BACKGROUND
since the inception of antibody technology twenty years ago, phage display is a powerful tool to generate antibodies for proteome research  <cit> , diagnostics  <cit>  or for therapeutic purposes  <cit> .
therapeutic antibodies are currently one of the fastest developing class of biologicals in the pharmaceutical market  <cit> .
the main indications for therapeutic antibodies are cancer and auto-immune diseases  <cit> .
to date,  <dig> antibodies and antibody conjugates are ema and/or fda approved   and about  <dig> antibodies and antibody fusion proteins were under development in  <dig>  <cit> .
two major strategies for generating fully human antibodies are: transgenic mice and antibody phage display.
in transgenic mice, the chromosome segments encoding antibody gene fragments are replaced with the corresponding human chromosome segments encoding human immunoglobulins.
these animals allow the generation of fully human antibodies by hybridoma technology  <cit> .
an advantage of transgenic mice is the in vivo affinity maturation of antibodies, but on the other hand, all in vivo antibody generations are restricted by the natural immune system itself: the limitation in antigen processing and presentation and the tolerance against conserved epitopes  <cit> .
antibody phage display is an alternative or complementing technology to generate human antibody fragments from universal antibody gene libraries as lead candidates for therapeutic development  <cit> .
here, the selection is an in vitro process and is not limited by the restrictions of the immune system and selection conditions can be adjusted and controlled, thus allowing to select for properties not achievable by in vivo immune systems  <cit> .
to isolate human antibodies by phage display, two types of antibody gene libraries are used: immune libraries and universal or “single-pot” libraries  <cit> .
immune libraries from patients are suited to select specific antibodies against a disease or pathogen, e.g.
cancer  <cit> , human immunodeficiency virus  <cit> or herpes simplex virus  <cit> .
“single-pot” libraries allow the selection of antibodies - in theory - against any target.
the human naive antibody gene libraries hal4/7/ <dig> are “single-pot” libraries.
antibodies against a panel of different antigens were selected from these hal libraries and applied for different purposes, e.g.
<cit> .
antibody fragments from these libraries can directly be cloned into a selection of compatible expression vectors to produce e.g.
in vivo biotinylated antibodies  <cit> , scfv-fc  <cit>  or full igg .
the scfv-fc format  is an alternative, functionally identical to igg in most assays.
due to its quicker and easier production, it provides a robust format for screening of large numbers of antibody candidates, and can be converted to full igg afterwards.
in this work, the scfv phagemid vector design was optimized and the “single-pot” antibody gene libraries hal9/ <dig> were constructed and analyzed, demonstrating significant improvements over previous designs.
methods
construction of phage display vectors
the phage display vector phal <dig> was constructed by cloning a dna fragment encoding his-/c-myc tag flanked by noti and bamhi, which was generated with two pcr primers  into phal <dig>  scfv coding sequences from phal <dig> were cloned in phal <dig> using the restriction sites ncoi and noti.
the c-terminal phenylalanine of the vК was deleted from scfv coding sequences by pcr using the primer set mkpelb_f  and mhkappaclscfv-noti_r <dig> .
the pcr products were cloned into the vector phal <dig>  <cit>  and phal <dig> between the vector encoded signal peptide and the c-myc/ his-tag or his/ c-myc-tag sequences, respectively, using the restriction sites ncoi and noti.
production of soluble antibodies in microtitre plates
96-well mtps with polypropylene  wells  containing 150 μl 2 × yt-ga  <cit> ⁠ were inoculated with the bacteria bearing scfv expressing phagemids.
mtps were incubated overnight at 37°c at 800 rpm in a mtp shaker .
a volume of 180 μl phosphate-buffered 2 × yt-ga in a pp-mtp well was inoculated with 10 μl of the overnight culture and grown at 37°c and 800 rpm for 2 h. bacteria were harvested by centrifugation for 10 min at  <dig>  × g and 180 μl supernatants were removed.
the pellets were resuspended in 180 μl 2 × yt supplemented with 100 μg/ml ampicillin, 100 mm sucrose and 50 μm isopropyl-beta d thiogalacto pyranoside  and incubated at 30°c and 800 rpm overnight.
bacteria were pelleted by centrifugation for 10 min at  <dig>  × g and 4°c.
the scfv-containing supernatant was transferred to a new pp-mtp and stored at 4°c before analysis.
production of antibody phage
50 ml 2 × yt medium + 100 μg/ml ampicillin + 100 mm glucose were inoculated with an overnight culture to o.d.600 =  <dig> .
bacteria were grown to o.d.600 =  <dig> – <dig>  at 37°c and 250 rpm.
2 ml bacteria  were infected with 2 ×  <dig> helper phage hyperphage  <cit> , incubated at 37°c for 30 min without shaking, followed by 30 min at 250 rpm.
infected cells were harvested by centrifugation for 10 min at  <dig>  × g and the pellet was resuspended in 30 ml 2 × yt + 100 μg/ml ampicillin + 50 μg/ml kanamycin.
phage were produced at 30°c and 250 rpm for 16 h. cells were pelleted for 10 min at  <dig>  × g. phage in supernatant were precipitated with 1/ <dig> volume of 20% peg/ <dig>  m nacl solution for 1 h on ice and pelleted by centrifugation 1 h at  <dig>  × g at 4°c.
precipitated phage were resuspended in 300 μl phage dilution buffer, and cell debris was pelleted by additional centrifugation for 5 min at  <dig>  × g at 20°c.
the supernatant containing the scfv phage was stored at 4°c.
phage titration  was done according to  <cit> .
antigen elisa
100 ng of antigen was coated to  <dig> well microtitre plates  in pbs ph  <dig>  or 50 mm nahco <dig> ph  <dig>  overnight at 4°c.
after coating, the wells were washed three times with pbst and blocked with 2%mpbst for  <dig>  h at rt, followed by three washing steps with pbst.
108 cfu scfv-phage and helperphage as control were loaded in the first well of each line of the plate.
each sample was diluted 1: <dig> in pbs along the plate ending with 100 μl proteinaceous solution per well.
the loaded plate was incubated for  <dig>  h at rt, followed by three pbst washing cycles.
bound scfv phage were detected with mouse anti-m <dig> hrp conjugate  .
visualization was performed using tmb  as a substrate and the staining reaction was stopped by adding 100 μl 1 n sulphuric acid.
absorbance at 450 nm  was measured by using a sunrise™ microtitre plate reader .
sds-page
antigens were analyzed by 12% sds-page using a protean ii minigel system  according to  <cit> .
protein gels were stained with coomassie brilliant blue.
western blotting and immunostaining
protein samples in sds polyacrylamide gels were transferred to and immobilized on polyvinylidene difluoride  membranes  by a semidry procedure .
the membrane was blocked with 2%  skimmed milk powder in pbst for 1 h at rt.
scfvs were detected by mouse anti c-myc mab myc1-9e <dig>   for  <dig>  h at rt and goat anti-mouse hrp mab   for  <dig>  h at rt.
for visualization super signal® westpico chemiluminescence substrate  was applied and protein bands were detected by enhanced chemiluminescence  on a luminometer .
for detection of antibody phage, the minor coat protein piii was detected with 1: <dig>  diluted mouse mab anti-piii  for  <dig>  h at rt, followed by goat anti-mouse  mab  conjugated with ap .
the development was performed by nbt/bcip.
library construction
the study was performed in accordance with the declaration of helsinki.
the study participants were selected from blood donors of the institute for clinical transfusion medicine, städtisches klinikum braunschweig ggmbh, braunschweig, germany.
all voluntary donors were informed about the project and gave their informed consent.
the use of blood samples for the amplification of antibody gene fragments to develop antibody phage display libraries was approved by the ethical commitee of the technische universität braunschweig .
lymphocytes were isolated from  <dig> donors with various ethnical backgrounds using the lymphoprep kit  according to the manufacturers instructions.
total rna was isolated using trizol  and mrna was isolated using the oligotex mrna minikit .
then cdna was synthesized using superscript iii , random hexamer oligonucleotide primers and 50–250 ng mrna.
to amplify the antibody gene fragments   <dig> individual first pcrs of each cdna sample were performed separately for each cdna preparation in a volume of 50 μl using gotaq  and  <dig>  μm of each primer  <cit>  for 30 cycles  followed by a 10 min final synthesis step.
the pcr products were purified by agarose gel electrophoresis using the nucleospin gel and pcr clean-up kit .
vh, kappa or lambda pcr products were pooled separately.
to add restriction sites for cloning, 100 ng of the purified and pooled vh, kappa or lambda pcr products of the first pcr for each of the 27 second pcr reactions were used in a volume of 100 μl using gotaq and  <dig>  μm of each primer for 20 cycles  followed by a 10 min final synthesis step at 72°c.
pcr products were purified by agarose gel electrophoresis using the nucleospin gel and pcr clean-up kit .
vh, kappa or lambda pcr products were pooled separately.
in total  <dig> first pcr and 1458 second pcr reactions were performed.table  <dig>
production of soluble scfv antibody fragments randomly chosen from the hal <dig> antibody gene library
production level
clone
swi6-2
swi6-10
swi6-14
swi6-26
swi6-30
swi6-50
swi6-51
swi6-52
swi6-55
swi6-60
swi6-46
production level
clone
swi6-48
swi28-1
swi28-2
swi28-3
swi6-4
swi28-5
swi28-6
swi28-7
swi28-8
swi128-9
swi128-10
production level
clone
swi28-11
swi28-12
swi28-13
swi28-14
swi28-15
swi28-16
swi28-17
swi28-18
swi28-19
swi28-20
the scfvs were detected by western blot analysis in 10 μl supernatant from e.coli xl- <dig> blue mrf’ production in  <dig> well microtiter plates.
the production yield was evaluated according to the band intensities.
+++ best yield, ++ medium yield, + low yield,  <dig> no yield.
wt wild-type scfv coding sequence, df deletion of the c-terminal phenylalanine from the scfv coding sequence.
for vl cloning 5 μg vector phal <dig> and 2 μg kappa or lambda pcr products were digested in a volume of 100 μl using  <dig> u mlui and noti  at 37°c for 3 h. this step was performed multiple times to produce enough material for up to  <dig> transformations.
for quality control each digestion was performed separately with each enzyme in parallel.
the digestions were inactivated at 80°c for 20 min, followed by adding  <dig>  u calf intestine phosphatase   and incubation at 37°c for 30 min, this step was repeated once.
vector and pcr products were purified using the nucleospin gel and pcr clean-up kit, removing short stuffer fragments between mlui and noti in phal <dig>  each ligation was performed with 1 μg digested vector and 270 ng pcr product using  <dig> u t <dig> ligase  in a volume of 100 μl overnight at 16°c.
ligations were inactivated at 70°c for 10 min and precipitated with 10 μl 3 m sodium acetate ph  <dig>  and 250 μl ethanol for 2 min at rt, followed by 5 min centrifugation at 16000 × g and 4°c.
pellet was washed two times with 500 μl 70%  ethanol.
the dried pellet was resuspended in 35 μl dh2o and mixed on ice with 25 μl electrocompetent e. coli xl1-blue mrf’.
electroporation was performed with  <dig>  cm prechilled cuvettes using a micropulser electroporator  at  <dig>  kv.
immediately, 1 ml prewarmed 37°c soc medium ph  <dig>   tryptone,  <dig> %  yeast extract,  <dig> %  nacl, 20 mm mg solution, 20 mm glucose) was added and incubated for 1 h at 600 rpm and 37°c.
transformation was plated out on 25 cm square petri dishes with 2xyt-gat agar  tryptone, 1%  yeast extract,  <dig> %  nacl, 100 mm glucose, 100 μg/ml ampiciline, 20 μg/ml tetracycline,  <dig> %  agar-agar) and incubated overnight at 37°c.
in parallel 10− <dig> dilutions of each transformation reaction were plated out to determine the transformation rate.
these plates were used also for quality control by colony pcr using the oligonucleotide primers mhlacz-pro_f and mhgiii_r to verify the insert size.
the colonies were scraped from the 25 cm plates using 40 ml 2xyt medium  tryptone, 1%  yeast extract,  <dig> %  nacl) and 5 ml were directly used for midi plasmid preparation using the nucleobond plasmid midi kit .
for vh cloning material from  <dig> donors of the previous described hal7/ <dig> libraries  <cit>  was used in addition to material of  <dig> new donors.
in a first step 5 μg phal30-vl sublibraries and 2 μg vh pcr products were digested in a volume of 100 μl using  <dig> u ncoi-hf and  <dig> u hindiii-hf  at 37°c for 3 h. this step was performed several times to produce enough material for 150– <dig> transformations.
the digestions, ligations and transformations were performed as described for vl cloning with following modifications.
ligation was performed with 250 ng vh pcr product.
after transformation of xl1-blue mrf’, overnight incubation on 25 cm 2 × yt-gat plates and resuspension in 25 ml 2 × yt medium, glycerol stocks of each library were made using 800 μl bacteria solution  and 200 μl glycerol  and stored at −80°c.
for the final library one glycerol stock of each sublibrary was thawed, mixed together, aliquoted  and stored at −80°c.
the antibody gene libraries hal9/ <dig> were packaged separately inoculating 400 ml 2 × yt-ga  with a library glycerol stock.
the bacteria were grown to an optical density at 600 nm  of  <dig> – <dig>  at 37°c and 250 rpm.
25 ml bacterial culture  were infected with  <dig>  ×  <dig> hyperphage particles  <cit> , incubated at 37°c for 30 min without shaking followed by 30 min at 250 rpm.
infected cells were harvested by centrifugation for 10 min at 3220xg.
the pellet was resuspended in 400 ml 2 × yt-ak .
phage were produced at 30°c and 250 rpm over night.
the bacteria were centrifuged for 20 min at  <dig>  × g. phage particles in the supernatant were precipitated with 1/ <dig> volume of 20%  polyethylene glycol / <dig>  m nacl solution for one hour on ice with gentle shaking and pelleted by centrifugation for one hour at  <dig>  × g at 4°c.
the precipitated phage were resuspended in 10 ml phage dilution buffer , 1/ <dig> volume of peg solution was added and incubated on ice for 20 min, followed by centrifugation for 30 min at  <dig>  × g and 4°c.
the pellet was resupended in 1 ml phage dilution buffer.
residual bacteria and cell debris were removed by additional centrifugation for 5 min at 16000 × g at 20°c.
supernatants containing antibody phage were stored at 4°c.
phage titration was done as described before  <cit> .
the scfv display rates of the packaged libraries were analyzed by 10% sds-page, western blot and anti-piii immunostain .
wildtype piii has a calculated molecular mass of  <dig>  kda, but it runs at an apparent molecular mass of 65 kda in sds-page  <cit> .
accordingly, the scfv::piii fusion protein runs at about 95 kda.
antibody selection
antibody selections were performed against proteins or peptides as described before  <cit> .
the elution with trypsin - phal <dig> and the former vector phal <dig> contain a trypsin site between the tags and giii - is more efficient as elution by ph shift .
RESULTS
analysis of the new phage display vector phal30
a prerequisite for a good up to date antibody gene library is a phagemid that allows both, a high display level of functional antibody fragments on phage and a good expression of soluble antibodies for screening.
the new design of the phagemid generation phal <dig>  is based on the phal <dig>  <cit> .
in the first optimization step and independent of kappa or lambda light chains, the tag order in the phal <dig> phagemid was changed from the initial his/myc-tag in phal <dig> to myc/his tag.
for evaluation of the expression capacity of both phagemids, three different soluble scfv antibody fragments were produced in 150 ml e.coli xl- <dig> blue mrf’ culture for 4 h at 25°c and 250 rpm.
functional soluble scfv antibody fragments were quantified by antigen elisa in the production supernatant, the periplasmatic extract, the osmotic shock fraction and the eluate after imac purification .
except for the osmotic shock preparation, the production level with the phal <dig> phagemid was always significantly improved.
after imac purification of the supernatants, the yields of ht186-d <dig> were 1 mg/l for phal <dig> and 2 mg/l for phal <dig>  in case of tm43-e <dig> the yields were 1 mg/l for both vectors and for d <dig>  the yields increased from  <dig>  mg/l for phal <dig> to 1 mg/l for phal <dig>  the production yields in the periplasmic fraction of scfvs ht186-d <dig> and tm43-e <dig> after imac purification were improved from  <dig>  mg/l, and  <dig>  mg/l with phal <dig> to  <dig>  mg/l and  <dig>  mg/l, respectively, with phal <dig> figure  <dig>
schematic drawing of phal <dig> and phal <dig>  abbreviations: lacz promoter: promoter of the bacterial lac operon; rbs: ribosome binding site; pelb: signal peptide sequence of bacterial pectate lyase, mediating secretion into the periplasmic space; vh: variable fragment of the heavy chain; blue box: first six amino acids of ch <dig>  part of the linker; lc: light chain; dark blue box: first  <dig> / <dig>  aminoacids of cl; ochre: ochre stop codon; amber: amber stop codon; his-tag: 6xhistidine tag; terminator: sequence terminating transcription; myc-tag: eqkliseedln tag.
the elements of the inserts are not drawn to scale.
comparision of phal <dig> and phal <dig>
comparision of the production of soluble antibodies.
sn supernatant, pe periplasmatic extract, os osmotic shock fraction, eluate after imac purification, od450nm-620nm optical density at 450 nm , scfv antibody fragments analyzed: d <dig> , ht186-d <dig> and tm43-e <dig>  antigens: lysozyme, muc- <dig> and ompd.
comparision of scfv-phage antigen binding.
od450nm-620nm optical density at 450 nm , scfv antibody fragments d <dig> , ht186-d <dig>  sh313-b <dig> and tm43-e <dig>  antigens: lysozyme, muc <dig>  cd <dig> and ompd.
next, four different phal <dig> and phal <dig> phagemids were packaged with hyperphage.
the resulting phage titers were comparable among each other.
they ranged from 6 ×  <dig> to 6 ×  <dig> cfu/ ml culture medium.
the scfv display level on phage was identical, as confirmed by western immunoblot .
approximately 90% of g3p was fused to the scfv antibody fragments.
a functional comparison of phal <dig> and phal <dig> scfv-phage regarding antigen binding was performed by titration antigen elisa .
the titration curves were similar for three different scfv-phage, further illustrating similar display level.
for tm43-e <dig> more functional scfv were displayed on phage.
taken together, both phagemids are almost identical in phage display level and phage binding assays, but the phal <dig> phagemid provided a significant increase in production of soluble antibody fragments for screening which may improve the hit rate in initial screening assays.
influence of the phenylalanine residue in kappa cl on scfv phage display
target independent, it was observed that scfv antibody fragments bearing a vК light chain were less frequently isolated from hal7/ <dig> than those with a vλ light chain  <cit> .
a possible explanation could be a lower expression of antibody fragments with a vК light chain.
therefore, the phagemid was further optimized by deleting the bulky c-terminal phenylalanine of the vК light chain.
first, the soluble production level of five known scfv fragments in phal <dig> and six known kappa scfv fragments in phal <dig> was analyzed and compared by western immunoblot .
the deletion of the phenylalanine in the vК light chain resulted in a higher production level for all tested scfv.
further expression analysis by western immunblot included the comparison of  <dig> randomly chosen scfv fragments from the kappa hal <dig> antibody gene library and their phenylalanine deletion version .
the expression levels were higher with the phenylalanine deletion mutants in  <dig> cases, slightly lower for three clones and in the same range for the remaining  <dig> clones.
construction of hal <dig> and hal10
using blood samples obtained from  <dig> caucasian, african, indian and chinese non-immunized human donors, the new antibody libraries hal <dig> and hal <dig> were constructed using the improved phagemid backbone phal <dig>  in detail, blood lymphocytes from  <dig> caucasian, african, indian and chinese non-immunized human donors were isolated for library construction.
lymphocyte mrna was reverse transcribed to cdna and the antibody gene repertoire was amplified in two steps.
in the first step, vh and the full length light chains were amplified using a set of framework  <dig> forward primers and igm, kappa and lambda constant domain reverse primers  <cit> .
in the second step, specific restriction sites were incorporated for cloning into the phal <dig> phagemid vector.
for the second amplification step of vh and lambda subfamilies the dna antibody repertoire  from  <dig> donors of the previously constructed hal <dig> was added for construction of the new hal <dig> and hal <dig> libraries.
both libraries contain the same vh repertoire  but differ in their light chain repertoire.
hal <dig> includes all lambda subfamilies , hal <dig> all kappa subfamilies  except the pseudogene encoding vκ <dig>  cloning of the antibody genes was done in two steps.
first, light chain genes were cloned with 1 ×  <dig> independent clones for each library.
then heavy chain genes were cloned in the light chain containing phagemid leading to a final repertoire size of the hal <dig> and hal <dig> scfv libraries of  <dig>  ×  <dig> and  <dig>  ×  <dig>  respectively.
analysis of v-gene subfamily distribution
to assess the diversity of the libraries, bacterial colonies from library transformation plates were analyzed by colony pcr and sequencing.
in total  <dig> full length scfv encoding sequences for hal <dig> and  <dig> sequences for hal <dig> were aligned to human germline v gene segments using vbase <dig>  <cit> .
to compare the initial diversity of the libraries with the germline usage after selection,  <dig> antibodies selected against  <dig> targets were analyzed.
of these selected antibodies from libraries hal <dig> and hal <dig>   <dig> % were bearing a vκ light chain compared to 4% of antibodies selected from hal7/ <dig>  the antibody subfamily distribution of the unselected hal7/ <dig> libraries , the subfamily frequency of selected scfvs from hal7/ <dig>  and the in vivo distribution  <cit>  are shown in figure 3a-c. the heavy chain diversity of the unselected hal9/ <dig> libraries is similar to the subfamily distribution found in vivo .
vh <dig> and vh <dig> are the dominating vh subfamilies in the initial library as well as for the selected scfvs.
vh <dig> shows a slight underrepresentation in the initial library, whereas the vh <dig> subfamily is overrepresented in all unselected and selected hal libraries.
vκ <dig> and vκ <dig> are the most abundant subfamilies, which is consistent with findings in vivo .
vκ <dig> is overrepresented in the unselected hal <dig> library but could not be retrieved after selection and in contrast vκ <dig> was significantly enriched during selection.
in the vλ repertoire of hal <dig>  the vλ1- <dig> are the most abundant subfamilies similar to the subfamily distribution found in vivo , but the frequency of vλ1- <dig> is lower compared to the in vivo frequency due to an overrepresentation of subfamilies vλ4/6/7/8/ <dig> which are found only in low frequency in vivo.figure  <dig>
antibody subfamily distribution found in the hal9/ <dig> libraries, in the selected scfvs from the hal9/ <dig> libraries, in the hal7/ <dig> libraries [
31
] and
in vivo
[
45
].
abundance of vh.
abundance of vκ.
abundance of vλ.
sequence analysis indicated a high antibody germline gene diversity for the heavy-chain and light-chain repertoires of the hal9/ <dig> libraries.
the identified heavy chain repertoire in this limited sample already covered  <dig> of  <dig> functional vh genes .
in addition, one vh gene  occurred in the unselected libraries that has not yet been confirmed to be functional  <cit> .
vh germline genes were observed in frequencies between  <dig> % and  <dig> % in the unselected hal <dig> and hal <dig> with no significant differences between the libraries.
the comparison of the gene usage before and after selection shows a clear enrichment of some vh genes.
the most abundant vh genes after selection were ighv3- <dig>  increased from  <dig> % in the unselected libraries to  <dig> % after selection, ighv1- <dig>  increased from  <dig> % to  <dig> % and ighv1- <dig>  increased from  <dig> % to  <dig> % after selection.
the frequency of the remaining vh germline genes remained constant or was lowered after selection.
most strikingly, the usage of all vh <dig> genes was considerably reduced in selected antibodies.
only  <dig> of  <dig> vh <dig> germline genes were found again after selection with a ten-fold reduction in total frequency, decreasing from  <dig> % in the unselected libraries to  <dig> % after selection .figure  <dig>
two-dimensional heatmap illustrating vh–vλ gene pairing frequencies in the unselected hal <dig> library  and in the selected scfvs from the hal <dig> library .
frequency of all functional vh genes  <cit>  and vλ genes  <cit>  are shown.
genes that are not confirmed to be functional, but were found in the library/were selected are marked in orange.
<dig> antibodies of the initial library and  <dig> selected scfvs were analyzed.
the percentual amounts of each germline gene are given separetely for vh  and vλ .
two-dimensional heatmap illustrating vh–vκ gene pairing frequencies in the unselected hal <dig> library  and in the selected scfvs from the hal <dig> library .
frequency of all functional vh genes  <cit>  and vκ genes  <cit>  are shown.
genes that are not confirmed to be functional, but were found in the library/were selected are marked in orange.
vκ <dig> genes are all classified as non-functional and not inclued in this overview.
<dig> antibodies of the initial library and  <dig> selected scfvs were analyzed.
the percentual amounts of each germline gene are given separetely for vh  and vκ .
<dig> of the  <dig> functional vλ genes were found in the hal <dig> library sample .
one vλ gene  was found in the unselected hal <dig> as well in selected scfvs that is predicted to be not functional  <cit> .
as seen for the heavy chain repertoire, the frequency of several vλ germline genes changed during the selection process.
usage of the vλ <dig> subfamily was increased after selection mostly due to a higher abundance of the iglv1- <dig> germline gene, increasing from  <dig> % in the unselected library to  <dig> % after selection and a higher abundance of iglv1- <dig>  increasing from  <dig> % to  <dig> % .
in the vλ <dig> subfamily, the frequency of the iglv2- <dig> germline gene showed a slight increase from  <dig> % to  <dig> % after selection but the overall abundance of vλ <dig> genes decreased due to a lower usage of the remaining germline genes.
three of nine different vλ <dig> germline genes were retrieved in high frequency before and after selection: iglv3- <dig>  iglv3- <dig> and iglv2- <dig>  the findings reflect the in vivo subfamily distribution, where iglv3- <dig> and iglv2- <dig> account for ~80% of vλ <dig>  <cit> .
after selection the frequency of iglv3- <dig> was reduced from  <dig> % to  <dig> % and increased for iglv3- <dig> from  <dig> % to  <dig> %.
usage of iglv3- <dig> remained constant.
the abundance of the most prevalent vλ gene iglv6- <dig> in the unselected hal <dig> was decreased from  <dig> % to  <dig> % after selection.
in the hal <dig> library  <dig> of  <dig> functional vκ germline genes were observed .
two vκ genes  found in the unselected library were described to be only potentially functional  <cit> .
the most abundant vκ germline gene before selection was igkv4- <dig> with a frequency of ~25%.
this is a more than twofold higher prevalence than found in vivo  <cit>  and usage of igkv4- <dig> after selection was reduced to ~4%.
the frequency of vκ <dig> subfamily genes was raised from 37% in the unselected library to 48% after selection .
three genes igkv1- <dig>  igkv1-d <dig> and igkv1-d <dig> increased from  <dig>  to  <dig> %,  <dig>  to  <dig> % and from  <dig>  to  <dig> %, respectively.
vh and vl germline gene pairings
the abundance of heavy- and light-chain pairings that were observed in the unselected libraries and within selected antibodies are illustrated in figure  <dig> for vh-vλ combinations and in figure  <dig> for vh-vκ combinations.
in the unselected libraries no particular vh-vl combination is dominating .
the pairings are evenly distributed depending on their total abundance.
vh-vλ pairings were observed in frequencies between  <dig> % and  <dig> % in the unselected hal <dig> with vh3-30/vλ6- <dig> being the most abundant combination.
in the unselected hal <dig> pairing frequencies up to  <dig> % were observed for vh-vκ due to the high abundance of the igkv4- <dig> germline gene.
however, after  <dig> individual selections a clear preference for particular vh-vl pairings was detected.
for vh-vλ pairings the most prevalent combination was vh3-30/vλ3- <dig> which was observed in  <dig> % of the selected antibodies.
the λ3- <dig> gene showed a preference for pairing with vh <dig> germline genes.
the vh3- <dig> germline gene was by far the most abundant vh gene after selection and paired with nearly all light chain genes in high frequency.
interestingly, the light chain gene vλ8- <dig> paired almost exclusively with vh3- <dig>  the remaining vλ germline genes showed preferential pairing with the vh <dig> and vh <dig> germline genes and with lower frequency also to the vh6- <dig> germline gene.
a second vh <dig> subfamily gene, vh3- <dig>  was also observed in high frequency after selection.
similar to vh3- <dig> no clear preference in pairing with any vλ genes segment was seen.
for three vh <dig> genes a more distinct preference for single vλ genes was observed.
the combinations vh1-46/vλ1- <dig> and vh1-69/vλ1- <dig> were enriched to  <dig> % and the combination vh1-18/vλ1- <dig> was enriched to  <dig> %.
the five most common vh-vλ combinations  account for nearly 20% of all selected antibodies.
an enrichment of the vh3- <dig> germline gene after selection was also observed for the vh-vκ gene pairing.
furthermore a high frequency of vκ <dig> and vκ <dig> genes occurred after selection, but due to the relatively small sample size of selected antibodies bearing a kappa light chain no significant conclusion can be made about enrichment of single vh-vκ combinations.
cdr <dig> length and amino acid distribution of light-chain and heavy-chain
length and amino acid distribution of cdr3-l and cdr3-h of the hal <dig> and hal <dig> libraries were analyzed.
for example,  <dig> cdr3-h sequences of the unselected libraries and  <dig> sequences of selected antibodies were analyzed and compared.
the cdr3-h length distribution before and after selection is depicted in figure 6a.
in the unselected libraries, the cdr3-h length ranges from  <dig> to  <dig> aa with a median length of about  <dig> aa.
cdr3-h longer than  <dig> aa are occurring only in low frequency.
after selection, the distribution is very slightly shifted towards a cdr3-h length with a median of  <dig> aa.
cdr <dig> length of  <dig> –  <dig> aa are found in high frequency after selection but cdr3-h length longer than  <dig> aa were not detected.
long cdr-h <dig> sequences are often internally stabilized by disulfide bridges in a very characteristic manner.
a first internal cysteine is always followed by four amino acids - often serine and glycine rich - and completed by the second cysteine .figure  <dig>
heavy and light chain cdr length distribution.
cdr-h <dig> length distribution in hal9/ <dig>  cdr-h <dig> lengths in unselected library  and in selected scfvs from hal9/ <dig> .
cdr-l <dig> length distribution in hal <dig>  cdr-l <dig> lengths in unselected library  and in selected scfvs from hal <dig> .
cdr-l <dig> length distribution in hal <dig>  cdr-l <dig> lengths in unselected library  and in selected scfvs from hal <dig> .
the cdr3-h amino acid composition was analyzed for the unselected hal9/ <dig> libraries .
the amino acid usage at each position is shown for cdrs with up to  <dig> aa in length.
the cdr3-h often starts with an alanine and arginine in the first two positions and throughout the whole cdr the amino acids glutamate, serine, tyrosine and glycine are favored.
at the last three positions the “fdy” motive of the ighj <dig> segment is often found.
significantly, the cdr3-h amino acid usage found in selected scfvs is largely the same compared to the amino acid usage in the initial libraries .figure  <dig>
heavy chain cdr amino acid distribution.
cdr-h <dig> amino acid distribution in unselected hal9/ <dig> .
cdr-h <dig> amino acid distribution in selected scfvs from hal9/ <dig> .
distribution of amino acids at each position of cdr-h <dig> in kabat numbering.
amino acids 100-j,  <dig> and  <dig> correspond to the last  <dig> residues of each cdr3-h <dig>
for the cdr3-l length distribution of hal <dig>  before and after selection  <dig> sequences of the unselected library and  <dig> sequences of selected antibodies were analyzed .
in the unselected library the cdr <dig> length ranges from  <dig> to  <dig> aa with a median length of about  <dig> aa.
the most common cdr <dig> length for lambda light chains are  <dig>   <dig> or  <dig> aa that account together for more than 80% of all found cdr3-l lengths.
after selection, cdrs with a length of  <dig> aa were found more frequently and the occurrence of cdrs with a length of  <dig> aa was decreased.
cdr3-l length distribution of hal <dig>  was analyzed with  <dig> sequences of the unselected library and  <dig> sequences of selected antibodies .
in the unselected library the cdr <dig> length ranges from  <dig> to  <dig> aa.
most kappa light chains are bearing a cdr <dig> with a length of  <dig> aa  and the length distribution did not change significantly after selection.
the cdr3-l amino acid distribution of the unselected libraries was analyzed separately for lambda and kappa light chains.
the amino acid usage at each position is shown for cdrs with up to  <dig> aa in length for lambda light chains  and for cdrs with up to  <dig> aa in length for kappa light chains .
at most positions of the light chain cdr <dig>  the usage of amino acids is restricted, e.g.
70% of antibodies have a aspartate at lambda cdr <dig> position  <dig>  or 90% have a proline at kappa cdr <dig> position  <dig>  but there is still a quite high diversity found in amino acid usage throughout the whole cdr.
again, the cdr3-l amino acid distribution found in selected scfvs is almost the same when compared to the amino acid usage of the initial libraries hal9/ <dig> .figure  <dig>
light chain cdr amino acid distribution.
cdr-l <dig> amino acid distribution in hal <dig> .
cdr-l <dig> amino acid distribution in selected scfvs from hal <dig> .
cdr-l <dig> amino acid distribution in hal <dig> .
cdr-l <dig> amino acid distribution in selected scfvs from hal <dig> .
distribution of amino acids at each position of cdr-l <dig> in kabat numbering.
discussion
since the development of phagemids for antibody phage display by breitling et al.
<cit> , the technology was continuously further developed.
the most used phage display vectors have the tag order his-myc when using both tags, e.g.
pcantab3his  <cit> , pces  <cit> , phen <dig>  <cit> , phal <dig>  <cit> , pit <dig>  <cit> , pmod <dig>  <cit>  or pmid <dig>  <cit> .
to our knowledge, there is only one phage display vector using the opposite orientation: psd <dig>  <cit> .
comparing both tag orders, the myc-his order  results in improved production of functional scfv compared to his-myc  whereas the display of functional scfv on phage is not effected.
using a kappa  and a lambda  antibody gene library in the same selection, we have observed that the output of selected kappa antibodies was always lower compared to lambda antibodies  <cit> .
løset et al.
and tiller et al.
also describe a lower production yield of kappa scfvs or fabs compared to lambda antibodies that confirms our observation with the hal libraries  <cit> .
the scfv design in phal <dig> included the first six amino acids of ch <dig> as part of the linker and the first  <dig> amino acids of cl lambda, respectively the first nine amino acids of cl kappa.
the last amino acid in cl kappa used in the scfv design is a phenylalanine.
phenylalanine is encoded by only two codons which may lead to a reduced translation and has a bulky hydrophobic benzol side group which may hamper solubility.
in projects with macaque immune libraries using also phal <dig> and derived phal vectors, the phenylalanine was omitted.
the selected kappa scfv were produced well, leading to a generation of kappa scfv against different targets  <cit> .
for human scfv, deletion of phenylalanine improved the expression rate of known kappa antibodies and randomly chosen kappa clones.
this modification increased the rate of selected kappa antibodies from 4% using hal4/7/ <dig> to  <dig> % when using hal9/ <dig>
using the novel vector phal <dig> and scfv design, two new universal human naive antibody gene libraries were constructed.
the theoretical diversity of the hal9/ <dig> libraries is with  <dig>  ×  <dig> independent clones in the same range like other published scfv or fab libraries with a theoretical diversity in the range of 1x1010-1x <dig>  e.g.
the naive mccafferty scfv library   <cit> , the naive pfizer scfv library   <cit> , the naive cat <dig>  scfv library   <cit> , the naive/synthetic dyax fab   <cit>  library, the synthetic ylanthia fab library   <cit>  or very recently published the philodiamond scfv library   <cit> .
the representation of antibody subfamilies in the hal9/ <dig> libraries is comparable with the hal7/ <dig> library  <cit> , it differs only in some minor points, e.g.
vh <dig>  vκ <dig> and vλ <dig> are more abundant in hal9/ <dig>  in general, vh gene usage is dominated by vh <dig> and vh <dig>  dominant vl are usually vκ <dig>  vκ <dig>  vκ <dig> and vκ <dig> and vλ by vλ <dig>  vλ <dig>  vλ <dig> and vλ <dig>  in the new libraries, the distribution of v genes is comparable with their frequency in vivo  <cit>  but with following exceptions.
the subfamily vh <dig> is more abundant in vivo whereas vκ <dig> and vλ <dig> are more frequent in hal antibody gene libraries and rare in vivo.
the main difference is the frequency of vλ1 > vλ2 > vλ <dig> in vivo compared to vλ3 > vλ1 > vλ <dig> in hal9/ <dig>  the ylanthia library  <cit>  fits perfectly with the in vivo distribution.
the distribution of v genes for vh and vκ of hal9/ <dig> is in accordance with the pfizer library  <cit> .
a comparison of vλ with hal <dig> is not possible, because the pfizer library lacks most vλ genes.
compared to hal9/ <dig>  the distribution of v genes in the cat <dig>  library  <cit>  differs more from in vivo situation.
here, vh is dominated by vh <dig> and vκ is dominated by one vκ <dig> gene.
with ~ <dig> amino acids, the average hal9/ <dig> cdr-h <dig> length is longer than in the naive pfizer  <cit>  or synthetic ylanthia  <cit>  libraries , but slightly shorter compared to the dyax library with ~ <dig> amino acids  <cit> .
in addition more very long cdr-h <dig>  are found in hal9/ <dig> compared to the pfizer library.
the average length of cdr-l <dig> for λ is eleven amino acids and therefore two amino acids longer as the average length of cdr-l <dig> for κ. in hal9/ <dig>   <dig> or  <dig> different aa are occurring at each cdr-h <dig> position whereas for ylanthia  <dig> to  <dig> different aa are possible at each position, planned by rational design  <cit> .
in ylanthia, the cdr-h <dig> is dominated by serine, tyrosine and glycine .
in the naive hal9/ <dig> libraries, the amino acid repertoire in cdr-h <dig> is more balanced, but the frequency of tyrosine increases from n’terminus to c’terminus as well .
significantly, within the group of selected scfvs, the representation of vh antibody subfamilies is largely in accordance with the mccafferty library  <cit>  and pfizer library  <cit> , but not with the cat <dig>  library  <cit> , where vh is dominated by vh1 > vh <dig> compared to vh3 > vh <dig> for mccafferty, hal9/ <dig> or pfizer library.
for vκ, more vκ <dig> than vκ <dig> were selected from hal <dig> or mccafferty, whereas from pfizer or cat <dig>  mostly vκ <dig> were selected.
regarding vλ, here vλ1- <dig> and  <dig> are mainly isolated from mccaffery and hal <dig>  whereas vλ <dig> is rarely selected from cat <dig> .
the frequency of selected vh <dig>  vκ <dig> and vλ <dig> antibodies from hal9/ <dig> is very low compared with the frequency in the initial library.
the same was observed for hal7/ <dig>  <cit>  and cat <dig>   <cit> .
the vh4- <dig> antibody gene is described as toxic for b-cells  <cit> .
as consequence, two vh4- <dig> and vh4- <dig> genes were excluded when constructing the synthetic ylanthia library, despite the fact, that these vh <dig> genes are very frequent in the natural human antibody repertoire  <cit> .
remarkably, a majority of antibodies selected from macaque immune antibody gene libraries against botulinum a toxin are vh <dig> antibodies, especially vh4- <dig>  <cit> .
the macaque antibody genes are very similar to their human counterparts.
therefore, the vh <dig> gene family may be preadapted to some targets, or at least best suited to structurally complement the respective epitopes.
the average cdr length of cdr-h <dig> is only very slightly shorter after selection compared with the initial library, presumably due to a better growth of bacteria producing shorter antibody genes during antibody selection.
the length of the cdr-l <dig> does not significantly differ in selected antibodies.
the cdr composition in the cdr-l <dig> is completely different between λ and κ light chains, giving a hint why two different kinds of light chains have been evolved.
very importantly, the frequency of amino acids at each cdr <dig> position does not significantly change after selection, clearly demonstrating that any bacterial expression bias is minor, and all amino acids used in the naive human gene repertoire can be found in selected, functional antibodies.
some vh-genes are preferred after selection, e.g.
vh1- <dig>  vh1- <dig>  vh3- <dig>  vh3- <dig>  these are also v-genes often used in ylanthia  <cit>  and cat <dig>   <cit> .
notably, the very common vh3- <dig> gene results in a low igg <dig> expression rate, but is most frequent in the natural human antibody repertoire  <cit> .
this v-gene is a very stable and was used also for semisynthetic libraries, e.g.
tomlinson library  <cit> .
for κ light chain, igkv1- <dig>  igkv1d- <dig>  igkv1d- <dig> and igkv3- <dig> are selected frequently.
igkv3- <dig> is the most used κ gene in the natural repertoire and is used for ylanthia  <cit> .
the λ v-genes iglv1- <dig>  iglv1- <dig>  iglv2- <dig>  iglv3- <dig>  iglv3- <dig> and iglv6- <dig> were most frequently found after hal selection.
iglv2- <dig> is the most used λ v-gene in the natural antibody repertoire and is used for ylanthia, iglv1- <dig> and iglv1- <dig> are also often used in nature, but iglv1- <dig> was excluded from the ylanthia design  <cit> .
CONCLUSIONS
the naive antibody gene libraries hal9/ <dig> have unique features compared to the libraries published earlier.
the libraries have a slightly greater maximum diversity than the mccafferty library, they comprise more lambda v-genes and have longer cdr-h <dig> compared to the pfizer library, the distribution of v-genes resembles more the natural antibody repertoire compared to cat <dig>  and they show more cdr-h <dig> diversity than ylanthia.
the successful generation of > <dig> antibodies against > <dig> targets with overwhelming success and in short time with miniaturized systems illustrates the huge advances in human library construction and use achieved since the first description of this method.
mark schütte and michael hust contributed equally to this work.
competing interests
the majority of authors of this work are employed by merck kgaa, mab-factory gmbh or yumab gmbh, or are shareholders of these companies.
authors’ contributions
jk and sw performed experiments, participated in the design of the study, analyzed data and drafted the manuscript.
dm and ft performed experiments.
af and ts participated in the design of the study and analyzed data.
sd participated in the design of the study, analyzed data and drafted the manuscript.
hg provided material and performed experiments.
lt and bh participated in the design and coordination of the study and analyzed data.
ms performed experiments, participated in the design and coordination of the study, analyzed data and drafted the manuscript.
mh participated in the design and coordination of the study, analyzed data and drafted the manuscript.
all authors read and approved the final manuscript.
authors’ information
mark schütte and michael hust, both senior authors.

 since the inception of antibody technology twenty years ago, phage display is a powerful tool to generate antibodies for proteome research, diagnostics or for therapeutic purposes. therapeutic antibodies are currently one of the fastest developing class of biologicals in the pharmaceutical market. the main indications for therapeutic antibodies are cancer and auto-immune diseases. to date, antibodies and antibody conjugates are ema and/or fda approved and about antibodies and antibody fusion proteins were under development in. two major strategies for generating fully human antibodies are: transgenic mice and antibody phage display. in transgenic mice, the chromosome segments encoding antibody gene fragments are replaced with the corresponding human chromosome segments encoding human immunoglobulins. these animals allow the generation of fully human antibodies by hybridoma technology. an advantage of transgenic mice is the in vivo affinity maturation of antibodies, but on the other hand, all in vivo antibody generations are restricted by the natural immune system itself: the limitation in antigen processing and presentation and the tolerance against conserved epitopes. antibody phage display is an alternative or complementing technology to generate human antibody fragments from universal antibody gene libraries as lead candidates for therapeutic development. here, the selection is an in vitro process and is not limited by the restrictions of the immune system and selection conditions can be adjusted and controlled, thus allowing to select for properties not achievable by in vivo immune systems. to isolate human antibodies by phage display, two types of antibody gene libraries are used: immune libraries and universal or “single-pot” libraries. immune libraries from patients are suited to select specific antibodies against a disease or pathogen, e.g. cancer, human immunodeficiency virus or herpes simplex virus. “single-pot” libraries allow the selection of antibodies - in theory - against any target. the human naive antibody gene libraries hal4/7/ are “single-pot” libraries. antibodies against a panel of different antigens were selected from these hal libraries and applied for different purposes, e.g.. antibody fragments from these libraries can directly be cloned into a selection of compatible expression vectors to produce e.g. in vivo biotinylated antibodies, scfv-fc or full igg. the scfv-fc format is an alternative, functionally identical to igg in most assays. due to its quicker and easier production, it provides a robust format for screening of large numbers of antibody candidates, and can be converted to full igg afterwards. in this work, the scfv phagemid vector design was optimized and the “single-pot” antibody gene libraries hal9/ were constructed and analyzed, demonstrating significant improvements over previous designs. methods construction of phage display vectors the phage display vector phal was constructed by cloning a dna fragment encoding his-/c-myc tag flanked by noti and bamhi, which was generated with two pcr primers into phal scfv coding sequences from phal were cloned in phal using the restriction sites ncoi and noti. the c-terminal phenylalanine of the vК was deleted from scfv coding sequences by pcr using the primer set mkpelb_f and mhkappaclscfv-noti_r. the pcr products were cloned into the vector phal and phal between the vector encoded signal peptide and the c-myc/ his-tag or his/ c-myc-tag sequences, respectively, using the restriction sites ncoi and noti. production of soluble antibodies in microtitre plates 96-well mtps with polypropylene wells containing 150 μl 2 × yt-ga ⁠ were inoculated with the bacteria bearing scfv expressing phagemids. mtps were incubated overnight at 37°c at 800 rpm in a mtp shaker. a volume of 180 μl phosphate-buffered 2 × yt-ga in a pp-mtp well was inoculated with 10 μl of the overnight culture and grown at 37°c and 800 rpm for 2 h. bacteria were harvested by centrifugation for 10 min at  × g and 180 μl supernatants were removed. the pellets were resuspended in 180 μl 2 × yt supplemented with 100 μg/ml ampicillin, 100 mm sucrose and 50 μm isopropyl-beta d thiogalacto pyranoside and incubated at 30°c and 800 rpm overnight. bacteria were pelleted by centrifugation for 10 min at  × g and 4°c. the scfv-containing supernatant was transferred to a new pp-mtp and stored at 4°c before analysis. production of antibody phage 50 ml 2 × yt medium + 100 μg/ml ampicillin + 100 mm glucose were inoculated with an overnight culture to o.d.600 = . bacteria were grown to o.d.600 =  – at 37°c and 250 rpm. 2 ml bacteria were infected with 2 ×  helper phage hyperphage, incubated at 37°c for 30 min without shaking, followed by 30 min at 250 rpm. infected cells were harvested by centrifugation for 10 min at  × g and the pellet was resuspended in 30 ml 2 × yt + 100 μg/ml ampicillin + 50 μg/ml kanamycin. phage were produced at 30°c and 250 rpm for 16 h. cells were pelleted for 10 min at  × g. phage in supernatant were precipitated with 1/ volume of 20% peg/  m nacl solution for 1 h on ice and pelleted by centrifugation 1 h at  × g at 4°c. precipitated phage were resuspended in 300 μl phage dilution buffer, and cell debris was pelleted by additional centrifugation for 5 min at  × g at 20°c. the supernatant containing the scfv phage was stored at 4°c. phage titration was done according to. antigen elisa 100 ng of antigen was coated to well microtitre plates in pbs ph or 50 mm nahco ph  overnight at 4°c. after coating, the wells were washed three times with pbst and blocked with 2%mpbst for  h at rt, followed by three washing steps with pbst. 108 cfu scfv-phage and helperphage as control were loaded in the first well of each line of the plate. each sample was diluted 1: in pbs along the plate ending with 100 μl proteinaceous solution per well. the loaded plate was incubated for  h at rt, followed by three pbst washing cycles. bound scfv phage were detected with mouse anti-m hrp conjugate. visualization was performed using tmb as a substrate and the staining reaction was stopped by adding 100 μl 1 n sulphuric acid. absorbance at 450 nm was measured by using a sunrise™ microtitre plate reader. sds-page antigens were analyzed by 12% sds-page using a protean ii minigel system according to. protein gels were stained with coomassie brilliant blue. western blotting and immunostaining protein samples in sds polyacrylamide gels were transferred to and immobilized on polyvinylidene difluoride membranes by a semidry procedure. the membrane was blocked with 2% skimmed milk powder in pbst for 1 h at rt. scfvs were detected by mouse anti c-myc mab myc1-9e for  h at rt and goat anti-mouse hrp mab for  h at rt. for visualization super signal® westpico chemiluminescence substrate was applied and protein bands were detected by enhanced chemiluminescence on a luminometer. for detection of antibody phage, the minor coat protein piii was detected with 1: diluted mouse mab anti-piii for  h at rt, followed by goat anti-mouse mab conjugated with ap. the development was performed by nbt/bcip. library construction the study was performed in accordance with the declaration of helsinki. the study participants were selected from blood donors of the institute for clinical transfusion medicine, städtisches klinikum braunschweig ggmbh, braunschweig, germany. all voluntary donors were informed about the project and gave their informed consent. the use of blood samples for the amplification of antibody gene fragments to develop antibody phage display libraries was approved by the ethical commitee of the technische universität braunschweig. lymphocytes were isolated from donors with various ethnical backgrounds using the lymphoprep kit according to the manufacturers instructions. total rna was isolated using trizol and mrna was isolated using the oligotex mrna minikit. then cdna was synthesized using superscript iii, random hexamer oligonucleotide primers and 50–250 ng mrna. to amplify the antibody gene fragments individual first pcrs of each cdna sample were performed separately for each cdna preparation in a volume of 50 μl using gotaq and  μm of each primer for 30 cycles followed by a 10 min final synthesis step. the pcr products were purified by agarose gel electrophoresis using the nucleospin gel and pcr clean-up kit. vh, kappa or lambda pcr products were pooled separately. to add restriction sites for cloning, 100 ng of the purified and pooled vh, kappa or lambda pcr products of the first pcr for each of the 27 second pcr reactions were used in a volume of 100 μl using gotaq and  μm of each primer for 20 cycles followed by a 10 min final synthesis step at 72°c. pcr products were purified by agarose gel electrophoresis using the nucleospin gel and pcr clean-up kit. vh, kappa or lambda pcr products were pooled separately. in total first pcr and 1458 second pcr reactions were performed.table production of soluble scfv antibody fragments randomly chosen from the hal antibody gene library production level clone swi6-2 swi6-10 swi6-14 swi6-26 swi6-30 swi6-50 swi6-51 swi6-52 swi6-55 swi6-60 swi6-46 production level clone swi6-48 swi28-1 swi28-2 swi28-3 swi6-4 swi28-5 swi28-6 swi28-7 swi28-8 swi128-9 swi128-10 production level clone swi28-11 swi28-12 swi28-13 swi28-14 swi28-15 swi28-16 swi28-17 swi28-18 swi28-19 swi28-20 the scfvs were detected by western blot analysis in 10 μl supernatant from e.coli xl- blue mrf’ production in well microtiter plates. the production yield was evaluated according to the band intensities. +++ best yield, ++ medium yield, + low yield, no yield. wt wild-type scfv coding sequence, df deletion of the c-terminal phenylalanine from the scfv coding sequence. for vl cloning 5 μg vector phal and 2 μg kappa or lambda pcr products were digested in a volume of 100 μl using u mlui and noti at 37°c for 3 h. this step was performed multiple times to produce enough material for up to transformations. for quality control each digestion was performed separately with each enzyme in parallel. the digestions were inactivated at 80°c for 20 min, followed by adding u calf intestine phosphatase and incubation at 37°c for 30 min, this step was repeated once. vector and pcr products were purified using the nucleospin gel and pcr clean-up kit, removing short stuffer fragments between mlui and noti in phal each ligation was performed with 1 μg digested vector and 270 ng pcr product using u t ligase in a volume of 100 μl overnight at 16°c. ligations were inactivated at 70°c for 10 min and precipitated with 10 μl 3 m sodium acetate ph  and 250 μl ethanol for 2 min at rt, followed by 5 min centrifugation at 16000 × g and 4°c. pellet was washed two times with 500 μl 70% ethanol. the dried pellet was resuspended in 35 μl dh2o and mixed on ice with 25 μl electrocompetent e. coli xl1-blue mrf’. electroporation was performed with  cm prechilled cuvettes using a micropulser electroporator at  kv. immediately, 1 ml prewarmed 37°c soc medium ph  tryptone, % yeast extract, % nacl, 20 mm mg solution, 20 mm glucose) was added and incubated for 1 h at 600 rpm and 37°c. transformation was plated out on 25 cm square petri dishes with 2xyt-gat agar tryptone, 1% yeast extract, % nacl, 100 mm glucose, 100 μg/ml ampiciline, 20 μg/ml tetracycline, % agar-agar) and incubated overnight at 37°c. in parallel 10− dilutions of each transformation reaction were plated out to determine the transformation rate. these plates were used also for quality control by colony pcr using the oligonucleotide primers mhlacz-pro_f and mhgiii_r to verify the insert size. the colonies were scraped from the 25 cm plates using 40 ml 2xyt medium tryptone, 1% yeast extract, % nacl) and 5 ml were directly used for midi plasmid preparation using the nucleobond plasmid midi kit. for vh cloning material from donors of the previous described hal7/ libraries was used in addition to material of new donors. in a first step 5 μg phal30-vl sublibraries and 2 μg vh pcr products were digested in a volume of 100 μl using u ncoi-hf and u hindiii-hf at 37°c for 3 h. this step was performed several times to produce enough material for 150– transformations. the digestions, ligations and transformations were performed as described for vl cloning with following modifications. ligation was performed with 250 ng vh pcr product. after transformation of xl1-blue mrf’, overnight incubation on 25 cm 2 × yt-gat plates and resuspension in 25 ml 2 × yt medium, glycerol stocks of each library were made using 800 μl bacteria solution and 200 μl glycerol and stored at −80°c. for the final library one glycerol stock of each sublibrary was thawed, mixed together, aliquoted and stored at −80°c. the antibody gene libraries hal9/ were packaged separately inoculating 400 ml 2 × yt-ga with a library glycerol stock. the bacteria were grown to an optical density at 600 nm of – at 37°c and 250 rpm. 25 ml bacterial culture were infected with  ×  hyperphage particles, incubated at 37°c for 30 min without shaking followed by 30 min at 250 rpm. infected cells were harvested by centrifugation for 10 min at 3220xg. the pellet was resuspended in 400 ml 2 × yt-ak. phage were produced at 30°c and 250 rpm over night. the bacteria were centrifuged for 20 min at  × g. phage particles in the supernatant were precipitated with 1/ volume of 20% polyethylene glycol /  m nacl solution for one hour on ice with gentle shaking and pelleted by centrifugation for one hour at  × g at 4°c. the precipitated phage were resuspended in 10 ml phage dilution buffer, 1/ volume of peg solution was added and incubated on ice for 20 min, followed by centrifugation for 30 min at  × g and 4°c. the pellet was resupended in 1 ml phage dilution buffer. residual bacteria and cell debris were removed by additional centrifugation for 5 min at 16000 × g at 20°c. supernatants containing antibody phage were stored at 4°c. phage titration was done as described before. the scfv display rates of the packaged libraries were analyzed by 10% sds-page, western blot and anti-piii immunostain. wildtype piii has a calculated molecular mass of  kda, but it runs at an apparent molecular mass of 65 kda in sds-page. accordingly, the scfv::piii fusion protein runs at about 95 kda. antibody selection antibody selections were performed against proteins or peptides as described before. the elution with trypsin - phal and the former vector phal contain a trypsin site between the tags and giii - is more efficient as elution by ph shift.  analysis of the new phage display vector phal30 a prerequisite for a good up to date antibody gene library is a phagemid that allows both, a high display level of functional antibody fragments on phage and a good expression of soluble antibodies for screening. the new design of the phagemid generation phal is based on the phal. in the first optimization step and independent of kappa or lambda light chains, the tag order in the phal phagemid was changed from the initial his/myc-tag in phal to myc/his tag. for evaluation of the expression capacity of both phagemids, three different soluble scfv antibody fragments were produced in 150 ml e.coli xl- blue mrf’ culture for 4 h at 25°c and 250 rpm. functional soluble scfv antibody fragments were quantified by antigen elisa in the production supernatant, the periplasmatic extract, the osmotic shock fraction and the eluate after imac purification. except for the osmotic shock preparation, the production level with the phal phagemid was always significantly improved. after imac purification of the supernatants, the yields of ht186-d were 1 mg/l for phal and 2 mg/l for phal in case of tm43-e the yields were 1 mg/l for both vectors and for d the yields increased from  mg/l for phal to 1 mg/l for phal the production yields in the periplasmic fraction of scfvs ht186-d and tm43-e after imac purification were improved from  mg/l, and  mg/l with phal to  mg/l and  mg/l, respectively, with phal figure schematic drawing of phal and phal abbreviations: lacz promoter: promoter of the bacterial lac operon; rbs: ribosome binding site; pelb: signal peptide sequence of bacterial pectate lyase, mediating secretion into the periplasmic space; vh: variable fragment of the heavy chain; blue box: first six amino acids of ch part of the linker; lc: light chain; dark blue box: first / aminoacids of cl; ochre: ochre stop codon; amber: amber stop codon; his-tag: 6xhistidine tag; terminator: sequence terminating transcription; myc-tag: eqkliseedln tag. the elements of the inserts are not drawn to scale. comparision of phal and phal comparision of the production of soluble antibodies. sn supernatant, pe periplasmatic extract, os osmotic shock fraction, eluate after imac purification, od450nm-620nm optical density at 450 nm, scfv antibody fragments analyzed: d, ht186-d and tm43-e antigens: lysozyme, muc- and ompd. comparision of scfv-phage antigen binding. od450nm-620nm optical density at 450 nm, scfv antibody fragments d, ht186-d sh313-b and tm43-e antigens: lysozyme, muc cd and ompd. next, four different phal and phal phagemids were packaged with hyperphage. the resulting phage titers were comparable among each other. they ranged from 6 ×  to 6 ×  cfu/ ml culture medium. the scfv display level on phage was identical, as confirmed by western immunoblot. approximately 90% of g3p was fused to the scfv antibody fragments. a functional comparison of phal and phal scfv-phage regarding antigen binding was performed by titration antigen elisa. the titration curves were similar for three different scfv-phage, further illustrating similar display level. for tm43-e more functional scfv were displayed on phage. taken together, both phagemids are almost identical in phage display level and phage binding assays, but the phal phagemid provided a significant increase in production of soluble antibody fragments for screening which may improve the hit rate in initial screening assays. influence of the phenylalanine residue in kappa cl on scfv phage display target independent, it was observed that scfv antibody fragments bearing a vК light chain were less frequently isolated from hal7/ than those with a vλ light chain. a possible explanation could be a lower expression of antibody fragments with a vК light chain. therefore, the phagemid was further optimized by deleting the bulky c-terminal phenylalanine of the vК light chain. first, the soluble production level of five known scfv fragments in phal and six known kappa scfv fragments in phal was analyzed and compared by western immunoblot. the deletion of the phenylalanine in the vК light chain resulted in a higher production level for all tested scfv. further expression analysis by western immunblot included the comparison of randomly chosen scfv fragments from the kappa hal antibody gene library and their phenylalanine deletion version. the expression levels were higher with the phenylalanine deletion mutants in cases, slightly lower for three clones and in the same range for the remaining clones. construction of hal and hal10 using blood samples obtained from caucasian, african, indian and chinese non-immunized human donors, the new antibody libraries hal and hal were constructed using the improved phagemid backbone phal in detail, blood lymphocytes from caucasian, african, indian and chinese non-immunized human donors were isolated for library construction. lymphocyte mrna was reverse transcribed to cdna and the antibody gene repertoire was amplified in two steps. in the first step, vh and the full length light chains were amplified using a set of framework forward primers and igm, kappa and lambda constant domain reverse primers. in the second step, specific restriction sites were incorporated for cloning into the phal phagemid vector. for the second amplification step of vh and lambda subfamilies the dna antibody repertoire from donors of the previously constructed hal was added for construction of the new hal and hal libraries. both libraries contain the same vh repertoire but differ in their light chain repertoire. hal includes all lambda subfamilies, hal all kappa subfamilies except the pseudogene encoding vκ cloning of the antibody genes was done in two steps. first, light chain genes were cloned with 1 ×  independent clones for each library. then heavy chain genes were cloned in the light chain containing phagemid leading to a final repertoire size of the hal and hal scfv libraries of × and × respectively. analysis of v-gene subfamily distribution to assess the diversity of the libraries, bacterial colonies from library transformation plates were analyzed by colony pcr and sequencing. in total full length scfv encoding sequences for hal and sequences for hal were aligned to human germline v gene segments using vbase. to compare the initial diversity of the libraries with the germline usage after selection, antibodies selected against targets were analyzed. of these selected antibodies from libraries hal and hal % were bearing a vκ light chain compared to 4% of antibodies selected from hal7/ the antibody subfamily distribution of the unselected hal7/ libraries, the subfamily frequency of selected scfvs from hal7/ and the in vivo distribution are shown in figure 3a-c. the heavy chain diversity of the unselected hal9/ libraries is similar to the subfamily distribution found in vivo. vh and vh are the dominating vh subfamilies in the initial library as well as for the selected scfvs. vh shows a slight underrepresentation in the initial library, whereas the vh subfamily is overrepresented in all unselected and selected hal libraries. vκ and vκ are the most abundant subfamilies, which is consistent with findings in vivo. vκ is overrepresented in the unselected hal library but could not be retrieved after selection and in contrast vκ was significantly enriched during selection. in the vλ repertoire of hal the vλ1- are the most abundant subfamilies similar to the subfamily distribution found in vivo, but the frequency of vλ1- is lower compared to the in vivo frequency due to an overrepresentation of subfamilies vλ4/6/7/8/ which are found only in low frequency in vivo.figure antibody subfamily distribution found in the hal9/ libraries, in the selected scfvs from the hal9/ libraries, in the hal7/ libraries [ 31 ] and in vivo [ 45 ]. abundance of vh. abundance of vκ. abundance of vλ. sequence analysis indicated a high antibody germline gene diversity for the heavy-chain and light-chain repertoires of the hal9/ libraries. the identified heavy chain repertoire in this limited sample already covered of functional vh genes. in addition, one vh gene occurred in the unselected libraries that has not yet been confirmed to be functional. vh germline genes were observed in frequencies between % and % in the unselected hal and hal with no significant differences between the libraries. the comparison of the gene usage before and after selection shows a clear enrichment of some vh genes. the most abundant vh genes after selection were ighv3- increased from % in the unselected libraries to % after selection, ighv1- increased from % to % and ighv1- increased from % to % after selection. the frequency of the remaining vh germline genes remained constant or was lowered after selection. most strikingly, the usage of all vh genes was considerably reduced in selected antibodies. only of vh germline genes were found again after selection with a ten-fold reduction in total frequency, decreasing from % in the unselected libraries to % after selection.figure two-dimensional heatmap illustrating vh–vλ gene pairing frequencies in the unselected hal library and in the selected scfvs from the hal library. frequency of all functional vh genes and vλ genes are shown. genes that are not confirmed to be functional, but were found in the library/were selected are marked in orange. antibodies of the initial library and selected scfvs were analyzed. the percentual amounts of each germline gene are given separetely for vh and vλ. two-dimensional heatmap illustrating vh–vκ gene pairing frequencies in the unselected hal library and in the selected scfvs from the hal library. frequency of all functional vh genes and vκ genes are shown. genes that are not confirmed to be functional, but were found in the library/were selected are marked in orange. vκ genes are all classified as non-functional and not inclued in this overview. antibodies of the initial library and selected scfvs were analyzed. the percentual amounts of each germline gene are given separetely for vh and vκ. of the functional vλ genes were found in the hal library sample. one vλ gene was found in the unselected hal as well in selected scfvs that is predicted to be not functional. as seen for the heavy chain repertoire, the frequency of several vλ germline genes changed during the selection process. usage of the vλ subfamily was increased after selection mostly due to a higher abundance of the iglv1- germline gene, increasing from % in the unselected library to % after selection and a higher abundance of iglv1- increasing from % to %. in the vλ subfamily, the frequency of the iglv2- germline gene showed a slight increase from % to % after selection but the overall abundance of vλ genes decreased due to a lower usage of the remaining germline genes. three of nine different vλ germline genes were retrieved in high frequency before and after selection: iglv3- iglv3- and iglv2- the findings reflect the in vivo subfamily distribution, where iglv3- and iglv2- account for ~80% of vλ. after selection the frequency of iglv3- was reduced from % to % and increased for iglv3- from % to %. usage of iglv3- remained constant. the abundance of the most prevalent vλ gene iglv6- in the unselected hal was decreased from % to % after selection. in the hal library of functional vκ germline genes were observed. two vκ genes found in the unselected library were described to be only potentially functional. the most abundant vκ germline gene before selection was igkv4- with a frequency of ~25%. this is a more than twofold higher prevalence than found in vivo and usage of igkv4- after selection was reduced to ~4%. the frequency of vκ subfamily genes was raised from 37% in the unselected library to 48% after selection. three genes igkv1- igkv1-d and igkv1-d increased from to %, to % and from to %, respectively. vh and vl germline gene pairings the abundance of heavy- and light-chain pairings that were observed in the unselected libraries and within selected antibodies are illustrated in figure  for vh-vλ combinations and in figure  for vh-vκ combinations. in the unselected libraries no particular vh-vl combination is dominating. the pairings are evenly distributed depending on their total abundance. vh-vλ pairings were observed in frequencies between % and % in the unselected hal with vh3-30/vλ6- being the most abundant combination. in the unselected hal pairing frequencies up to % were observed for vh-vκ due to the high abundance of the igkv4- germline gene. however, after individual selections a clear preference for particular vh-vl pairings was detected. for vh-vλ pairings the most prevalent combination was vh3-30/vλ3- which was observed in % of the selected antibodies. the λ3- gene showed a preference for pairing with vh germline genes. the vh3- germline gene was by far the most abundant vh gene after selection and paired with nearly all light chain genes in high frequency. interestingly, the light chain gene vλ8- paired almost exclusively with vh3- the remaining vλ germline genes showed preferential pairing with the vh and vh germline genes and with lower frequency also to the vh6- germline gene. a second vh subfamily gene, vh3- was also observed in high frequency after selection. similar to vh3- no clear preference in pairing with any vλ genes segment was seen. for three vh genes a more distinct preference for single vλ genes was observed. the combinations vh1-46/vλ1- and vh1-69/vλ1- were enriched to % and the combination vh1-18/vλ1- was enriched to %. the five most common vh-vλ combinations account for nearly 20% of all selected antibodies. an enrichment of the vh3- germline gene after selection was also observed for the vh-vκ gene pairing. furthermore a high frequency of vκ and vκ genes occurred after selection, but due to the relatively small sample size of selected antibodies bearing a kappa light chain no significant conclusion can be made about enrichment of single vh-vκ combinations. cdr length and amino acid distribution of light-chain and heavy-chain length and amino acid distribution of cdr3-l and cdr3-h of the hal and hal libraries were analyzed. for example, cdr3-h sequences of the unselected libraries and sequences of selected antibodies were analyzed and compared. the cdr3-h length distribution before and after selection is depicted in figure 6a. in the unselected libraries, the cdr3-h length ranges from to aa with a median length of about aa. cdr3-h longer than aa are occurring only in low frequency. after selection, the distribution is very slightly shifted towards a cdr3-h length with a median of aa. cdr length of – aa are found in high frequency after selection but cdr3-h length longer than aa were not detected. long cdr-h sequences are often internally stabilized by disulfide bridges in a very characteristic manner. a first internal cysteine is always followed by four amino acids - often serine and glycine rich - and completed by the second cysteine.figure heavy and light chain cdr length distribution. cdr-h length distribution in hal9/ cdr-h lengths in unselected library and in selected scfvs from hal9/. cdr-l length distribution in hal cdr-l lengths in unselected library and in selected scfvs from hal. cdr-l length distribution in hal cdr-l lengths in unselected library and in selected scfvs from hal. the cdr3-h amino acid composition was analyzed for the unselected hal9/ libraries. the amino acid usage at each position is shown for cdrs with up to aa in length. the cdr3-h often starts with an alanine and arginine in the first two positions and throughout the whole cdr the amino acids glutamate, serine, tyrosine and glycine are favored. at the last three positions the “fdy” motive of the ighj segment is often found. significantly, the cdr3-h amino acid usage found in selected scfvs is largely the same compared to the amino acid usage in the initial libraries.figure heavy chain cdr amino acid distribution. cdr-h amino acid distribution in unselected hal9/. cdr-h amino acid distribution in selected scfvs from hal9/. distribution of amino acids at each position of cdr-h in kabat numbering. amino acids 100-j, and correspond to the last residues of each cdr3-h for the cdr3-l length distribution of hal before and after selection sequences of the unselected library and sequences of selected antibodies were analyzed. in the unselected library the cdr length ranges from to aa with a median length of about aa. the most common cdr length for lambda light chains are or aa that account together for more than 80% of all found cdr3-l lengths. after selection, cdrs with a length of aa were found more frequently and the occurrence of cdrs with a length of aa was decreased. cdr3-l length distribution of hal was analyzed with sequences of the unselected library and sequences of selected antibodies. in the unselected library the cdr length ranges from to aa. most kappa light chains are bearing a cdr with a length of aa and the length distribution did not change significantly after selection. the cdr3-l amino acid distribution of the unselected libraries was analyzed separately for lambda and kappa light chains. the amino acid usage at each position is shown for cdrs with up to aa in length for lambda light chains and for cdrs with up to aa in length for kappa light chains. at most positions of the light chain cdr the usage of amino acids is restricted, e.g. 70% of antibodies have a aspartate at lambda cdr position or 90% have a proline at kappa cdr position but there is still a quite high diversity found in amino acid usage throughout the whole cdr. again, the cdr3-l amino acid distribution found in selected scfvs is almost the same when compared to the amino acid usage of the initial libraries hal9/.figure light chain cdr amino acid distribution. cdr-l amino acid distribution in hal. cdr-l amino acid distribution in selected scfvs from hal. cdr-l amino acid distribution in hal. cdr-l amino acid distribution in selected scfvs from hal. distribution of amino acids at each position of cdr-l in kabat numbering. discussion since the development of phagemids for antibody phage display by breitling et al., the technology was continuously further developed. the most used phage display vectors have the tag order his-myc when using both tags, e.g. pcantab3his, pces, phen, phal, pit, pmod or pmid. to our knowledge, there is only one phage display vector using the opposite orientation: psd. comparing both tag orders, the myc-his order results in improved production of functional scfv compared to his-myc whereas the display of functional scfv on phage is not effected. using a kappa and a lambda antibody gene library in the same selection, we have observed that the output of selected kappa antibodies was always lower compared to lambda antibodies. løset et al. and tiller et al. also describe a lower production yield of kappa scfvs or fabs compared to lambda antibodies that confirms our observation with the hal libraries. the scfv design in phal included the first six amino acids of ch as part of the linker and the first amino acids of cl lambda, respectively the first nine amino acids of cl kappa. the last amino acid in cl kappa used in the scfv design is a phenylalanine. phenylalanine is encoded by only two codons which may lead to a reduced translation and has a bulky hydrophobic benzol side group which may hamper solubility. in projects with macaque immune libraries using also phal and derived phal vectors, the phenylalanine was omitted. the selected kappa scfv were produced well, leading to a generation of kappa scfv against different targets. for human scfv, deletion of phenylalanine improved the expression rate of known kappa antibodies and randomly chosen kappa clones. this modification increased the rate of selected kappa antibodies from 4% using hal4/7/ to % when using hal9/ using the novel vector phal and scfv design, two new universal human naive antibody gene libraries were constructed. the theoretical diversity of the hal9/ libraries is with × independent clones in the same range like other published scfv or fab libraries with a theoretical diversity in the range of 1x1010-1x e.g. the naive mccafferty scfv library, the naive pfizer scfv library, the naive cat scfv library, the naive/synthetic dyax fab library, the synthetic ylanthia fab library or very recently published the philodiamond scfv library. the representation of antibody subfamilies in the hal9/ libraries is comparable with the hal7/ library, it differs only in some minor points, e.g. vh vκ and vλ are more abundant in hal9/ in general, vh gene usage is dominated by vh and vh dominant vl are usually vκ vκ vκ and vκ and vλ by vλ vλ vλ and vλ in the new libraries, the distribution of v genes is comparable with their frequency in vivo but with following exceptions. the subfamily vh is more abundant in vivo whereas vκ and vλ are more frequent in hal antibody gene libraries and rare in vivo. the main difference is the frequency of vλ1 > vλ2 > vλ in vivo compared to vλ3 > vλ1 > vλ in hal9/ the ylanthia library fits perfectly with the in vivo distribution. the distribution of v genes for vh and vκ of hal9/ is in accordance with the pfizer library. a comparison of vλ with hal is not possible, because the pfizer library lacks most vλ genes. compared to hal9/ the distribution of v genes in the cat library differs more from in vivo situation. here, vh is dominated by vh and vκ is dominated by one vκ gene. with ~ amino acids, the average hal9/ cdr-h length is longer than in the naive pfizer or synthetic ylanthia libraries, but slightly shorter compared to the dyax library with ~ amino acids. in addition more very long cdr-h are found in hal9/ compared to the pfizer library. the average length of cdr-l for λ is eleven amino acids and therefore two amino acids longer as the average length of cdr-l for κ. in hal9/ or different aa are occurring at each cdr-h position whereas for ylanthia to different aa are possible at each position, planned by rational design. in ylanthia, the cdr-h is dominated by serine, tyrosine and glycine. in the naive hal9/ libraries, the amino acid repertoire in cdr-h is more balanced, but the frequency of tyrosine increases from n’terminus to c’terminus as well. significantly, within the group of selected scfvs, the representation of vh antibody subfamilies is largely in accordance with the mccafferty library and pfizer library, but not with the cat library, where vh is dominated by vh1 > vh compared to vh3 > vh for mccafferty, hal9/ or pfizer library. for vκ, more vκ than vκ were selected from hal or mccafferty, whereas from pfizer or cat mostly vκ were selected. regarding vλ, here vλ1- and are mainly isolated from mccaffery and hal whereas vλ is rarely selected from cat. the frequency of selected vh vκ and vλ antibodies from hal9/ is very low compared with the frequency in the initial library. the same was observed for hal7/ and cat. the vh4- antibody gene is described as toxic for b-cells. as consequence, two vh4- and vh4- genes were excluded when constructing the synthetic ylanthia library, despite the fact, that these vh genes are very frequent in the natural human antibody repertoire. remarkably, a majority of antibodies selected from macaque immune antibody gene libraries against botulinum a toxin are vh antibodies, especially vh4-. the macaque antibody genes are very similar to their human counterparts. therefore, the vh gene family may be preadapted to some targets, or at least best suited to structurally complement the respective epitopes. the average cdr length of cdr-h is only very slightly shorter after selection compared with the initial library, presumably due to a better growth of bacteria producing shorter antibody genes during antibody selection. the length of the cdr-l does not significantly differ in selected antibodies. the cdr composition in the cdr-l is completely different between λ and κ light chains, giving a hint why two different kinds of light chains have been evolved. very importantly, the frequency of amino acids at each cdr position does not significantly change after selection, clearly demonstrating that any bacterial expression bias is minor, and all amino acids used in the naive human gene repertoire can be found in selected, functional antibodies. some vh-genes are preferred after selection, e.g. vh1- vh1- vh3- vh3- these are also v-genes often used in ylanthia and cat. notably, the very common vh3- gene results in a low igg expression rate, but is most frequent in the natural human antibody repertoire. this v-gene is a very stable and was used also for semisynthetic libraries, e.g. tomlinson library. for κ light chain, igkv1- igkv1d- igkv1d- and igkv3- are selected frequently. igkv3- is the most used κ gene in the natural repertoire and is used for ylanthia. the λ v-genes iglv1- iglv1- iglv2- iglv3- iglv3- and iglv6- were most frequently found after hal selection. iglv2- is the most used λ v-gene in the natural antibody repertoire and is used for ylanthia, iglv1- and iglv1- are also often used in nature, but iglv1- was excluded from the ylanthia design.  the naive antibody gene libraries hal9/ have unique features compared to the libraries published earlier. the libraries have a slightly greater maximum diversity than the mccafferty library, they comprise more lambda v-genes and have longer cdr-h compared to the pfizer library, the distribution of v-genes resembles more the natural antibody repertoire compared to cat and they show more cdr-h diversity than ylanthia. the successful generation of > antibodies against > targets with overwhelming success and in short time with miniaturized systems illustrates the huge advances in human library construction and use achieved since the first description of this method. mark schütte and michael hust contributed equally to this work. competing interests the majority of authors of this work are employed by merck kgaa, mab-factory gmbh or yumab gmbh, or are shareholders of these companies. authors’ contributions jk and sw performed experiments, participated in the design of the study, analyzed data and drafted the manuscript. dm and ft performed experiments. af and ts participated in the design of the study and analyzed data. sd participated in the design of the study, analyzed data and drafted the manuscript. hg provided material and performed experiments. lt and bh participated in the design and coordination of the study and analyzed data. ms performed experiments, participated in the design and coordination of the study, analyzed data and drafted the manuscript. mh participated in the design and coordination of the study, analyzed data and drafted the manuscript. all authors read and approved the final manuscript. authors’ information mark schütte and michael hust, both senior authors. 
we show that changing the tag order to myc/his improved the production of soluble antibodies, but did not affect antibody phage display. for several published antibody libraries, the selected number of kappa scfvs were lower compared to lambda scfvs, probably due to a lower kappa scfv or fab expression rate. the hal libraries and antibodies selected against targets were analyzed regarding the used germline v-genes, used v-gene combinations and cdr-h3/-l length and composition. the naive antibody gene libraries hal and hal with a combined theoretical diversity of × independent clones, were constructed from healthy donors using improved phage display vectors. deletion of a phenylalanine at the end of the cl linker sequence in our new phagemid design increased scfv production rate and frequency of selected kappa antibodies significantly. antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. here we describe the design, construction and characterization of an optimized antibody phage display library. in detail, most common phagemids employed for antibody phage display are using a combined his/myc tag for detection and purification. the highly diverse universal antibody gene libraries hal9/ were constructed using an optimized scfv phagemid vector design. the amino acid diversity and distribution in the cdr-h of the initial library was retrieved in the cdr-h of selected antibodies showing that all cdr-h amino acids occurring in the human antibody repertoire can be functionally used and is not biased by e. coli expression or phage selection.
 antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. from naive antibody gene libraries - in theory - antibodies against any target can be selected. here we describe the design, construction and characterization of an optimized antibody phage display library.  the naive antibody gene libraries hal and hal with a combined theoretical diversity of × independent clones, were constructed from healthy donors using improved phage display vectors. in detail, most common phagemids employed for antibody phage display are using a combined his/myc tag for detection and purification. we show that changing the tag order to myc/his improved the production of soluble antibodies, but did not affect antibody phage display. for several published antibody libraries, the selected number of kappa scfvs were lower compared to lambda scfvs, probably due to a lower kappa scfv or fab expression rate. deletion of a phenylalanine at the end of the cl linker sequence in our new phagemid design increased scfv production rate and frequency of selected kappa antibodies significantly. the hal libraries and antibodies selected against targets were analyzed regarding the used germline v-genes, used v-gene combinations and cdr-h3/-l length and composition. the amino acid diversity and distribution in the cdr-h of the initial library was retrieved in the cdr-h of selected antibodies showing that all cdr-h amino acids occurring in the human antibody repertoire can be functionally used and is not biased by e. coli expression or phage selection. further, the data underline the importance of cdr length variations.  the highly diverse universal antibody gene libraries hal9/ were constructed using an optimized scfv phagemid vector design. analysis of selected antibodies revealed that the complete amino acid diversity in the cdr-h was also found in selected scfvs showing the functionality of the naive cdr-h diversity. keywords scfvphage displayantibody engineeringlibrarypanningscreeningissue-copyright-statement© the author 2015 