INTERNAL CONTROL AND METHOD FOR SURVEILLANCE OF Gap-LCR

Abstract: There is disclosed an internal control for being used in a "Gap-filling Ligase Chain Reaction" (Gap-LCR). The synthetic oligonucleotide functioning as the internal control has approximately the same length and identical four LCR probe sites as the target nucleic acid. The internal control and the target DNA is consequently amplified in a Gap-LCR with substantially equal efficiency. Additionally the synthetic oligonucleotide is modified in the gap-sequence between the hybridised LCR-probes in such a way that it contains a site for a restriction enzyme. By treating the LCR product with this restriction enzyme, the enzyme will cleave the PCR product from the internal control, whereas the LCR product from the target may be analyzed separately. The disclosed internal control may thus be used both in qualitative and in quantitative LCR-based analyses.

Description: INTERNAL CONTROL AND METHOD FOR SURVEILLANCE OF Gap-LCR. The present invention concerns an internal control for use in the "gap-filing ligase chain reaction" (Gap-LCR) . The internal control being a synthetic nucleotide, has substantially the same length and contains the hybridi¬ zation sites for the same four LCR-probes as the target nucleic acid (the target sequence) . The internal control and the target become accordingly amplified in a GAP-LCR with substantially the same effectiveness. Additionally the synthetic oligonucleotide is modified in the gap between the LCR-probes in such a way that it comprises a unique site for a restriction enzyme. Treatment of the LCR product with such a restriction enzyme will cut the internal control LCR product so that the LCR product from the target may be analyzed separately. The disclosed internal control may be used both in qualitative and quantitative LCR-based analysis. Background Analyses based on enzymatic amplification of nucleic acids sometimes give false negative results e.g. on ac¬ count of the presence of inhibitors in the samples. An inhibitor may for instance keep the enzymes from per- forming the reactions effectively. Samples containing inhibitors may be erroneously considered to lack a given target since their analyses does not give any signal. An addition of an internal control to the samples will re¬ veal the presence of inhibitors since it is expected that the internal control always will be amplified and will give a signal. The internal control functions thus as a qualitative control. The use of an internal control in polymerase chain re- action (PCR) based analyses has been disclosed by Matsu- mara et al. (Jpn. J. Clin. Oncol. 1992, 22:335-341). Their PCR with two sets of primers amplify a target of interest, but simultaneously another target functioning as an internal control in the reaction is amplified. Becker and Hahlbroeck (Nucl. Acid Res. 1989, 17:9437- 9446) disclose a PCR based on a procedure wherein both target and internal control DNA is amplified by using the same two primers. Their internal control has become mutated in vitro so that it contains a unique site for a restriction enzyme. The PCR product from the internal control may be cleaved with the restriction enzyme and then be separated from the PCR product from the target by gel electrophoresis. Gilliland et al. (Proc. Natl. Acad Sci. USA 1990, 87:2725-2729) and Ursi et al. (APMIS 1992, 100:635-639) discloses internal controls which contain extra blocks of DNA between the PCR primer-sites. After PCR-amplification by using the same two primers the PCR- product from the internal control will have a different length than the target PCR product. These two may either be separated by gel electrophoresis or by hybridization with two selective probes. Also for "nucleic acid se- quence amplification" (the NASBA system) there has been disclosed by Kievits and Lens (WO 94/04706) a procedure wherein both target and a longer/shorter internal control become amplified simultaneously by using the same pri¬ mers. Both the PCR and the NASBA internal controls may be used for quantitative analyses, for instance by densiometric measurements of the two bands appearing in gel electro¬ phoresis of the amplification product. So far ligase chain reaction (LCR) based analyses have lacked an internal control to be used in quantitative analyses. In a standard LCR disclosed by Backman (Euro¬ pean Patent Office - 320.380 - 1987) the amplification of the target is being performed with only DNA ligase. In the reaction four probes are hybridised in pairs adjacent to each other on each strand in the target DNA. The nicks between the probes are closed by the DNA ligase so that two new DNA strands are produced. These may be used as a target in the next cycle of the process, see figure la. The LCR internal control disclosed by Griffiths and Emery (WO 93/02215) has a different sequence than the target DNA on one side of the nick. The LCR amplification of the internal control requires thus the use of two extra LCR probes. These hybridise to the unique part of the control DNA, whereas the two LCR probes being common, hybridise to that part which is identical between the control and target DNA. In this way the nicks being ligated by the enzyme are being made. This has been shown schematically in fig. lb. The amplification pro¬ ducts from the target and from the internal control may be separated e.g. by sequence specific hybridisation with selective probes. Even if this internal control may work as a qualitative control and reveal the presence of pos- sible LCR inhibitors its effectivity in the amplification of the target and control DNA will be different on ac¬ count of unequal sequences in the LCR probes. This lim¬ its the applicability and usefulness of such designed internal controls. Fig. la is a schematical diagram of a standard LCR ampli¬ fication. Fig. lb shows the LCR amplification of an internal con- trol wherein two extra probes are used as disclosed by Griffiths and Emery. Detection of the two LCR products may be done by hybridisation with selective probes an account of different sequences on the right side of the nicks. Fig. 2 is a schematic diagram depicting a gap-filling ligase chain reaction amplification (Gap-LCR) wherein both DNA polymerase and DNA ligase is used. Fig. 3 a-c shows examples of modifications in the control DNA with the purpose of creating a unique site for a restriction enzyme in the LCR product from the internal control. Only the polymerase step in the Gap-LCR process is indicated. In relation to fig. la, please notice that the LCR of the internal control is being performed by using different probes as compared to the LCT of the target. The two LCR products get thus different sequences. A modified LCR being disclosed by Backman et al (European Patent Office - 439.182A - 1991) gives an increased spec¬ ificity. In this gap-filling LCR (Gap-LCR) two gaps arising between each of the probes in the two pairs of hybridised LCR probes are filled in with DNA polymerase before the ligation reaction may occur, see figure 2. Disclosure The present invention concerns an internal standard to be used both in qualitative and in quantitative LCR-based analyses. It has the following basis: The gap between the probes in Gap-LCR allows some modification of the sequence in the gap, e.g. creation/deletion of a site for a restriction enzyme. This modification of the control DNA sequence is very limited and is dependent on the gap and probe sequences. This is in sharp contrast with the internal controls containing unique sites for restriction enzymes to be used in PCR. The modification of the Gap- LCR internal control sequence may comprise addition/dele¬ tion/exchange (see figure 3) . of one or two deoxy- nucleoside triphosphates in addition to the base(s) which are necessary in the LCR of the target DNA. In PCR, on the other hand, a modification creating/deleting a site for a restriction enzyme is easily performed since there exist a relatively long distance between the PCR primers and all the four deoxynucleoside triphosphates which are present in the reaction. However, a larger modification of the control DNA in the Gap-LCR, which would lead to a need for all four the deoxynucleoside triphosphates to get the gap filled, would convert the LCR to a PCR. The amplification with the use of only DNA polymerase has significantly different reaction kinetics than the Gap- LCR wherein two enzymes, DNA polymerase and DNA ligase, are used. When the differences in sequence between the target and control DNA are small, the control DNA will be amplified in Gap-LCR with approximately the same effec- tivity as the target DNA. The amplification products from the present internal control and from the target DNA may be separated according to a simple treatment with restriction enzymes. This is the key to the present invention. The present internal control may thus func¬ tion as both a qualitative and a quantitative internal standard for which there exists a need in qualitative enuring of LCR-based analyses, something which gives a significantly expanded area of use for such analyses. With respect to fig. 3 a-c, the process indicated in this chart may obviously also be followed when removing a unique restriction site in the LCR product from the in¬ ternal control DNA when target DNA contains a correspond¬ ing structure in its gap sequence. EXAMPLE The principle behind the present method is a construction of a nucleotide sequence in the internal control which is of mainly the same length and identical LCR probe sites as the target DNA. The internal control is designed with a unique site for a restriction enzyme in contrast with and as opposed to the target DNA. Accordingly the target and the internal control are amplified in Gap-LCR with approximately the same effectivity. A uniquely coding sequence from Hepatitis B virus (HBV) was chosen as a suitable target for the Gap-LCR amplification and for designing the internal standard. Target nucleic acid sequence (50 nucleotides) : The chosen HBV sequence contains the same sequences as the probes 1 and 3 joined together with -GCC- (the gap sequence) . Notice that only one single DNA strand has been depicted in the figure. Gap sequence Site for PROBE 2 -GCC- Site for PROBE 4 Internal control sequence (synthetic oligonucleotide) (51 nucleotides) . The sequence of the synthetic oligonucleotide (the in- ternal control) is equal to the target nucleic acid sequ¬ ence except for the gap sequence which has been modified to -GGCC-. Gap sequence Site for probe 2 -GGCC- Site for probe 4 The nucleotide sequence for the synthetic oligonucleotide (the internal control) has a unique site for the restric- tion enzyme Haelll (-GGCC-) , whereas the sequence in the target does not. Thus when treating the amplified mate¬ rial with Haelll, the amplified internal control will be cut whereas the amplified target remains unchanged. Gap-LCR of target (HBV sequence) : The probes 1 and 2 have been conjugated with carbazole (Ca) and the probes 3 and 4 with adamantane (Ad) . t "Gap-filling reaction" (Dna polymerase) ; Λ Ligation reaction (DNA ligase) . Cycle 1: HBV sequence 5' 3' A - C- l«©.\* -Ad 3' Probe 2 Λ t t Probe 4 5' Cycle 2: Complementary HBV sequence (cDNA) 3' Probe 2 Probe 4 5' and HBV sequence 5' I I I I I I I I I I I I I I I I I I I I Ca- A - C- 3' Probe 2 Λ t t Probe 4 5' Repeat cycles (amplified product of target HBV.: 3' Probe 2 Probe 4 Gap-LCR of the internal control: The probes 1 and 2 have been conjugated with carbazole (Ca) and the probes 3 and 4 with adamantane (Ad) . t "Gap-filling reaction" (DNA polymerase) ; Λ Ligation reaction (DNA ligase) . Cycle 1: Internal control sequence Cycle 2: Complementary internal control sequence (cDNA) 3' Probe 2 Probe 4 5' and Internal control sequence Repeat cycles (amplified product of internal control): Haem 3' Probe 2 U Probe 4 5' I I I I I I I I I I I I I I I I I I I I I 5' Probe 1 ft Probe 3 3' Haem The amplified internal control contains a unique site for the restrictions enzyme Haelll. Haelll cuts the LCR- product from the internal control in such a way that this may not be detected in the IMx-system which requires both carbazole and adamantane on one and the same DNA strand. Detection of amplified material: The quantity of amplified product is measured by using the IMx-system (Abbott) . The amplified material (target and internal control) reacts with particles coated with anti-carbazole. The quantity of bound material on the particles is detected by using anti-adamantane conjugated with alkaline phosphatase. This enzyme gives a colour response. The amplified control contains a unique site for the restriction enzyme Haelll (-CCGG-) , whereas the amplified target DNA does not. After a mixture of the two LCR products have been treated with Haelll, the quantity of amplified target may be measured alone. The difference in signal between the untreated (uncut) and the Haelll- treated (cut) material gives the original quantity of target DNA in the sample by a simple ratio calculation, see infra. The disclosed method may accordingly be used both in qualitative and in quantitative Gap-LCR-based analyses. Typical LCR-results: The Gap-LCR was performed as described by Marchall et al. (PCR Methods and Applications, 1994, 4:80-84) with the following modifications: The 55 repeated cycles of the LCR comprised: Denaturing the double-stranded DNA at 85°C followed by hybridisation/elongation/ligation at 55°C. The amplification was started by using a "Wax mediated Hot Start" and the denaturing of the first cycle lasted for 5 minutes. Table 1: IMx-results of a synthetic control and a HBV- positive sample, untreated and treated with Haelll (the original amount of synthetic control DNA: 10 3 molecules) LCR product ; IMx-rate Synthetic control DNA 206,0 Haelll-treated synthetic control DNA 30,6 Synthetic control DNA + HBV sample DNA 922,1 Haelll-treated synthetic control DNA + HBV sample DNA 857,7 DNA negative control (H 2 0 control sample) 7,7 HBV DNA negative control (serum sample) 16,8 Positive/negative value: I x rate 50 Since the internal control and HBV DNA in the sample are amplified with approximately equal efficiency, the ratio between the control and the HBV DNA in the Gap-LCR pro¬ cess will be substantially constant during all cycles. The sensitivity level in the Gap LCR is shown in table 2, about 10 HBV DNA copies. By combining the DNA from the control and from the unknown sample, the HBV DNA from an unknown sample can be measured directly after the Gap-LCR and the Haelll treatment, since the amount of control DNA is known. Table 2: IMx test-results of different amounts of com- mercial standard ("Abbott positive control, hepatitis B viral DNA", 3xl0 7 copies/ml) HBV copies IMx-rate 1500 446,0 15 75,6 0,15 20,2 0 14,2 Positive/negative value: IMx-rate 50 Specifically the present invention concerns a method for surveillance of the result of Gpa-LCR (Gapfilling Ligase Chain Reaction) wherein a target nucleic acid sequence enzymatically is amplified to yield amplification pro¬ ducts, wherein an enzyme utilises: a nucleic acid initi¬ ator, the target sequence or amplification product to which it hybridises as a template, and at least one addi¬ tional nucleoside-containing reactant which can be enzym¬ atically assembled to form amplification products which are complementary to the target sequence as well as a second enzyme acting on the amplified parts of the nu- cleic acid being hybridised to the template to combine the elongated part of the nucleic acid sequence with a second nucleic acid sequence probe, the constructed pro¬ ducts serving as further templates for additional comple¬ mentary nucleic acid sequences after dissociation from the target nucleic acid sequence, the improvement re¬ siding in that there is added to the reaction medium an extra target nucleic acid sequence as an internal control sequence, said internal control sequence being capable of hybridising to two nucleic acid sequences being present forming a gap between them, the sequence of extra target internal nucleic acid sequence being modified; to form or remove at least one (cleavage and/or attachment) site for a restriction endonuclease compared to the original tar¬ get nucleic acid sequence, thus producing a substantially identical nucleic acid sequence as the target sequence , except for the introduced/removed modified site for a restriction endonuclease, whereupon the amplification product of the modified nucleic acid sequence is detected and optionally compared to the amplification product of the target sequence after digestion with a restriction endonuclease. Furthermore, the improvement of the method according to the present invention resides in that the modification of the sequence in the gap comprises addition or deletion or replacement of at least one of the nucleotides. Additionally, the method according to the present in¬ vention includes that at least one of the nucleosides of at least one of the sequences forming the probes in the LCR is modified to become detectable. Such a modi- fication may involve adding at least one detectable com¬ pound to at least one of the nucleosides, said compound preferably, but not necessarily, being a protein, e.g. an antibody, an enzyme, a radioactive label, a substrate for a detectable enzymatic reaction, a chemiluminescent or phosphorescent substance, a detectable compound, e.g. a dye or a magnetic substance. The method according to the present invention may be performed with a material wherein at least one of the nucleotide sequences comprises DNA. At least one of the nucleotide sequences may optionally comprise RNA. The nucleoside sequence to be used as an internal control in the method according to the present invention, is a nucleoside sequence being able to hybridise to a comple¬ mentary nucleoside sequence being elongated, forming or removing, when being combined with the second nucleoside sequence hybridising to the nucleoside sequence wherein the sequence of nucleosides in the internal control se- quence is different from the target sequence, at lest one unique recognition and/or cleavage site for a restriction endonuclease. The nucleoside sequence according to the present in- vention may furthermore comprise at least one nucleotide in the product from the internal control nucleoside se¬ quence which is modified with at least one detectable compound such as a protein, e.g. an antibody, an enzyme, a radioactive label, a substrate for a detectable enzym¬ atic reaction, a chemiluminescent or phosphorescent sub¬ stance, a detectable compound, e.g. a dye or a magnetic substance. The nucleoside sequence according to the present in¬ vention may include a nucleoside sequence comprising DNA or optionally RNA. The Nucleoside sequence being disclosed supra and acting as an internal control in a LCR, may be included in a kit also comprising other reagents being required or pre¬ ferred to perform a LCR. The method and the nucleoside sequences according to the present invention may be used for both quantitative de¬ termination and qualitative surveillance of the progress and/or the results of a LCR, specifically Gap-LCR.

Claims: C l a i m s 1. Method for surveillance of the result of Gap-LCR (Gapfilling Ligase Chain Reaction) wherein a target nu- cleic acid sequence enzymatically is amplified to yield amplification products, wherein an enzyme utilises: a nucleic acid initiator, the target sequence or ampli¬ fication product to which it hybridises as a template, and at least one additional nucleoside-containing re- actant which can be enzymatically assembled to form amp¬ lification products which are complementary to the target sequence as well as a second enzyme acting on the ampli¬ fied parts of the nucleic acid being hybridised to the template to combine the elongated part of the nucleic acid sequence with a second nucleic acid sequence probe, the constructed products serving as further templates for additional complementary nucleic acid sequences after dissociation from the target nucleic acid sequence, c h a r a c t e r i z e d i n that there is added to the reaction medium an extra target nucleic acid sequence as an internal control sequence, said internal control sequence being capable of hybridising to two nucleic acid sequences being present forming a gap between them, the sequence of extra target internal nucleic acid sequence being modified; to form or remove at least one (cleavage and/or attachment) site for a restriction endonuclease compared to the original target nucleic acid sequence, thus producing a substantially identical nucleic acid sequence as the target sequence , except for the intro- duced/removed modified site for a restriction endo¬ nuclease, whereupon the amplification product of the modified nucleic acid sequence is detected and optionally compared to the amplification product of the target se¬ quence after digestion with a restriction endonuclease. 2 . Method according to claim 1 , c h a r a c t e r i z e d i n that the modification of the sequence in the gap between the hybridised areas comprises addition or deletion or substitution of at lest one of the nucleotides. 3. Method according to claim 1 or 2, c h a r a c t e r i s e d i n that at least one of the nucleotides of at least one of the sequences in the LCR product is modified to become detectable. 4. Method according to claim 3, c h a r a c t e r i s e d i n that the modification comprises introducing at least one detectable material on at least one of the nucleosides, wherein said material preferably, but not necessarily, being a protein, e.g. an antibody; an enzyme; a radioactive label; a substrate for a detectable enzymatic reaction; a chemiluminescent or phosphorescent substance; a detectable material e.g. a dye or a magnetic substance. 5. Method according to any of the preceding claims, c h a r a c t e r i z e d i n that at least one of the nucleoside sequences comprises DNA. 6. Method according to any of the claim 1 - 4, c h a r a c t e r i s e d i n that at least one of the nucleoside sequences comprises RNA. 7. Nucleic acid sequence suited as an internal control in the method according to any of the claims 1 - 6, said nucleic acid sequence being able to hybridise to a target sequence with a complementary nucleic acid sequence being elongated, c h a r a c t e r i z e d i n that it creates or removes, when combined to a second nucleic acid sequence hybridising to the nucleic acid sequence wherein the sequence of nucleotides in the internal control sequence is different from the target sequence, at least one un- ique recognition and/or cleavage site for a restriction endonuclease. 8. Nucleic acid sequence according to claim 7, c h a r a c t e r i z e d i n that at least one nu¬ cleic acid in the product from the internal control nu¬ cleic acid sequence is modified with at least one detect¬ able material, such as, but not limited to, a protein, e.g. an antibody; an enzyme; a radioactive label; a sub- strate for a detectable enzymatic reaction; a chemi¬ luminescent or phosphorescent substance; a detectable material e.g. a dye or a magnetic substance. 9. Nucleic acid sequence according to claim 7 or 8, c h a r a c t e r i z e d i n that the nucleic acid sequence comprises DNA. 10. Nucleic acid sequence according to claim 7 or 8, c h a r a c t e r i z e d i n that the nucleic acid sequence comprises RNA.

Inventors: BERG EINAR SVERRE, SKAUG KJELL, BERG, EINAR, SVERRE, SKAUG, KJELL
Applicants: BERG EINAR SVERRE, SKAUG KJELL, STATENS INST FOR FOLKEHELSE, BERG, EINAR, SVERRE, SKAUG, KJELL, STATENS INSTITUTT FOR FOLKEHELSE
Application year: 1996
Main classification: C12Q1
IPC codes: C12Q1