BACKGROUND
reverse transcription pcr , a protocol widely used to produce dna copies of an rna strand of interest, involves a lower temperature reverse transcription step followed by an elevated temperature pcr step  <cit> .
rt-pcr reactions are typically separated into two separate steps.
however, as the number of manipulations in a reaction protocol increases, so does the probability of contamination.
reduction of the two separate manipulation procedures into a one-step rt-pcr protocol provides a more streamlined, high-throughput technique that lowers the probability of contamination by minimizing the number of handling steps  <cit> .
however, one-step rt-pcr protocols are not without inherent limitations and have often been found to be less sensitive than the corresponding two-step protocols  <cit> .
one likely cause for this lower sensitivity is competing extension of pcr primers by reverse transcriptase  <cit>  or dna polymerase  <cit> .
at lower, less discriminatory temperatures of reverse transcription, pcr primer extension may result in off-target amplification products such as primer dimer and mispriming products.
to improve the specificity of rt-pcr, it is necessary to block such primer extension at lower temperatures.
rt-pcr is commonly used in routine molecular diagnostics as a tool for detection of genetic diseases  <cit> .
multiplex rt-pcr is an advanced application of this technique that allows for detection of two or more rna targets in a single tube reaction.
this approach has been used to rapidly detect viral subtypes  <cit>  or to simultaneously identify different disease mutations  <cit> .
multiplex one-step rt-pcr protocols enable the detection of multiple rna targets in a single reaction and allow for quantification of relative mrna expression levels using real-time detection  <cit> .
this technique requires extensive optimization because the use of multiple primer pairs in a single reaction increases the likelihood of primer dimer and mispriming product formation, which may interfere with the amplification of the desired products.
another pitfall of multiplex rt-pcr is the preferential elongation of certain targets, both at the cdna synthesis and pcr amplification stages of the reaction, especially when the targets differ greatly in relative abundance  <cit> .
these difficulties make multiplex one-step rt-pcr a challenging technique with rewarding results when successful.
to overcome the main drawbacks of one-step rt-pcr protocols, researchers have tried several approaches.
one strategy is to employ hot start dna polymerases.
as hot start dna polymerases are designed to only be active at the elevated, more stringent temperatures of pcr thermocycling, dna polymerase-mediated formation of off-target amplicons during the less stringent temperatures of reverse transcription can be significantly reduced.
another approach to prevent primer-mediated formation of off-target amplicon during the cdna synthesis step is the use of modified reverse transcriptases that are stable and active at higher temperatures, such as the superscript® iii rt .
by performing cdna synthesis at higher temperatures, the binding of pcr primers to regions of lesser complementarity during the reverse transcription  step should be reduced.
however, since both the rt primer and pcr primers are present in the same reaction, there is the possibility of further complications due to extension of all three primers during the rt step.
a different approach is to enhance one-step rt-pcr performance through the use of a physical barrier such as ampliwax® pcr gems .
ampliwax® pcr gems separate a single tube into two compartments, allowing for the rt step to occur independent of the dna polymerase and pcr primers  <cit> .
at the elevated temperatures of pcr, the wax melts to allow introduction of the dna polymerase and primers into the rt reaction product.
while this approach provides a means of further improving reaction performance in one-step rt-pcr, the preparation of the wax barrier presents an additional step that needs to be introduced into typical workflows.
an alternative approach uses microfluidics to allow for the sequential introduction of primers in a reaction  <cit> .
while this approach allows streamlined control over the introduction of the primer into the reaction this approach requires investment in highly sophisticated equipment.
with these concepts in mind, it was of interest to learn whether blocking pcr primer extension during the rt step would afford a similar benefit.
herein, we will investigate the use of primers containing thermolabile protecting groups for improved multiplex one-step rt-pcr performance.
previous studies revealed that the introduction of two thermolabile phosphotriester protecting groups  into the 3'-terminal and 3'-penultimate internucleotide linkages of a gene specific primer pair provided enhanced one-step rt-pcr performance  <cit> .
the use of temperature-sensitive primer modifications aims to significantly reduce pcr primer extendability until the elevated temperatures of pcr are reached.
this ability to block the extension of the pcr primers allows for the unmodified rt primer of choice, such as the oligo <dig> primer depicted in figure  <dig>  to be utilized during the cdna synthesis step.
the temperature-mediated removal of the thermolabile primer modification group allows for selective extension of the pcr primer pair during pcr thermal cycling.
this study will build upon the early work of lebedev et al.
<cit>  to examine the use of two or more modified primer pairs in multiplex one-step rt-pcr protocols.
the significance of this approach to one-step rt-pcr is great as researchers are more frequently relying on rt-pcr as the "gold standard" for accurate validation of microarray-based gene expression profile  <cit> .
RESULTS
in these studies, the potential benefit of thermolabile pcr primers in multiplex one-step rt-pcr was investigated.
in particular, one-step rt-pcr amplifications in this paper employed an unmodified oligo <dig> or random decamer primer for the rt step and one or more thermolabile primer pairs for the pcr step.
an initial singleplex one-step rt-pcr experiment on three literature-defined targets  <cit>  compared the performance of an unmodified pcr primer pair to pcr primers modified at both the 3' terminal and penultimate positions with thermolabile phosphotriester groups   <cit>  .
results revealed further improvement using precision modified pcr primers, regardless of the rt primer utilized.
while the use of precision primer modifications provided improved one-step rt-pcr specificity when an unmodified reverse gene specific primer was used, the greatest improvement in specificity was obtained when unmodified oligo <dig> or random decamer primers were used for the rt step.
based on these findings, a combination of precision pcr primer modifications and an unmodified oligo <dig> or random decamer rt primer was selected for extensive evaluation in the following multiplex one-step rt-pcr experiments.
three abc transporter primer pairs for the human  abca <dig>  abca <dig> and abca <dig> genes  <cit>  were prepared as unmodified and precision modified primers for examination of their performance in amplifying a single target.
the previous studies of langmann et al.
<cit>  were expanded to multiplex reactions that simultaneously amplified two or three targets .
in a singleplex set-up, rt-pcr with both unmodified and precision primers amplified the correct amplicon.
however, reactions with unmodified primers yielded less amplicon, and the longest target , formed a higher molecular weight off-target amplicon.
when all duplex combinations of the three targets were amplified, reactions containing unmodified primers were plagued by off-target amplification.
in contrast, reactions containing precision primers amplified all duplex combinations correctly with a lower level of primer dimer formation than reactions containing unmodified primers.
when all three targets were amplified simultaneously, the use of precision pcr primers showed high specificity for the targeted amplicons compared to the unmodified pcr primers.
since it has been described that reverse transcription at elevated temperatures improves the quality of cdna synthesis products and resultant pcr product quality  <cit> , we next investigated whether an increase in the temperature of the reverse transcription reaction from 42°c to 55°c would improve the performance of reactions employing unmodified primers.
a protocol using superscript® iii rt , a reverse transcriptase that is stable at higher temperatures, was developed to amplify three targets individually and together as a triplex .
the amplification of single targets using ssiii rt with unmodified primers provided more specific amplicon formation than when the rt step was at 42°c, using m-mlv rt.
however, simultaneous amplification of all three targets was poor, yielding robust formation of only the abca <dig> target, with lower yields of abca <dig> and abca <dig>  and strong primer dimer formation.
when the ssiii rt experiments were performed with precision primers , amplicon formation in both singleplex and triplex reaction formats was successful, providing similar findings as with m-mlv rt.
next, taq dna polymerase was substituted with one of two hot start dna polymerases  <cit>  to determine whether formation of non-specific extension products was due to dna polymerase activity at the lower temperatures of reverse transcription.
in conjunction, we also wanted to investigate whether the use of a more specific reverse transcriptase, such as ssiii rt, would improve the specificity of the reverse transcription and subsequent pcr steps.
towards that goal, we evaluated triplex amplifications using m-mlv rt  or ssiii rt  as the reverse transcriptase, and taq, amplitaq gold® or platinum® taq as the dna polymerase .
when hot start dna polymerases  and unmodified pcr primers were employed, a slight improvement was observed with ssiii rt.
however, amplicon yield was compromised by predominant primer dimer formation.
the three dna polymerases were subsequently evaluated with precision primers to assess whether product enrichment could be further improved by such combination.
for all combinations, the three targets were amplified with high specificity when modified primers were utilized, providing much better performance than with unmodified primers.
there were indications of reduced amplicon yield with the slower-activating amplitaq gold® dna polymerase  <cit> , but still the yield was better than that obtained with unmodified primers.
the ability of precision primers to support multiplex real-time one-step rt-pcr was next evaluated.
to correlate copy number with real-time detection of rt-pcr products, rna standards were prepared using by in vitro transcription of pcr amplified fragments of the abca <dig>  abca <dig>  and abca <dig> genes using the ribomax™ large scale rna production system-t <dig>  these rna standards were employed in subsequent experiments to allow for quantification of the number of copies of a gene of interest in total rna or other rna samples.
for each real-time one-step rt-pcr experiment where unknown sample quantification was performed, triplicate serial dilutions of the abca <dig>  abca <dig> and abca <dig> rna standards were performed in singleplex.
dilutions of the rna standards, ranging from ~ <dig> to ~ <dig> copies were robustly amplified, and produced resultant standard curves with efficiencies of 80-85% .
next, three human total rna tissues were selected and amplified in singleplex and multiplex one-step rt-pcr experiments for detection of the abca <dig>  abca <dig>  and abca <dig> genes .
each reaction, which amplified ~ <dig>  μg of total rna, was performed in triplicate and was compared to the appropriate dilutions of each rna standard.
results revealed high abca <dig> expression in the brain, high abca <dig> expression in the trachea, and very similar expression levels for abca <dig>  abca <dig>  and abca <dig> in the thymus.
for almost all genes, the experimentally determined copy number was similar for singleplex and multiplex one-step rt-pcr experiments, with the exception of the abca <dig> gene in brain.
this was likely due to a poorly-formed shape of the amplification curve for the triplicate reaction, which resulted in a large standard deviation in copy number determination for the abca <dig> gene .
analysis of the amplification products by agarose gel electrophoresis  revealed that the relative abundances calculated in real-time could be largely verified by endpoint analysis of the reaction products.
to determine whether the amount of input total rna would influence the resultant quantification of the sample, we repeated these studies using ~ <dig> , ~ <dig>  and ~ <dig> ng of total rna from trachea, thymus, and brain .
while the quantification cycle  values  <cit>  determined in singleplex and multiplex assays agreed well with one another for a given input concentration of total rna, we found that the amplification of the abca <dig> target was problematic, as it amplified with different efficiencies than abca <dig> and abca <dig>  this finding is not uncommon in multiplex experiments and may be due to a number of factors, including preferential amplification when targets are significantly unbalanced  <cit> .
to further investigate the factors that may influence the relative quantification of abca <dig>  abca <dig>  and abca <dig> in a multiplex experiment we first sought to determine whether the cdna priming strategy would affect quantification.
since the use of oligo <dig> primers will preferentially amplify the 3' end of transcripts, we next compared reactions which employed oligo primers, random decamer primers, or a combination of both for the cdna synthesis step.
these one-step rt-pcr studies were performed in triplicate using precision primers, with singleplex or triplex detection of the three genes in  <dig>  μg of human thymus total rna.
when the cq values were determined, there was very little variation in the calculated values from priming strategy to priming strategy .
not surprisingly, the resultant copies of each target determined from extrapolation to a standard curve were similar for singleplex and triplex detection of the abca <dig>  abca <dig>  and abca <dig> targets .
expanding further upon these studies, we next investigated the effect of significantly unbalanced target abundances on one-step rt-pcr performance.
eight mixtures of the abca <dig>  abca <dig>  and abca <dig> rna standards were prepared, where each component was present at  <dig>   <dig>  or  <dig> copies/μl.
each of these mixtures was evaluated in triplicate in a triplex real-time one-step rt-pcr experiment, determining the experimental number of copies by extrapolation to a standard curve.
for each mixture, the experimentally determined number of copies was typically less than the actual input by an order of magnitude .
to learn whether the relative abundance of the three targets could be accurately determined in the mix, the determined copies of each of the targets was normalized to that of the abca <dig> target .
while the relative abundances varied from the actual input, in most cases, the trends were maintained.
the notable exception in this study was that abca <dig> was detected at higher levels, especially in instances where abca <dig> was one of the more abundant targets.
further analysis of the reaction products by agarose gel electrophoresis revealed that the relative abundances of the three targets in each mix could largely be determined using endpoint analysis .
in a final set of experiments, conditions were evaluated that would increase the number of targets that could be simultaneously amplified using the modified primers.
using m-mlv as the reverse transcriptase, cleanamp™ precision primers supported multiplex amplification of up to five targets , where the unmodified primers could not amplify any of the specific targets.
when the more specific reverse transcriptase ssiii rt was used, amplicon formation became more robust, indicating that as the number of targets in a one-step rt-pcr protocol increases, so does the need for a higher temperature cdna synthesis step to support the downstream pcr amplification.
overall, the use of primers containing thermolabile protecting group has provided a significant improvement to one-step rt-pcr protocols, allowing for greater specificity in singleplex and multiplex amplification schemes.
discussion
multiplex one-step rt-pcr is a powerful technique that provides several advantages for molecular diagnostics, facilitating genetic screening and analysis of changes in gene expression levels in different tissues among other applications.
performing multiplex rt-pcr in one step instead of two offers a more streamlined process that allows for increased throughput of samples  <cit> .
however, the use of multiple primer pairs in the same reaction requires extensive optimization because amplicons are often amplified with differing efficiencies  <cit> .
moreover, extension of the pcr primers during the lower temperatures of the reverse transcription step, may result in mispriming and less efficient amplification of the target amplicons.
to further improve one-step rt-pcr performance, a number of different approaches have been developed to block the dna polymerase activity during the rt-pcr step  <cit>  but they require either a significant investment in equipment or a dramatic change in protocols  <cit> .
on the other hand, cleanamp™ precision primers present a novel approach that relies on the introduction of two thermolabile modification groups into a primer sequence of interest.
this approach is much more amenable to existing protocols and does not require additional manipulation steps or the need for additional equipment.
these modification groups prevent primer extension during the lower set-up temperatures thereby reducing non-specific amplification.
once the higher temperatures are reached, the thermolabile modifications are released and allow the primers to amplify the desired region of the cdna product.
the present study describes the benefit of using primers containing thermolabile phosphotriester modification groups  in multiplex one-step rt-pcr.
successful simultaneous amplification of three targets was observed in endpoint pcr, in cases where the unmodified primers could not amplify any of the specific amplicons .
this improved performance using precision pcr primers is likely the result of the modification blocking the extension of the pcr primers during the rt step of the reaction.
the preparation of rna standards allowed for evaluation of the quantification of abca <dig>  abca <dig>  and abca <dig> in real-time pcr, hence permitting a means for relative quantification of expression levels .
real-time results reveal that the quantification is not largely affected by the reaction format, as similar copy numbers are determined in both singleplex and multiplex formats.
these studies, which encompassed the evaluation of different cdna priming strategies, different input levels of total rna, and artificially prepared rna mixtures with different abundances of the three targets , gave largely reliable results, with some indication of amplification biases.
this bias was most evident for the abca <dig> target, which was observed to vary in some instances, especially when present at high abundance.
this phenomenon was consistent with what has been observed in the literature for largely unbalanced expression levels and is therefore not unexpected  <cit> .
although precision primers can also be combined in amplification schemes with sophisticated hot start dna polymerases such as platinum™ taq and amplitaq gold® and with more thermostable reverse transcriptases like ssiii rt, the results are comparable to those obtained with more-affordable non-hot start dna polymerases, m-mlv rt, and cleanamp™ precision primers as reaction components .
in fact, the amplicon yield decreased when ssiii rt and amplitaq gold® where combined with cleanamp™ precision primers, which is most likely due to the synergistic effect of limited release of unmodified primer and unmodified dna polymerase in the same reaction.
nevertheless, ssiii rt proved to enhance the amplification of more than four targets simultaneously when combined with precision primers and non-hot start taq dna polymerase .
overall, cleanamp™ precision primers provide a significant benefit in multiplex one-step rt-pcr, allowing for cleaner results with the potential for further development as a tool for relative quantification.
CONCLUSIONS
the increasing need for a rapid and accurate way to perform multiplex one-step rt-pcr to diagnose diseases or identify pathogens, makes cleanamp™ precision primers a viable choice.
the presence of the thermolabile cleanamp™ primer modifications improves the specificity of cdna synthesis by blocking the extension of primers during the lower-temperature rt-pcr step.
this higher stringency cdna synthesis allows for more robust amplification of each of the targets, with less interference by primer dimer formation and mispriming.
moreover, the ability to use these modified primers for one-step rt-pcr amplification of multiple targets offers a great opportunity for further development of this technology for use in measuring the relative expression levels of genes in different tissues, both in singleplex and multiplex assays.

 reverse transcription pcr, a protocol widely used to produce dna copies of an rna strand of interest, involves a lower temperature reverse transcription step followed by an elevated temperature pcr step. rt-pcr reactions are typically separated into two separate steps. however, as the number of manipulations in a reaction protocol increases, so does the probability of contamination. reduction of the two separate manipulation procedures into a one-step rt-pcr protocol provides a more streamlined, high-throughput technique that lowers the probability of contamination by minimizing the number of handling steps. however, one-step rt-pcr protocols are not without inherent limitations and have often been found to be less sensitive than the corresponding two-step protocols. one likely cause for this lower sensitivity is competing extension of pcr primers by reverse transcriptase or dna polymerase. at lower, less discriminatory temperatures of reverse transcription, pcr primer extension may result in off-target amplification products such as primer dimer and mispriming products. to improve the specificity of rt-pcr, it is necessary to block such primer extension at lower temperatures. rt-pcr is commonly used in routine molecular diagnostics as a tool for detection of genetic diseases. multiplex rt-pcr is an advanced application of this technique that allows for detection of two or more rna targets in a single tube reaction. this approach has been used to rapidly detect viral subtypes or to simultaneously identify different disease mutations. multiplex one-step rt-pcr protocols enable the detection of multiple rna targets in a single reaction and allow for quantification of relative mrna expression levels using real-time detection. this technique requires extensive optimization because the use of multiple primer pairs in a single reaction increases the likelihood of primer dimer and mispriming product formation, which may interfere with the amplification of the desired products. another pitfall of multiplex rt-pcr is the preferential elongation of certain targets, both at the cdna synthesis and pcr amplification stages of the reaction, especially when the targets differ greatly in relative abundance. these difficulties make multiplex one-step rt-pcr a challenging technique with rewarding results when successful. to overcome the main drawbacks of one-step rt-pcr protocols, researchers have tried several approaches. one strategy is to employ hot start dna polymerases. as hot start dna polymerases are designed to only be active at the elevated, more stringent temperatures of pcr thermocycling, dna polymerase-mediated formation of off-target amplicons during the less stringent temperatures of reverse transcription can be significantly reduced. another approach to prevent primer-mediated formation of off-target amplicon during the cdna synthesis step is the use of modified reverse transcriptases that are stable and active at higher temperatures, such as the superscript® iii rt. by performing cdna synthesis at higher temperatures, the binding of pcr primers to regions of lesser complementarity during the reverse transcription step should be reduced. however, since both the rt primer and pcr primers are present in the same reaction, there is the possibility of further complications due to extension of all three primers during the rt step. a different approach is to enhance one-step rt-pcr performance through the use of a physical barrier such as ampliwax® pcr gems. ampliwax® pcr gems separate a single tube into two compartments, allowing for the rt step to occur independent of the dna polymerase and pcr primers. at the elevated temperatures of pcr, the wax melts to allow introduction of the dna polymerase and primers into the rt reaction product. while this approach provides a means of further improving reaction performance in one-step rt-pcr, the preparation of the wax barrier presents an additional step that needs to be introduced into typical workflows. an alternative approach uses microfluidics to allow for the sequential introduction of primers in a reaction. while this approach allows streamlined control over the introduction of the primer into the reaction this approach requires investment in highly sophisticated equipment. with these concepts in mind, it was of interest to learn whether blocking pcr primer extension during the rt step would afford a similar benefit. herein, we will investigate the use of primers containing thermolabile protecting groups for improved multiplex one-step rt-pcr performance. previous studies revealed that the introduction of two thermolabile phosphotriester protecting groups into the 3'-terminal and 3'-penultimate internucleotide linkages of a gene specific primer pair provided enhanced one-step rt-pcr performance. the use of temperature-sensitive primer modifications aims to significantly reduce pcr primer extendability until the elevated temperatures of pcr are reached. this ability to block the extension of the pcr primers allows for the unmodified rt primer of choice, such as the oligo primer depicted in figure to be utilized during the cdna synthesis step. the temperature-mediated removal of the thermolabile primer modification group allows for selective extension of the pcr primer pair during pcr thermal cycling. this study will build upon the early work of lebedev et al. to examine the use of two or more modified primer pairs in multiplex one-step rt-pcr protocols. the significance of this approach to one-step rt-pcr is great as researchers are more frequently relying on rt-pcr as the "gold standard" for accurate validation of microarray-based gene expression profile.  in these studies, the potential benefit of thermolabile pcr primers in multiplex one-step rt-pcr was investigated. in particular, one-step rt-pcr amplifications in this paper employed an unmodified oligo or random decamer primer for the rt step and one or more thermolabile primer pairs for the pcr step. an initial singleplex one-step rt-pcr experiment on three literature-defined targets compared the performance of an unmodified pcr primer pair to pcr primers modified at both the 3' terminal and penultimate positions with thermolabile phosphotriester groups. results revealed further improvement using precision modified pcr primers, regardless of the rt primer utilized. while the use of precision primer modifications provided improved one-step rt-pcr specificity when an unmodified reverse gene specific primer was used, the greatest improvement in specificity was obtained when unmodified oligo or random decamer primers were used for the rt step. based on these findings, a combination of precision pcr primer modifications and an unmodified oligo or random decamer rt primer was selected for extensive evaluation in the following multiplex one-step rt-pcr experiments. three abc transporter primer pairs for the human abca abca and abca genes were prepared as unmodified and precision modified primers for examination of their performance in amplifying a single target. the previous studies of langmann et al. were expanded to multiplex reactions that simultaneously amplified two or three targets. in a singleplex set-up, rt-pcr with both unmodified and precision primers amplified the correct amplicon. however, reactions with unmodified primers yielded less amplicon, and the longest target, formed a higher molecular weight off-target amplicon. when all duplex combinations of the three targets were amplified, reactions containing unmodified primers were plagued by off-target amplification. in contrast, reactions containing precision primers amplified all duplex combinations correctly with a lower level of primer dimer formation than reactions containing unmodified primers. when all three targets were amplified simultaneously, the use of precision pcr primers showed high specificity for the targeted amplicons compared to the unmodified pcr primers. since it has been described that reverse transcription at elevated temperatures improves the quality of cdna synthesis products and resultant pcr product quality, we next investigated whether an increase in the temperature of the reverse transcription reaction from 42°c to 55°c would improve the performance of reactions employing unmodified primers. a protocol using superscript® iii rt, a reverse transcriptase that is stable at higher temperatures, was developed to amplify three targets individually and together as a triplex. the amplification of single targets using ssiii rt with unmodified primers provided more specific amplicon formation than when the rt step was at 42°c, using m-mlv rt. however, simultaneous amplification of all three targets was poor, yielding robust formation of only the abca target, with lower yields of abca and abca and strong primer dimer formation. when the ssiii rt experiments were performed with precision primers, amplicon formation in both singleplex and triplex reaction formats was successful, providing similar findings as with m-mlv rt. next, taq dna polymerase was substituted with one of two hot start dna polymerases to determine whether formation of non-specific extension products was due to dna polymerase activity at the lower temperatures of reverse transcription. in conjunction, we also wanted to investigate whether the use of a more specific reverse transcriptase, such as ssiii rt, would improve the specificity of the reverse transcription and subsequent pcr steps. towards that goal, we evaluated triplex amplifications using m-mlv rt or ssiii rt as the reverse transcriptase, and taq, amplitaq gold® or platinum® taq as the dna polymerase. when hot start dna polymerases and unmodified pcr primers were employed, a slight improvement was observed with ssiii rt. however, amplicon yield was compromised by predominant primer dimer formation. the three dna polymerases were subsequently evaluated with precision primers to assess whether product enrichment could be further improved by such combination. for all combinations, the three targets were amplified with high specificity when modified primers were utilized, providing much better performance than with unmodified primers. there were indications of reduced amplicon yield with the slower-activating amplitaq gold® dna polymerase, but still the yield was better than that obtained with unmodified primers. the ability of precision primers to support multiplex real-time one-step rt-pcr was next evaluated. to correlate copy number with real-time detection of rt-pcr products, rna standards were prepared using by in vitro transcription of pcr amplified fragments of the abca abca and abca genes using the ribomax™ large scale rna production system-t these rna standards were employed in subsequent experiments to allow for quantification of the number of copies of a gene of interest in total rna or other rna samples. for each real-time one-step rt-pcr experiment where unknown sample quantification was performed, triplicate serial dilutions of the abca abca and abca rna standards were performed in singleplex. dilutions of the rna standards, ranging from ~ to ~ copies were robustly amplified, and produced resultant standard curves with efficiencies of 80-85%. next, three human total rna tissues were selected and amplified in singleplex and multiplex one-step rt-pcr experiments for detection of the abca abca and abca genes. each reaction, which amplified ~ μg of total rna, was performed in triplicate and was compared to the appropriate dilutions of each rna standard. results revealed high abca expression in the brain, high abca expression in the trachea, and very similar expression levels for abca abca and abca in the thymus. for almost all genes, the experimentally determined copy number was similar for singleplex and multiplex one-step rt-pcr experiments, with the exception of the abca gene in brain. this was likely due to a poorly-formed shape of the amplification curve for the triplicate reaction, which resulted in a large standard deviation in copy number determination for the abca gene. analysis of the amplification products by agarose gel electrophoresis revealed that the relative abundances calculated in real-time could be largely verified by endpoint analysis of the reaction products. to determine whether the amount of input total rna would influence the resultant quantification of the sample, we repeated these studies using ~, ~ and ~ ng of total rna from trachea, thymus, and brain. while the quantification cycle values determined in singleplex and multiplex assays agreed well with one another for a given input concentration of total rna, we found that the amplification of the abca target was problematic, as it amplified with different efficiencies than abca and abca this finding is not uncommon in multiplex experiments and may be due to a number of factors, including preferential amplification when targets are significantly unbalanced. to further investigate the factors that may influence the relative quantification of abca abca and abca in a multiplex experiment we first sought to determine whether the cdna priming strategy would affect quantification. since the use of oligo primers will preferentially amplify the 3' end of transcripts, we next compared reactions which employed oligo primers, random decamer primers, or a combination of both for the cdna synthesis step. these one-step rt-pcr studies were performed in triplicate using precision primers, with singleplex or triplex detection of the three genes in μg of human thymus total rna. when the cq values were determined, there was very little variation in the calculated values from priming strategy to priming strategy. not surprisingly, the resultant copies of each target determined from extrapolation to a standard curve were similar for singleplex and triplex detection of the abca abca and abca targets. expanding further upon these studies, we next investigated the effect of significantly unbalanced target abundances on one-step rt-pcr performance. eight mixtures of the abca abca and abca rna standards were prepared, where each component was present at or copies/μl. each of these mixtures was evaluated in triplicate in a triplex real-time one-step rt-pcr experiment, determining the experimental number of copies by extrapolation to a standard curve. for each mixture, the experimentally determined number of copies was typically less than the actual input by an order of magnitude. to learn whether the relative abundance of the three targets could be accurately determined in the mix, the determined copies of each of the targets was normalized to that of the abca target. while the relative abundances varied from the actual input, in most cases, the trends were maintained. the notable exception in this study was that abca was detected at higher levels, especially in instances where abca was one of the more abundant targets. further analysis of the reaction products by agarose gel electrophoresis revealed that the relative abundances of the three targets in each mix could largely be determined using endpoint analysis. in a final set of experiments, conditions were evaluated that would increase the number of targets that could be simultaneously amplified using the modified primers. using m-mlv as the reverse transcriptase, cleanamp™ precision primers supported multiplex amplification of up to five targets, where the unmodified primers could not amplify any of the specific targets. when the more specific reverse transcriptase ssiii rt was used, amplicon formation became more robust, indicating that as the number of targets in a one-step rt-pcr protocol increases, so does the need for a higher temperature cdna synthesis step to support the downstream pcr amplification. overall, the use of primers containing thermolabile protecting group has provided a significant improvement to one-step rt-pcr protocols, allowing for greater specificity in singleplex and multiplex amplification schemes. discussion multiplex one-step rt-pcr is a powerful technique that provides several advantages for molecular diagnostics, facilitating genetic screening and analysis of changes in gene expression levels in different tissues among other applications. performing multiplex rt-pcr in one step instead of two offers a more streamlined process that allows for increased throughput of samples. however, the use of multiple primer pairs in the same reaction requires extensive optimization because amplicons are often amplified with differing efficiencies. moreover, extension of the pcr primers during the lower temperatures of the reverse transcription step, may result in mispriming and less efficient amplification of the target amplicons. to further improve one-step rt-pcr performance, a number of different approaches have been developed to block the dna polymerase activity during the rt-pcr step but they require either a significant investment in equipment or a dramatic change in protocols. on the other hand, cleanamp™ precision primers present a novel approach that relies on the introduction of two thermolabile modification groups into a primer sequence of interest. this approach is much more amenable to existing protocols and does not require additional manipulation steps or the need for additional equipment. these modification groups prevent primer extension during the lower set-up temperatures thereby reducing non-specific amplification. once the higher temperatures are reached, the thermolabile modifications are released and allow the primers to amplify the desired region of the cdna product. the present study describes the benefit of using primers containing thermolabile phosphotriester modification groups in multiplex one-step rt-pcr. successful simultaneous amplification of three targets was observed in endpoint pcr, in cases where the unmodified primers could not amplify any of the specific amplicons. this improved performance using precision pcr primers is likely the result of the modification blocking the extension of the pcr primers during the rt step of the reaction. the preparation of rna standards allowed for evaluation of the quantification of abca abca and abca in real-time pcr, hence permitting a means for relative quantification of expression levels. real-time results reveal that the quantification is not largely affected by the reaction format, as similar copy numbers are determined in both singleplex and multiplex formats. these studies, which encompassed the evaluation of different cdna priming strategies, different input levels of total rna, and artificially prepared rna mixtures with different abundances of the three targets, gave largely reliable results, with some indication of amplification biases. this bias was most evident for the abca target, which was observed to vary in some instances, especially when present at high abundance. this phenomenon was consistent with what has been observed in the literature for largely unbalanced expression levels and is therefore not unexpected. although precision primers can also be combined in amplification schemes with sophisticated hot start dna polymerases such as platinum™ taq and amplitaq gold® and with more thermostable reverse transcriptases like ssiii rt, the results are comparable to those obtained with more-affordable non-hot start dna polymerases, m-mlv rt, and cleanamp™ precision primers as reaction components. in fact, the amplicon yield decreased when ssiii rt and amplitaq gold® where combined with cleanamp™ precision primers, which is most likely due to the synergistic effect of limited release of unmodified primer and unmodified dna polymerase in the same reaction. nevertheless, ssiii rt proved to enhance the amplification of more than four targets simultaneously when combined with precision primers and non-hot start taq dna polymerase. overall, cleanamp™ precision primers provide a significant benefit in multiplex one-step rt-pcr, allowing for cleaner results with the potential for further development as a tool for relative quantification.  the increasing need for a rapid and accurate way to perform multiplex one-step rt-pcr to diagnose diseases or identify pathogens, makes cleanamp™ precision primers a viable choice. the presence of the thermolabile cleanamp™ primer modifications improves the specificity of cdna synthesis by blocking the extension of primers during the lower-temperature rt-pcr step. this higher stringency cdna synthesis allows for more robust amplification of each of the targets, with less interference by primer dimer formation and mispriming. moreover, the ability to use these modified primers for one-step rt-pcr amplification of multiple targets offers a great opportunity for further development of this technology for use in measuring the relative expression levels of genes in different tissues, both in singleplex and multiplex assays. 
multiplex rt-pcr is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. herein, we report multiplex one-step rt-pcr experiments in which the pcr primers contain thermolabile phosphotriester modification groups. results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step rt-pcr specificity in both singleplex and multiplex reaction formats. however, intensive pcr optimization is often required to overcome competing undesired pcr primer extension during the rt step. the presence of these groups minimizes pcr primer extension during the rt step and allows for control of pcr primer extension until the more stringent, elevated temperatures of pcr are reached. the need for an accurate and sensitive technique to quantify mrna expression levels makes the described modified primer technology a promising tool for use in multiplex one-step rt-pcr.
 multiplex rt-pcr is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. the simplification of this protocol into a one-step procedure saves time and reagents. however, intensive pcr optimization is often required to overcome competing undesired pcr primer extension during the rt step.  herein, we report multiplex one-step rt-pcr experiments in which the pcr primers contain thermolabile phosphotriester modification groups. the presence of these groups minimizes pcr primer extension during the rt step and allows for control of pcr primer extension until the more stringent, elevated temperatures of pcr are reached. results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step rt-pcr specificity in both singleplex and multiplex reaction formats.  the need for an accurate and sensitive technique to quantify mrna expression levels makes the described modified primer technology a promising tool for use in multiplex one-step rt-pcr. a more accurate representation of the abundances in initial template sample is feasible with modified primers, as artifacts of biased pcr are reduced because of greater improvements in reaction specificity. 