DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications

@article{citeulike:838507, abstract = {Secondary structures in polymerase chain reaction (PCR) target sequences have a negative impact on amplification success rates and on downstream uses of PCR products. For example, signal strength and allele discrimination in single nucleotide polymorphism (SNP) genotyping methods can be compromised by allele-biased amplification and/or by PCR product folding that limits access of interrogating probes. To increase the fidelity and robustness of PCR, and to aid follow-on applications, we have developed DFold (http://dfold.cgb.ki.se) - a generalized software solution that creates PCR oligonucleotide primer designs devoid of stable secondary structures. We demonstrate the effectiveness of the tool by applying it to a range of dynamic allele-specific hybridization (DASH) assay designs, many of which we evaluate in the laboratory. We further consider how the system throughput may be made sufficiently high for use upon millions of target sequences in order to support whole-genome analyses. Hum Mutat 24:1-8, 2004. {\copyright} 2004 Wiley-Liss, Inc.}, address = {Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden}, author = {Fredman, David and Jobs, M. and Str\"{o}mqvist, L. and Brookes, A. J. }, citeulike-article-id = {838507}, doi = {10.1002/humu.20066}, journal = {Human Mutation}, keywords = {oligo-design, software}, number = {1}, pages = {1--8}, posted-at = {2006-09-10 22:46:08}, priority = {2}, title = {DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications}, url = {http://dx.doi.org/10.1002/humu.20066}, volume = {24}, year = {2004} }

TY - JOUR ID - citeulike:838507 L3 - citeulike-article-id:838507 TI - DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications JF - Human Mutation VL - 24 IS - 1 SP - 1 EP - 8 AD - Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden N2 - Secondary structures in polymerase chain reaction (PCR) target sequences have a negative impact on amplification success rates and on downstream uses of PCR products. For example, signal strength and allele discrimination in single nucleotide polymorphism (SNP) genotyping methods can be compromised by allele-biased amplification and/or by PCR product folding that limits access of interrogating probes. To increase the fidelity and robustness of PCR, and to aid follow-on applications, we have developed DFold (http://dfold.cgb.ki.se) - a generalized software solution that creates PCR oligonucleotide primer designs devoid of stable secondary structures. We demonstrate the effectiveness of the tool by applying it to a range of dynamic allele-specific hybridization (DASH) assay designs, many of which we evaluate in the laboratory. We further consider how the system throughput may be made sufficiently high for use upon millions of target sequences in order to support whole-genome analyses. Hum Mutat 24:1-8, 2004. © 2004 Wiley-Liss, Inc. KW - oligo-design KW - software AU - Fredman, David AU - Jobs, M AU - Strömqvist, L AU - Brookes, AJ PY - 2004/// UR - http://dx.doi.org/10.1002/humu.20066 ER -