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• W1441552867 abstract "Polymerase Chain Reaction (PCR) is a widely used technology in molecular bi-ology for DNA amplification. To generate multiple copies of a DNA molecule, a pair ofprimers (two synthesized DNA sequences with a total length of 15-30 bases) are annealedto the boundaries of the targeted DNA molecule. Then, the new replicated DNA fragmentelongates from one primer to the other.Though primers always hybridize to their respective complements within DNAsequences, primer pairs for targeted DNA sequences can also anneal non-targeted DNAfragments containing common DNA sub-sequences also found in targeted DNA molecules.During the PCR process, primer pairs that offer high specificity and coverage rates fortargeted fragments among all the copies are preferred.To provide primer pairs with high selectivity, several computational algorithmshave been proposed. Most state-of-the-art algorithms take into account signature primers,or common short DNA fragments in the targeted DNA molecules. However, these algorithmsdo not account for the fact that during the PCR process in which primer pairs designedusing signature primers are used, DNA fragments that do not have signature primers willnot become amplified. These algorithms are, then, limited in various ways.Predicting primers' respective binding affinities is crucial in primer design be-cause, during the PCR process, the annealing between the targeted DNA fragments andthe primers with low binding affinity degenerates during the PCR process's thermal cycles.Because of this degeneration, targeted fragments expected to be reproduced by the primerpairs go missing during DNA amplification.It is important to note that a particular primer's nucleic acids do not contributeequally to the binding affinity. Specifically, this binding affinity is determined by the nucleicacids in the 3' end of the primer more than the nucleic acids in the 5' end. Existingalgorithms typically oversimplify their predictions by either ignoring primers with highbinding affinity or including primers with low binding affinity.To address current algorithms' limitations, we created PRISE2, a robust computa-tional tool for sequence-selective PCR primer design. This innovative tool considers all sub-sequences of potential primer pairs to increase the coverage rate of the targeted fragments.This tool also provides a flexible mechanism with which to formulate positional bias whenestimating primers' binding affinity. Importantly, the execution time of locating bindingsites for all potential primers is positively proportion to the number of the subsequences. Toaccelerate searching for the binding sites, this tool clusters subsequences according to theirsequence prefices to reduce the searching space. PRISE2 not only provides a user-friendlyinterface, but also offers full functionality for primer-design tasks. It was implemented usingC++ and Qt frameworks to guarantee efficiency and achieve a cross-platform requirement.In applications where a collection of similar sequences need to be amplified usingPCR, degenerate primers can be used to improve the efficiency and accuracy of ampli-fication, since they can hybridize into multiple, unique DNA fragments. Conceptually,degenerate primers allow multiple bases at various positions. However, in reality, they aremixtures of regular primers that differ on certain bases. Specific degenerate primers' de-generacy refers to the number of regular primers in a mixture. Higher degeneracy allows aprimer to amplify more targeted sequences simultaneously and also leads to low specificityfor targeted sequences that adversely affect the quality and quantity of amplification. It isessential to find a good balance between high coverage and low degeneracy, a balance thata tool like PRISE2 helps achieve.For degenerate primer design, we proposed a new heuristic algorithm, RRD2P , tocompute degenerate primer pairs with near-optimal coverage to targets under the specifieddegeneracy threshold. RRD2P runs in polynomial time and is confirmed to produce primerpairs with good coverage on three biological data sets. This production compares favorablywith a similar tool called HYDEN. The fundamental goal driving RRD2P : to representcomputing optimal primers as an integer linear program, solve their fractional relaxation,and then apply randomized rounding to obtain an integral solution." @default.
• W1441552867 created "2016-06-24" @default.
• W1441552867 creator A5014676064 @default.
• W1441552867 date "2015-01-01" @default.
• W1441552867 modified "2023-09-27" @default.
• W1441552867 title "Algorithms and Software for PCR Primer Design" @default.
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• W1441552867 hasPublicationYear "2015" @default.
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