ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups

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ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups

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Title: ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups
Author: Peacock-Villada, Alexandra; Coljee, Vincent; Danilowicz, Claudia; Prentiss, Mara

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Citation: Peacock-Villada, Alexandra, Vincent Coljee, Claudia Danilowicz, and Mara Prentiss. 2015. “ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups.” PLoS ONE 10 (6): e0130875. doi:10.1371/journal.pone.0130875. http://dx.doi.org/10.1371/journal.pone.0130875.
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Abstract: Accurate sequence dependent pairing of single-stranded DNA (ssDNA) molecules plays an important role in gene chips, DNA origami, and polymerase chain reactions. In many assays accurate pairing depends on mismatched sequences melting at lower temperatures than matched sequences; however, for sequences longer than ~10 nucleotides, single mismatches and correct matches have melting temperature differences of less than 3°C. We demonstrate that appropriately grouping of 35 bases in ssDNA using abasic sites increases the difference between the melting temperature of correct bases and the melting temperature of mismatched base pairings. Importantly, in the presence of appropriately spaced abasic sites mismatches near one end of a long dsDNA destabilize the annealing at the other end much more effectively than in systems without the abasic sites, suggesting that the dsDNA melts more uniformly in the presence of appropriately spaced abasic sites. In sum, the presence of appropriately spaced abasic sites allows temperature to more accurately discriminate correct base pairings from incorrect ones.
Published Version: doi:10.1371/journal.pone.0130875
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482597/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:17295592
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