Predicting stability of DNA bulge at mononucleotide microsatellite
| dc.citation.firstpage | 7901 | |
| dc.citation.issueNumber | 14 | |
| dc.citation.journalTitle | Nucleic Acids Research | |
| dc.citation.lastpage | 7908 | |
| dc.citation.volumeNumber | 49 | |
| dc.contributor.author | Bae, Jin H. | |
| dc.contributor.author | Zhang, David Yu | |
| dc.contributor.org | Systems, Synthetic, and Physical Biology | |
| dc.date.accessioned | 2021-09-21T15:37:53Z | |
| dc.date.available | 2021-09-21T15:37:53Z | |
| dc.date.issued | 2021 | |
| dc.description.abstract | Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites. | |
| dc.identifier.citation | Bae, Jin H. and Zhang, David Yu. "Predicting stability of DNA bulge at mononucleotide microsatellite." <i>Nucleic Acids Research,</i> 49, no. 14 (2021) Oxford University Press: 7901-7908. https://doi.org/10.1093/nar/gkab616. | |
| dc.identifier.digital | gkab616 | |
| dc.identifier.doi | https://doi.org/10.1093/nar/gkab616 | |
| dc.identifier.uri | https://hdl.handle.net/1911/111390 | |
| dc.language.iso | eng | |
| dc.publisher | Oxford University Press | |
| dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/), | |
| dc.title | Predicting stability of DNA bulge at mononucleotide microsatellite | |
| dc.type | Journal article | |
| dc.type.dcmi | Text | |
| dc.type.publication | publisher version |
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