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- W3178144829 endingPage "3624" @default.
- W3178144829 startingPage "3615" @default.
- W3178144829 abstract "The use of mesoscopic models to describe the thermodynamic properties of locked nucleic acid (LNA)-modified nucleotides can provide useful insights into their properties, such as hydrogen-bonding and stacking interactions. In addition, the mesoscopic parameters can be used to optimize LNA insertion in probes, to achieve accurate melting temperature predictions, and to obtain duplex opening profiles at the base-pair level. Here, we applied this type of model to parameterize a large set of melting temperatures for LNA-modified sequences, from published sources, covering all possible nearest-neighbor configurations. We have found a very large increase in Morse potentials, which indicates very strong hydrogen bonding as the main cause of improved LNA thermodynamic stability. LNA-modified adenine–thymine (AT) was found to have similar hydrogen bonding to unmodified cytosine–guanine (CG) base pairs, while for LNA CG, we found exceptionally large hydrogen bonding. In contrast, stacking interactions, which were thought to be behind the stability of LNA, were similar to unmodified DNA in most cases. We applied the new LNA parameters to the design of BRAF, KRAS, and EGFR oncogene variants by testing all possible LNA modifications. Selected sequences were then synthesized and had their hybridization temperatures measured, achieving a prediction accuracy within 1 °C. We performed a detailed base-pair opening analysis to discuss specific aspects of these probe hybridizations that may be relevant for probe design." @default.
- W3178144829 created "2021-07-19" @default.
- W3178144829 creator A5009022895 @default.
- W3178144829 creator A5015559679 @default.
- W3178144829 creator A5036492620 @default.
- W3178144829 creator A5085726797 @default.
- W3178144829 date "2021-07-12" @default.
- W3178144829 modified "2023-09-25" @default.
- W3178144829 title "Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design" @default.
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- W3178144829 doi "https://doi.org/10.1021/acs.jcim.1c00470" @default.
- W3178144829 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34251211" @default.
- W3178144829 hasPublicationYear "2021" @default.
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