Complete mesoscopic parameterization of single LNA modifications in DNA applied to oncogene probe design
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Universidade Federal de Minas Gerais
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The use of mesoscopic models to describe thethermodynamic properties of locked nucleic acid (LNA)-modifiednucleotides can provide useful insights into their properties, such ashydrogen-bonding and stacking interactions. In addition, themesoscopic parameters can be used to optimize LNA insertionin probes, to achieve accurate melting temperature predictions, andto obtain duplex opening profiles at the base-pair level. Here, weapplied this type of model to parameterize a large set of meltingtemperatures for LNA-modified sequences, from publishedsources, covering all possible nearest-neighbor configurations. Wehave found a very large increase in Morse potentials, whichindicates very strong hydrogen bonding as the main cause ofimproved LNA thermodynamic stability. LNA-modified adenine−thymine (AT) was found to have similar hydrogen bonding tounmodified 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. Weapplied the new LNA parameters to the design ofBRAF,KRAS, andEGFRoncogene variants by testing all possible LNAmodifications. Selected sequences were then synthesized and had their hybridization temperatures measured, achieving a predictionaccuracy within 1°C. We performed a detailed base-pair opening analysis to discuss specific aspects of these probe hybridizationsthat may be relevant for probe design.
Abstract
Assunto
Biofísica, Ácidos nucleicos, Oncogenes
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Locked Nucleic Acids, Oncogenes
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https://pubs.acs.org/doi/10.1021/acs.jcim.1c00470