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Modeling Peptide Nucleic Acid Binding Enthalpies Using MM-GBSA.

ABSTRACT: The binding enthalpies of peptide nucleic acid (PNA) homoduplexes were predicted using a molecular mechanics generalized Born surface area approach. Using the nucleic acid nearest-neighbor model, these were decomposed into sequence parameters which could replicate the enthalpies from thermal melting experiments with a mean error of 8.7%. These results present the first systematic computational investigation into the relationship between sequence and binding energy for PNA homoduplexes and identified a stabilizing helix initiation enthalpy not observed for nucleic acids with phosphoribose backbones.

SUBMITTER: Goodman J

PROVIDER: S-EPMC9706560 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Modeling Peptide Nucleic Acid Binding Enthalpies Using MM-GBSA.

Goodman Jack J Attwood David D Kiely Janice J Coladas Mato Pablo P Luxton Richard R

The journal of physical chemistry. B 20221114 46

The binding enthalpies of peptide nucleic acid (PNA) homoduplexes were predicted using a molecular mechanics generalized Born surface area approach. Using the nucleic acid nearest-neighbor model, these were decomposed into sequence parameters which could replicate the enthalpies from thermal melting experiments with a mean error of 8.7%. These results present the first systematic computational investigation into the relationship between sequence and binding energy for PNA homoduplexes and identi ...[more]

PMID: 36375178

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