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B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.
Nieuwland, Celine; Hamlin, Trevor A; Fonseca Guerra, Célia; Barone, Giampaolo; Bickelhaupt, F Matthias.
Afiliación
  • Nieuwland C; Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands.
  • Hamlin TA; Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands.
  • Fonseca Guerra C; Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands.
  • Barone G; Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 CC, Leiden (The, Netherlands.
  • Bickelhaupt FM; Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Edificio 17, 90128, Palermo, Italy.
ChemistryOpen ; 11(2): e202100231, 2022 02.
Article en En | MEDLINE | ID: mdl-35083880
We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN Forma B Tipo de estudio: Prognostic_studies Idioma: En Revista: ChemistryOpen Año: 2022 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Alemania
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN Forma B Tipo de estudio: Prognostic_studies Idioma: En Revista: ChemistryOpen Año: 2022 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Alemania