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EnglishWe 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.
Celine Nieuwland, Trevor A. Hamlin, C{'{e}}lia Fonseca Guerra, Giampaolo Barone, & F. Matthias Bickelhaupt (2022). B-{DNA} Structure and Stability: The Role of Nucleotide Composition and Order. CHEMISTRYOPEN, 11(2) [10.1002/open.202100231].
| Data di pubblicazione: | 2022 | |
| Titolo: | B-{DNA} Structure and Stability: The Role of Nucleotide Composition and Order | |
| Autori: | ||
| Citazione: | Celine Nieuwland, Trevor A. Hamlin, C{'{e}}lia Fonseca Guerra, Giampaolo Barone, & F. Matthias Bickelhaupt (2022). B-{DNA} Structure and Stability: The Role of Nucleotide Composition and Order. CHEMISTRYOPEN, 11(2) [10.1002/open.202100231]. | |
| Rivista: | ||
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1002/open.202100231 | |
| Abstract: | 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. | |
| Settore Scientifico Disciplinare: | Settore CHIM/03 - Chimica Generale E Inorganica | |
| Appare nelle tipologie: | 1.01 Articolo in rivista |
File in questo prodotto:
| File | Descrizione | Tipologia | Licenza | |
|---|---|---|---|---|
| CO_2022_e202100231.pdf | Versione Editoriale | Open Access Visualizza/Apri |
http://hdl.handle.net/10447/537197
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