Quantum mechanical studies on the existence of AC mismatches through prototopic tautomerization pathway in adenine and cytosine recognition

Basumatary, Junu; Bezbaruah, Bipul; Kalita, Rinki Moni; Barman, Tapash Kumar; Medhi, C.

doi:10.1142/s0219633617500274

Cited by 5 publications

(5 citation statements)

References 22 publications

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“…AC AC type mismatches are generally thought to have one 77 or even two hydrogen bonds in anti-anti, 27,67,[78][79][80][81][82][83] and DFT calculations also suggest this. 84,85 However, the Morse potentials for AC shown in Fig. 7a, with few exceptions, do not appear to support the presence of strong hydrogen bonds.…”

Section: Ttmentioning

confidence: 96%

Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

et al. 2020

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Section: Ttmentioning

confidence: 96%

Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

et al. 2020

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“…Optimization and frequency calculations for all monomers and base pairs were performed at the B3LYP/6-31G(d,p) level of theory. B3LYP has been previously successfully used to study the effects of nucleobase methylation on the A:T and G:C base pairs, , as well as the base-pairing properties for a range of other DNA lesions (see, e.g., refs − ). Subsequently, the binding energies were determined using B3LYP-D3 with Becke-Johnson (BJ) damping and the 6-311++G(2df,2p) basis set.…”

Section: Computational Detailsmentioning

confidence: 99%

Quantum Chemical Studies of the Structure and Stability of N-Methylated DNA Nucleobase Dimers: Insights into the Mutagenic Base Pairing of Damaged DNA

2017

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DNA is constantly under attack from exogenous and endogenous sources that modify the chemical structure of the nucleobases. A common type of nucleobase damage is N-methylation, which can result in mutagenesis. Nevertheless, these lesions are often repaired by the DNA repair enzyme AlkB, albeit at varying rates. Herein we use density functional theory (B3LYP-D3(BJ)/6-311++G(2df,2p)//B3LYP/6-31G(d,p)) to comprehensively examine the structural and energetic properties of base pairs between seven nucleobase lesions resulting from N-methylation on the Watson-Crick (WC) binding face and each canonical nucleobase. By characterizing 105 stable nucleobase dimers, we provide fundamental details regarding the preferred lesion base pairings. Specifically, we reveal that the flexibility of the methylamino group resulting from methylation of an exocyclic amino substituent allows the 2MeG, 4MeC, and 6MeA lesions to maintain a preference for canonical WC base pairing, which correlates with the experimentally reported lack of mutagenicity for these damage products. In contrast, calculated distortions in key structural parameters and altered binding energies for base pairs involving adducts formed upon methylation of a ring nitrogen (namely, 1MeG, 3MeT, 1MeA, and 3MeC) help rationalize the associated mutagenicity and repair efficiencies. Most importantly, our work provides molecular-level information about the interactions between N-methylated and canonical nucleobases that is critical for future large-scale modeling of damaged DNA and enzyme-DNA complexes that strive to further uncover the mutagenicity and repair propensities of these detrimental lesions.

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“…The stacking interactions found were AC type mismatches are generally thought to have one 68 or even two hydrogen bonds in anti -anti , 18,58,[69][70][71][72][73][74] and DFT calculations also suggest this. 75,76 However, the Morse potentials for AC shown in Fig. 4a, with few exceptions, do not appear to support the presence of strong hydrogen bonds.…”

Section: Discussionmentioning

confidence: 88%

Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches

Oliveira¹,

Long²,

Brown³

et al. 2020

Preprint

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Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combination of canonical base pairs in the same location under the same conditions. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches.

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Quantum mechanical studies on the existence of AC mismatches through prototopic tautomerization pathway in adenine and cytosine recognition

Cited by 5 publications

References 22 publications

Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

Quantum Chemical Studies of the Structure and Stability of N-Methylated DNA Nucleobase Dimers: Insights into the Mutagenic Base Pairing of Damaged DNA

Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches

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