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

submitted on 13.03.2020, 01:01 and posted on 13.03.2020, 12:59 by Luciana M. Oliveira, Adam S. Long, Tom Brown, Keith R. Fox, Gerald Weber
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.


Fundação de Amparo a Pesquisa do Estado e Minas Gerais

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Coordenação de Aperfeicoamento de Nível Superior

The Forensic Science Service, Solihull Parkway, Birmingham Business Park, Birmingham, B37 7YN, UK


Email Address of Submitting Author


Universidade Federal de Minas Gerais



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest

Version Notes

First preprint version