Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms.

ABSTRACT: Regulatory protein access to the DNA duplex 'interior' depends on local DNA 'breathing' fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination

SUBMITTER: Beyerle ER 

PROVIDER: S-EPMC7913701 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature