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

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 of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.

Automated summary

Regulatory protein access to the interior of the DNA duplex is dependent on local DNA breathing fluctuations, primarily driven by thermally-induced base stacking-unstacking interactions. Using the dinucleotide dApdA as a model, researchers studied stacking-unstacking phenomena at a molecular level, revealing the role of ionic structure and water orientation in controlling DNA breathing fluctuations. Molecular Dynamics simulations and Markov State Model analyses were utilized to validate the findings, which were further supported by calculations of circular dichroism (CD) spectra. The study identified distinct chiral conformations in dApdA, representing different forms of base pairing and highlighting the importance of ion condensation and hydrogen bonding in duplex DNA dynamics.