The influence of terminal 3′,5′ phosphates on conformations of dApdA

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Abstract
Addition of 3′ and 5′ terminal phosphates to dApdA causes a decrease in conformational flexibility. pdApdAp has much fewer conformers with energies below 2.5 kcal./mole than dApdA. The A, B and Watson-Crick (34) helices are the most preferred forms. Other important conformations are in the trans domain of ψ. Thus, flexibility in ψ, as well as in ω and ω, and in the sugar pucker is indicated. The transformation from the B helix to the Watson-Crick helix follows a low energy path. This is significant since Watson-Crick conformations may be important for intercalation into nucleic acid polymers (40–42) above the dimer level. The B helix is preferred over the A form in these larger DNA subunits.