A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure
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The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5’-position and each of the natural bases in the 3’-position are examined, together with the analogous 5’- adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
Smith , D , Holroyd , L F , van Mourik , T & Jones , A 2016 , ' A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure ' Physical Chemistry Chemical Physics , vol 18 , no. 21 , pp. 14691-14700 . DOI: 10.1039/C5CP07816D
Physical Chemistry Chemical Physics
Copyright 2016 the Authors. This work is made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://dx.doi.org/10.1039/C5CP07816D
This work was supported by studentship funding from the Engineering and Physical Sciences Research Council Doctoral Training Account to DAS and LFH (EP/K503162/1); EaStCHEM, University of Edinburgh and University of St Andrews; University of Melbourne.
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