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dc.contributor.authorSmith, Darren
dc.contributor.authorHolroyd, Leo Frederick
dc.contributor.authorvan Mourik, Tanja
dc.contributor.authorJones, Anita
dc.identifier.citationSmith , 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 .
dc.identifier.otherPURE: 242548405
dc.identifier.otherPURE UUID: 23e7cc78-5ee4-4298-8601-75afffb0b517
dc.identifier.otherScopus: 84971350795
dc.identifier.otherORCID: /0000-0001-7683-3293/work/57088466
dc.identifier.otherWOS: 000378102700064
dc.descriptionThis 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.en
dc.description.abstractThe 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.
dc.relation.ispartofPhysical Chemistry Chemical Physicsen
dc.rightsCopyright 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
dc.subjectQD Chemistryen
dc.titleA DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structureen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews.School of Chemistryen
dc.contributor.institutionUniversity of St Andrews.EaSTCHEMen
dc.description.statusPeer revieweden

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