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A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure
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dc.contributor.author | Smith, Darren | |
dc.contributor.author | Holroyd, Leo Frederick | |
dc.contributor.author | van Mourik, Tanja | |
dc.contributor.author | Jones, Anita | |
dc.date.accessioned | 2017-05-10T23:33:48Z | |
dc.date.available | 2017-05-10T23:33:48Z | |
dc.date.issued | 2016-06-07 | |
dc.identifier | 242548405 | |
dc.identifier | 23e7cc78-5ee4-4298-8601-75afffb0b517 | |
dc.identifier | 84971350795 | |
dc.identifier | 000378102700064 | |
dc.identifier.citation | 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 . https://doi.org/10.1039/C5CP07816D | en |
dc.identifier.issn | 1463-9076 | |
dc.identifier.other | ORCID: /0000-0001-7683-3293/work/57088466 | |
dc.identifier.uri | https://hdl.handle.net/10023/10744 | |
dc.description | 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. | en |
dc.description.abstract | 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. | |
dc.format.extent | 10 | |
dc.format.extent | 1600118 | |
dc.language.iso | eng | |
dc.relation.ispartof | Physical Chemistry Chemical Physics | en |
dc.subject | QD Chemistry | en |
dc.subject | DAS | en |
dc.subject.lcc | QD | en |
dc.title | A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure | en |
dc.type | Journal article | en |
dc.contributor.institution | University of St Andrews. School of Chemistry | en |
dc.contributor.institution | University of St Andrews. EaSTCHEM | en |
dc.identifier.doi | 10.1039/C5CP07816D | |
dc.description.status | Peer reviewed | en |
dc.date.embargoedUntil | 2017-05-10 | |
dc.identifier.url | http://www.rsc.org/suppdata/c5/cp/c5cp07816d/c5cp07816d1.pdf | en |
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