A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure

Darren Smith, Leo Frederick Holroyd, Tanja van Mourik, Anita Jones

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)14691-14700
Number of pages10
JournalPhysical Chemistry Chemical Physics
Volume18
Issue number21
Early online date11 May 2016
DOIs
Publication statusPublished - 7 Jun 2016

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