Article

Ab Initio Optical Absorption Spectra of Size-Expanded xDNA Base Assemblies

National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, c/o Dipartimento di Fisica, Universita di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy
J. Phys. Chem. B, 2007, 111 (50), pp 14012–14021
DOI: 10.1021/jp075711z
Publication Date (Web): November 23, 2007
Copyright © 2007 American Chemical Society

Abstract

We present the results of time-dependent density functional theory calculations of the optical absorption spectra of synthetic nucleobases and of their hydrogen-bonded and stacked base pairs. We focus on size-expanded analogues of the natural nucleobases obtained through the insertion of a benzene ring bonded to the planar heterocycles (x-bases), according to the protocol designed and realized by the group of Eric Kool (e.g., see:  Gao, J.; Liu, H.; Kool, E.T. Angew. Chem., Int. Ed. 2005, 44, 3118, and references therein). We find that the modifications of the frontier electron orbitals with respect to natural bases, which are induced by the presence of the aromatic ring, also affect the optical response. In particular, the absorption onset is pinned by the benzene component of the HOMO of each x-base (xA, xG, xT, xC). In addition, the main trait of the H-bonding interbase coupling is a conspicuous red shift of spectral peaks in the low-energy range. Finally, the hypochromicity, a well-known fingerprint of stacking, is more pronounced in stacked xG−C and xA−T pairs than that in stacked G−C and A−T pairs, an index of enhanced stacking.

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Received 20 July 2007
Published online 23 November 2007
Published in print 1 December 2007
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