Elsevier

Chemical Physics Letters

Volume 537, 1 June 2012, Pages 94-100
Chemical Physics Letters

Quantum chemical study of hole transfer coupling in nucleic acid base complexes containing 7-deazaadenine

https://doi.org/10.1016/j.cplett.2012.04.018Get rights and content

Abstract

In this study, we report on the results of MD/QM computations of charge–transfer integrals for nucleic acid base complexes in stacked configurations containing 7-deazaadenine. A strong dependence of charge–transfer integrals on torsional parameters was observed in case of all studied complexes. However, a very important finding of this study is that in proximity of equilibrium configuration, the values of charge–transfer integral are not sensitive to the replacement of adenine with 7-deazaadenine. Likewise, the analysis of distribution of charge–transfer integrals, determined for structures taken from molecular dynamics simulations, revealed that their changes upon adenine modification are not a key factor influencing charge transport.

Highlights

► The substitution of adenine with 7-deazaadenine in selected complexes was considered. ► The interaction energy and charge transfer integrals profiles were calculated. ► The key parameters determining charge transport were discussed. ► The site energy seems to be a key factor determining charge transport.

Introduction

Due to its unique properties, including high flexibility, self-assembly, self-recognition and self-replication, DNA seems to be a very attractive material for nano electronics and molecular nanotechnology [1]. Understanding the charge transport through DNA can be helpful in resolving genomic instability problem and sensitivity of chromosomes to oxidative damages. Nucleic acids can be used to align molecules (due to the ability to create bonds with nanoparticles and proteins) and thus they might serve as building blocks of molecular switches, memory devices, biosensors or transistors [2], [3], [4], [5], [6]. Taniguchi and Kawai pointed out that various studies on DNA conductivity give inconsistent results because of large number of factors, including morphology, sequence and complexity of DNA molecules [7]. Another crucial factor is the environment, which may play an important role in conduction process [7], [8]. The majority of undertaken studies proved that random sequences of DNA have the resistivity within the range characterizing insulators [9], [10], [11]. It was also proved that some DNA periodic sequences exhibit properties similar to those of semiconductors and thus may be considered as semiconductors with a wide band gap [12], [13], [14], [15], [16]. There is still disagreement regarding the general mechanism of charge carrier transport through DNA. Two main approaches are widely employed in studying charge transport in DNA, namely quantum–mechanical tight binding models and semi-classical models having their roots in hopping mechanisms arising from Marcus theory [17], [18]. The results obtained in both theoretical and experimental studies confirmed that the most effective hole transport is observed in artificial sequences of poly (dG)  poly (dC) helix, where the charge migrates through guanine sites [19]. The hole transport between guanines occurs either by hopping across A–T bridges or as a result of superexchange interactions. It was also proved that consecutive A–T pairs between G sites drastically diminish charge transport between them. It is primarily caused by a high ionization energy of adenine and thymine in comparison with guanine. One of the most interesting aspects related to the charge transfer in systems of biological relevance, and in particular in DNA, is the crossing from superexchange to thermally induced hopping as discussed by Bixon and Jortner a decade ago [20]. As it was shown by these authors, there is an exponential dependence of superexchange rate on the bridge length (defined by N; in case of DNA N may correspond to the number of A–T pairs between neighbouring G sites) and a weak N-dependence for thermally induced hopping mechanism. The crossing between the two mechanisms is found to occur for N = 4 [20]. In case of (GGG) TTXTT (GGG) for X = G, 7-deazaadenine (from herein denoted as Z) thermally induced hopping dominated while for X = A there is a substantial contribution (around 25%) from the superexchange channel [20]. The essential parameter in the superexchange model is the electronic coupling which is defined in terms of charge–transfer integral (CTI) [21]. Nowadays, also more complicated theoretical models of charge transport in DNA are used but they are usually extensions of the models described above [22]. Recently, Kawai et al. have shown experimentally that the charge–transfer efficiency through DNA duplexes can be increased for a given sequence by replacing adenine with 7-deazaadenine, in which N7 nitrogen is replaced by C–H group [23]. Adenine modification changes its electronic properties and in a result leads to increase in charge–transfer through the strand. Moreover, 7-deazaadenine has ability to pair selectively with cytosine what does not cause instability of double helix.

The aim of our study is twofold. Firstly, we employ Kohn–Sham formulation of density functional theory to compute charge transfer integrals for nucleic acid base complexes composed of G, A and 7-deazaadenine. In doing so, we aim at determining if magnitudes of CTI between neighbouring nucleobases are affected by adenine modification. Moreover, the molecular site energies, calculated as nucleic acid base ionization energies, and reorganization energies for considered bases are determined and analyzed. Secondly, we analyze the effect of the complexes deformations on the hole transport in DNA containing 7-deazaadenine. This should provide additional insight into experimental finding reported by Kawai et al. that charge–transfer efficiency through DNA might be dramatically increased upon replacement of adenine with 7-deazaadenine [23]. To the best of our knowledge both aspects have not been addressed yet.

Section snippets

Computational methods

In the present study, we compute the charge–transfer integrals for complexes composed of two nucleic acid bases in the stacked configurations. The geometries of these complexes were generated in two distinct ways. First approach relies on monomer geometries, optimized at the MP2/aug-cc-pVDZ level of theory, used to probe a conformational space spanned by two parameters, namely R and α. The former is defined as the distance between centres of carbon–carbon bond of the molecules while the latter

Results and discussion

Figure 3, Figure 4 present the dependence of charge–transfer integrals and intermolecular interaction energies on considered degrees of freedom, R and α, for six complexes, namely A–A, A–Z, Z–Z, G–G, G–A and G–Z, where A and G denotes the standard DNA bases adenine and guanine and Z stands for 7-deazaadenine. Charge–transfer integral profiles should be discussed together with energy profiles, which reveal the structural disorder in the system. Similarly to other authors, we observe that the

Concluding remarks

In this study, we analyzed charge–transfer properties of nucleic acid base complexes in stacked configurations containing normal and modified adenine (where N7 atom was replaced by the C–H group). In particular, we reported on the results of computations of hopping matrix elements which are essential parameters in charge transport models based on the Marcus theory. A key finding of this study is that the shapes of the charge transfer integral profiles after substitution of adenine with

Acknowledgments

Authors are grateful to anonymous Reviewer for useful remarks regarding the manuscript. The work was supported by Polish Ministry of Science and Higher Education (Project No. N N507 388139), Czech Science Foundation (Project No. P205/10/2280) and by the Polish Ministry of Science and Higher Education and by the Ministry of Education, Youth, and Sports of the Czech Republic (Czech-Polish cooperation Project No. 8194/2010, MEB051010). One of the authors (UB) is the recipient of the fellowship

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