Vibrational Dynamics of the Double Hydrogen Bonds in Nucleic Acid Base Pairs

Abstract

The structural selectivity of complementary pairing of nucleic acid bases in DNA signifies the importance of hydrogen bonding in biology [1,2]. This fact has triggered a host of investigations, starting with gasphase and microsolvation studies of the stability and spectroscopy of nucleic acid bases as the fundamental building blocks [3,4]. Here, the specific changes in the infrared (IR) spectrum owing to hydrogen bonding provide a sensitive means of identification of bonding patterns, not only in gas but also in condensed phase [5,6]. For isolated adenine-thymine pairs, for instance, which were studied in gas phase using the IR-UV double-resonance technique [7], evidence was found that Watson-Crick pairing is not very likely under these conditions. In order to identify the dominant tautomer, it was necessary to perform quantum dynamical simulations of IR spectra, including anharmonicity [8]. Anharmonicity of the potential energy surface is characteristic of hydrogen-bonded species. Together with the quantum nature of the problem, it makes hydrogen bond (HB) dynamics a challenging task even in gas phase [9][10][11]. The issue of preferential association of nucleobases carries over to solution-phase studies. In a seminal work, Rich and coworkers [12] studied the homo-and heteropairing of various adenine and uracil derivatives in deuterochloroform solution using IR spectroscopy. This work triggered investigations of a number of nucleic acid base pairs [13-17]; a review of IR bands in the 800-1800 cm À1 range in aqueous solution can be found in Ref. [18].Linear IR spectroscopy cannot disentangle the rich information on the HB dynamics that is encoded in the broad and often structured lineshapes of IR spectra, especially in the condensed phase. Ultrafast nonlinear IR spectroscopy, on the other hand, has been proven to provide the means for addressing this dynamical information, thus giving access to anharmonic couplings, fluctuation timescales and pathways of vibrational

Geometric correlations and infrared spectrum of adenine–uracil hydrogen bonds in CDCl3 solution

“…Comparing the correlation curves in Fig. 6 with those obtained from crystal structure data 33,35 we notice a qualitatively similar behavior with the difference essentially reducing to an off-set of À420 cm À1 and À370 cm À1 for the N-HÁ Á ÁN and N-HÁ Á ÁO HB, respectively. In ref.…”

“…34 In a previous work we compiled a more complete set of N-HÁ Á ÁO data involving also HBs formed by amine groups. 35 The advantage of such relations is obvious, it allows to assign stretching frequencies along a trajectory on the basis of atomic co-ordinates only. This information can be used to efficiently determine IR line shapes.…”