Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations

Abstract

We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 +/- 2 water molecules per nucleotide instead of 21 +/-1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

“…此外, 红外光谱可以区分 A、 B 型双螺旋 DNA [17] , 研究 dA n •dT n 化 学 学 报 Vol. 70, 2012 ×dT n 三链螺旋 [18] , 及其它各种各样的碱基配对结构 [19] 和碱基的叠加结构 [20] . 红外光谱技术的这些应用, 是基 [29] 、多肽模式间的耦合 [25,30～32] 、有机阳离 子模式间的能量转移 [33] 和 DNA 低聚物分子的对角非谐 性常数及相邻分子的耦合 [34,35] .…”

Beyond nucleic acid base pairs: From triads to heptads

“…Before these studies are discussed in more detail, molecular dynamics simulations on polyad‐containing structures are to be listed, however, for the reasons mentioned above. Simulations have been performed for triplexes135–142 and quadruplexes 31, 32, 143–147. In addition, more and more structural diverse RNA structures are studied.…”

Anharmonic Vibrational Dynamics of DNA Oligomers

“…One of the most prominent hydrogen-bonded systems is DNA. Despite numerous experimental and theoretical investigations on vibrational spectra of nucleic acid bases [7,8,9,10,11,12,13], information on inter-and intramolecular interactions in base pairs and DNA oligomers is still limited [14,15,16,17,18,19,20,21,22,23,24,25]. A recent example is the work on single adenine-uracil (AU) base pairs in the Watson-Crick geometry in solution, which showed an enhancement of vibrational energy relaxation of the NH stretching vibration by a factor of three as compared to the isolated uracil base [21].…”

“…DNA oligomers adopt different types of conformations, both in gas and condensed phases, such as the A, B, B', C, D, and Z form, depending on water and salt concentration, type of cations, pH, and base sequences [8,12,25,26,27,28,29]. In the condensed phase the conformations of DNA oligomers are stabilized by water molecules that form water networks, predominantly in the major and minor grooves, and near the phosphate groups of the backbone [12]. Among the different types of base sequences, adenine-thymine (AT) oligomers are special because they do not undergo transitions from the B to the A form upon reducing the water content.…”

“…Among the different types of base sequences, adenine-thymine (AT) oligomers are special because they do not undergo transitions from the B to the A form upon reducing the water content. Instead, AT oligomers adopt the B' form at low water concentrations, with 4 to 6 water molecules per base pair that may be hydrogen-bonded to the oligomer [12,30,31,32]. In the B' form of the AT DNA oligomer two HBs are formed in the Watson-Crick configuration, i.e., between oxygen (O4) of the thymine and the NH 2 group of the adenine (N6), and between the NH group of the thymine (N3T) and the nitrogen atom of the adenine (N1), see Fig.…”