Nucleic acid structures energetics

In summary, then, there is little quantitative information derived from ab initio calculations that pertain to the energetic contribution of CH- - -X bonds to nucleic acid structure. The best data available at present derives from the pyrimidine dimer [126] wherein a value on the order of 1.6 kcal/mol was suggested. However, this quantity pertains to angularly distorted CH- - -N bonds in vacuo, with no account taken of the surroundings. 

N. Foloppe, L. Nilsson, J. MacKerell, E. Alexander, Ab initio conformational analysis of nucleic acid components Intrinsic energetic contributions to nucleic acid structure and dynamics. Biopolymers 61 (1999) 61-76. 

Of central importance for the formation of a specific protein-DNA complex are hydrogen bonds. The H-bonds are clearly identifiable in high resolution structures. H-bonds occur where a H-bond donor and acceptor he with 0.27-0.31 nm of each other. Energetically most favorable is the hnear arrangement of the H-bond, with deviations from hnearity leading to a reduction in energy. This characteristic is responsible for the stereospecific orientation of H-bond acceptors and donors. The H-bond thus contributes significantly to the spatial orientation between protein and nucleic acid. 

Ionic strength influences are well known with respect to the rate and energetics of nucleic acid hybridization [17]. Charge and ionic radius are both important in terms of stabilizing the structure of the duplex as well as stabilizing the stem portion of the molecular beacon [17]. The stem structure stability was increased when a divalent cation was incorporated into the hybridization buffer solution [17]. It was reported that cations were best at stabilizing the duplex formed upon hybridization in the order Ca2+ > Mg2+ K+ > Na+. The ultimate detection limit of the sensor configuration was calculated to be 1.1 nM [17]. 

P. Hobza et al., Structure, energetics, and dynamics of the nucleic acid base pairs Nonem-pirical ab initio calculations. Chem. Rev. 99, 3247-3276 (1999)... 

Lomant AJ, Fresco JR (1975) Structural and energetic consequences of noncomplementary base opposition in nucleic acid helices. Prog Nucl Acid Res Mol Biol 15 185-218... 

In this section, we present the results of computational studies of the five nucleic acid bases cytosine 13, guanine 14, adenine 15, thymine 16, and uracil 17. The canonical structures, those that are involved in the Watson-Crick base pairing within DNA, are drawn below. Other tautomers for each base can be energetically competitive with the canonical structure, and these other tautomers are invoked in some models of DNA mutations and anomalous DNA structures. The ensuing discussion focuses on the relative energies of the tautomers, in both the gas and solution phases. Structural changes that accompany this phase change are also noted. 

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