Thymine base pairing and

Kabelac, M. Zendlova, L. Reha, D. Hobza, P. Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules Molecular mechanics and correlated ab initio study, J. Phys. Chem. B 2005,109, 12206-12213. 

OCHg, SH, NHg, CHg, or COOH, ° adenine-thymine base pair - and its cationic and anionic forms (for the charge densities at C-5 and C-6 positions in uracil, thymine, 5-amino- 5-nitro- and 6-methyl-uracil, 6-azathymine and orotic acid, see refs. 187, 188) tt-HMO - -a-Del Re calculations on uracil, - 5-fluoro- and 5-bromouracil, 5,6-dihydrouracil and its anionic form tt-SCF MO -f a-Del Re... 

Besides the canonical triplexes formed, for example, between thymine and the adenine-thymine base pair and cytosine and the guanine-cytosine base pair other combinations have been suggested to form stable triplexes, e.g. G-TA, G-GC and T-GC [43], The stability of triplexes depends on pH, ionic strength, temperature, and, in cases where the Watson-Crick duplex is part of a plasmid DNA, it depends on supercoil density [44]. 

Samoylova E, Lippert H, Ullrich S, Hertel IV, Radloff W, Schultz T, (2005) Dynamics of photoinduced processes in adenine and thymine base pairs. J Am Chem Soc 127 1782—1786... 

Another pyrimidine base, uracil, is found in RNA instead of thymine. Base pairing between adenine and uracil involves two hydrogen bonds and resembles the adenine-thymine interaction. This type of base pairing is of importance in transcription, the synthesis of messenger RNA (see Section 14.2.5). 

Dimensions and hydrogen bonding of (a) thymine to adenine and (b) cytosine to guanine. Note that two hydrogen bonds are formed in the A-T base pair and three in the G-C base pair. The overall dimensions of the base pairs are the same. Consequently they fit at any position in an otherwise regular polymeric structure. (Source Adapted from S. Arnott, M. H. F. Wilkins, L. D. Hamilton, and R. Langridge, Fourier synthesis studies of lithium DNA, part III Hoogsteen models, J. Mol. Biol. I l 39l, 1965.)... 

Fig. 2 Schematic representations of two model duplexes composed of homopolymeric and alternating adenine-thymine base-pairs for clarity adenines are shown in green.

The BFPT process may take place whenever an excess electron is attached to a nucleobase interacting with a proton donor. In particular, the role of a proton donor could be filled by another nucleobase. Especially interesting are complementary base pairs, AT and GC, since these systems appear in DNA. In the case of the adenine-thymine base pair (AT), a combination of three proton donor and acceptor pairs of adenine with three proton donor and acceptor pairs of thymine leads to nine possible, planar, cyclic H-bonded complexes (see Figure 21-22 [49]). 

Hrouda, V., Florian, J., and Hobza, R, Structure, energetics and harmonic vibrational spectra of the adenine-thymine and adenine -thymine base pairs Gradient nonempirical and semi-empirical study, J. Phys. Chem. 97, 1542-1557 (1993). 

Gould, I. R. and Kollman, P. A., Theoretical investigation of the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs, J. Am. Chem. Soc. 116, 2493-2499 (1994). 

Considerable attention has also been devoted by several investigators to the theoretical study of the potential curves for hydrogen bonds of the guanine-cytosine and adenine-thymine base pairs. An accurate representation of this potential is important because the genetic code is contained in this interaction. Lowdin has suggested that mutations may be a result of a shift in position of the hydrogen bond protons in the base units of DNA via proton tunneling. " The idea of proton... 

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