Watson-Crick base pair adenine...thymine

Mazurkiewicz K, Haranczyk M, Gutowski M, Rak J (2007). Can an excess electron localize on a purine moiety in the adenine-thymine Watson-Crick base pair A computational study. Int J Quantum Chem DOI 10.1002/qua.21359. 

AT, adenine—thymine Watson—Crick base pair. 

In molecular biology, a set of two hydrogen-bonded nucleotides on opposite complementary nucleic acid strands is called a base pair. In the classical Watson-Crick base pairing in DNA, adenine (A) always forms a base pair with thymine (T) and guanine (G) always forms a base pair with cytosine (C). In RNA, thymine is replaced by uracil (U). 

Scheurer and Briischweiler71 calculated 2hJ(N,N) couplings in three nucleic acid base pairs, namely, Watson-Crick uracil-adenine (U A) [4a] and cytosine-guanine (C-G) base pairs [4b] and in the Hoogsteen adenine thymine (A-T) base pair [7]. 

FIG U RE 3.4 Watson-Crick base pairing in DNA. Adenine is complementary to thymine, and guanine is complementary to cytosine. 

Draw the structures of the Watson-Crick base pairs guanine-cytosine (GC) and adenine-thymine (AT). Also draw the GU pair, which is not a Watson-Crick pair. 

Fig. 1 Watson-Crick guanine-cytosine (G-C) and adenine-thymine (A-T) base-pairs.

O.V. Shishkin et al., Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs. J. Mol. Struct. 477, 15-21 (1999)... 

Nucleobases and nucleosides are common motifs for hydrogen-bonded supramolecular arrays. Ng et al. first reported a series of phthalocyanine-nucleobase conjugates [64], The tetra-adenine phthalocyanine 64 was prepared by standard <9-alkylation of zinc(II) tetrahydroxyphthalocyanine with 9-(2-bromoethyl)adenine in the presence of K2CO3. The fluorescence of 64 is quenched substantially upon addition of thymine-substituted 9,10-anthraquinone 65, and the rate is much faster compared with that for the situation when the unsubstituted 9,10-anthraquinone is used as the quencher. These results suggest that 64 forms a supramolecular complex with 65 through the Watson-Crick base-pairing interactions. 

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. 

Classic Watson-Crick base pairs are formed by unique hydrogen-bonding interactions between the nitrogenous bases of DNA and RNA. The purine adenine associates specifically with the pyrimidine thymine in DNA (or the related unmethylated analog, macil, in RNA), and the pmine guanine interacts with the pyrimidine cytosine. These complementarity rules. 

DNA is a right-handed, double-stranded helix, in which the bases essentially occupy the interior of the helix, whereas the phosphodiester backbone (sugar-phosphate backbone) more or less comprises the exterior. The bases on the individnal strands form intermolecular hydrogen bonds with each other (the complementary Watson-Crick base pairs). An adenine base on one strand interacts specifically with a thymine base on the other, forming two hydrogen bonds and an A-T base pair while a G-C base pair contains three hydrogen bonds. These interactions possess a specificity that is pivotal to both DNA repfication and transcription (see Figure 2). 

In triple helix formation the third strand, normally a homopyrimidine strand, is located in the major groove of a duplex consisting of Watson-Crick base pairing. The third strand is orientated parallel to that of the purine strand and the thymine and cytosine bases form Hoog-steen hydrogen bonds with adenine and guanine respectively. Since protonation of the cytosine bases is essential in order to provide the hydrogen bond between N-3 of cytosine and N-7 of... 

Generally, most publications concerning substituent effects or other structural changes in nucleobases provide information on effects observed in the base pairs. Therefore, the most frequently studied systems are structurally modified Watson—Crick base pairs, i.e., adenine—thymine (AT) and guanine—cytosine (GC) pairs. 

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