Watson-Crick base pairs in DNA

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). 

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

Low resolution Fourier syntheses of electron density with phases calculated from an approximate but erroneous model may nevertheless indicate another model and thus provide an unusually compelling indication that the phasing model is imperfect. This strategy has been used to reject Hoogsteen in favor of Watson-Crick base-pairing in DNA (60,61), to eliminate 10-fold in favor of 11-fold helicies in A-RNA (62), to favor nested chains rather than double helices in the case of one form of sodium hyaluronate (40). 

FIGURE 6.6 Watson-Crick base pairing in DNA nucleotides... 

The existence of Watson-Crick base-pairing in DNA and RNA is crucially dependent on the position of the chemical equilibria between tautomeric forms of the... 

As shown in Figure 7.7, cytosine has three major tautomeric forms which have different properties enol, keto, and keto-imine. In the gas phase, the keto-imine is the most unstable and the enol tautomer is shghtly more stable than the keto form by about 0.03 eV [59-61]. The keto form is the biologically important one, with Watson-Crick base-pairing in DNA, and predominant in solution. In matrix isolation, Szczesniak et al. [62] observed both keto and enol forms, with higher abundances for the latter and small contributions from the imino form. Brown et al. [63] have obtained the rotational constants for all three tautomeric forms by microwave spectroscopy. Schiedt et al. [64] also identified the existence of keto and enol tautomers of neutral cytosine in the gas phase by anion spectroscopy. 

White, S., J.W. Szewczyk, J.M. Turner, E.E. Baird, and P.B. Dervan. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998, 393, 468-471. 

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. 

Table 2 Average hydrogen-bonding geometry of Watson-Crick base pairs in high-resolution DNA structures ...

The incorporation into anti-parallel DNA of a cross-linked Watson-Crick base pair (120) has been described, " though no data for the duplexes formed are provided. A dissociable covalently bonded base pair (121), modelled to impose minimal distortion of the duplex, was used to replace a Watson-Crick base pair in ODNs. The second (complementary) strand was introduced by ligation of appropriate ODNs. The un-natural base pair between 2-amino-AT -dimethyl-purine and pyridin-2-one has been developed for specific transcription. " The ribo-triphosphate of pyridin-2-one and the 5-methyl derivative are selectively incorporated opposite 2-amino-Ar -dimethyl-purine by T7 RNA polymerase. The bulky dimethyl group prevents recognition and pairing by the natural bases. 

Figure 12.4 Watson-Crick base-pairing in B-DNA showing the locations of the exocyclic amino groups of guanine and adenine in the minor and major grooves, respectively.

Mismatches, or non-Watson-Crick base pairs in a DNA duplex, can arise through the following... 

C10H13N5O5 283.243 Constit. of nucleic acids. One of the four principal nucleosides involved in Watson-Crick base pairing in both DNA and RNA. 

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