Watson base-pairing

The Crick-Watson base pairing with the complementarity C-G and A-T (for DNA) or A-U (for RNA) is a consequence of the delicate balance between aromatic resonance energies and bond energies for CC, CO and CN single and double bonds. 

X-ray diffraction analyses of synthetic oligonucleotides has in some cases revealed departures from the ideal Crick-Watson base-pairing arrangement which has been described above [40,41] (10.74). 

Fig. 1. Elements of DNA stmcture (a) a deoxypolynucleotiide chain, which reads d(ACTG) from 3 — 5 or d(GTCA) from 3 — 5 and (b) and (c) the Watson-Crick purine—pyriinidine base pairs. A—T and G—C, respectively, where — represents attachment to the deoxyribose.

Fig. 6. Elements of RNA stmcture (a) uracil (b) a Watson-Crick A—U base pair and (c) a polynucleotide chain which reads from 5 — 3 ACUG, and...

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

Structural Equivalence of Watson-Crick Base Pairs... 

As indicated in Chapter 11, the base pairing in DNA is very specific the purine adenine pairs with the pyrimidine thymine the purine guanine pairs with the pyrimidine cytosine. Further, the A T pair and G C pair have virtually identical dimensions (Figure 12.10). Watson and Crick realized that units of such similarity could serve as spatially invariant substructures to build a polymer whose exterior dimensions would be uniform along its length, regardless of the sequence of bases. 

Owing to the increasing efficiency of computational methods, it has become possible to investigate base pairs in the gas phase and solution simulated by super-molecular approaches with up to six water molecules [98IJQ37, 98JPC(A) 10374, 98JPC(B)9109, 99JST107]. In the cytosine-isocytosine Watson-Crick base pair. 

The substituent effects on the H-bonding in an adenine-uracil (A-U) base pair were studied for a series of common functional groups [99JPC(A)8516]. Substitutions in the 5 position of uracil are of particular importance because they are located toward the major groove and can easily be introduced by several chemical methods. Based on DFT calculation with a basis set including diffuse functions, variations of about 1 kcal/mol were found for the two H-bonds. The solvent effects on three different Watson-Crick A-U base pairs (Scheme 100) have been modeled by seven water molecules creating the first solvation shell [98JPC(A)6167]. 

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

This is consistent with there not being enough space (20 °) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. These relationships are often called the rules of Watson-Crick base pairing. 

It has been found that 6-aminopyrazinone (Scheme 2), when incorporated as a pyrimidine base analog into an ohgonucleotide, might participate in a nonstandard base pair that retains Watson-Crick geometry [14],... 

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