Watson-Crick base

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

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... 

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],... 

Fig. 3.2 Pairing rules for polyamide recognition of all four Watson—Crick base pairs of DNA. Putative hydrogen bonds are shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimi-...

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. 

Fig. 4.3 Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), while the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advanta-...

The fundamental a-hehcal peptide nucleic acid (aPNA) concept is illustrated in Fig. 5.2. Our prototype aPNA module incorporated five nucleobases for Watson-Crick base pairing with a single-stranded nucleic acid target. These nucleobases... 

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