Watson-Crick hydrogen bonding

Egholm M., Buchardt O., Christensen L., Behrens C., Ereier S.M., Driver D.A., Berg, R. H., Kim, S.K., Nor-DEN B., Nielsen, P.E. PNA hybridizes to complementary oligonucleotides obeying the Watson—Crick hydrogen-bonding rules. Nature 1993, 365 566-568. 

P212121 Z — 8 Dx= 1.57 R = 0.085 for 1,743 intensities. The two independent molecules have similar conformations. The glycosyl dispositions are anti (90.1°, 91.2°), and the D-ribosyl groups are 3T4 (24.0°, 34.1° 15.6°, 35.5°). The exocyclic, C-4 -C-5 bond orientations are gauche+ (63.1°, 53.8°). The orientation of the methyl groups in both molecules is such that it is directed away from the imidazole moiety of the base, that is, the 0-6-C-7 bond is trans to the C-5-C-6 bond this arrangement constitutes an obstacle to formation of Watson-Crick hydrogen-bonds to the complementary base cytosine. In molecule A, 0-6 and C-7 are displaced from the purine plane by 79 and 87 pm, and, in molecule B, by 49 and 16 pm. The bases are stacked. 

DNA is a helical polyanion built by the union of two linear polymeric strands that are composed of sugars (deoxyribose) finked by phosphates. Each sugar contains an aromatic base (G,C,A, or T) bound to C-l of the sugar. The two strands are normally complementary so that when they combine to form the duplex, each base on one strand forms Watson-Crick hydrogen bonds with its counterpart (G with C and A with T) on the opposite... 

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

Both NER and BER forms of excision repair remove a great variety of defects, many of which are a result of oxidative damage.657 720 Most prominent among these is 7,8-dihydro-8-oxoguanine (8-OG), which is able to base pair with either cytosine (with normal Watson-Crick hydrogen bonding) or with adenine, which will yield a purine-purine mismatch and aC G —> A T transversion mutation (Eq. 27-24), a frequent mutation in human cancers.721 722... 

The relative magnitude of the large proflavine upfield complexation shifts requires that the dye intercalate into the duplex with its long axis colinear to the direction of the Watson-Crick hydrogen bonds of adjacent base pairs. This results in significant overlap of the proflavine ring system and base pairs at the intercalation site. 

Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA Hybridizes to Complementary Oligonucleotides Obeying the Watson-Crick Hydrogen Bonding Rules. Nature 1993 365 566-8. 

In double stranded DNA (RNA) the situation is different because several sites are occupied by the Watson-Crick hydrogen bonds [48] (Fig. 8). Thus, a carboxylic... 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

To build on the above promise and to generate systems that would be capable of effecting the through-membrane transport of mononucleotides, systems 10.47 and 10.48 (Figure 10.5.31) were synthesized by Sessler and coworkers.These contain Watson-Crick hydrogen bonding complements built into the molecule. 

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