Purines hydrogen bonding

Section 28.8 The most common fonn of DNA is B-DNA, which exists as a right-handed double helix. The car bohydrate-phosphate backbone lies on the outside, the purine and pyrimidine bases on the inside. The double helix is stabilized by complementary hydrogen bonding (base pauing) between adenine (A) and thymine (T), and guanine (G) and cytosine (C). 

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. 

Fig. 3.1 Schematic representation of the two modes of distamycin DNA complexes with putative hydrogen bonds shown as dashed lines. Circles with dots represent lone pairs of N(3) of purines and 0(2) of pyrimidines...

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... 

P2j Z = 2 D = 1.57 R = 0.048 for 931 intensities. The base exists in the thioxo form, with C-8=S and N-7 protonated. The 8-thio substituent causes the base to assume the syn (—102.6°) orientation. The o-ribosyl group is 2T3 (174.8 °, 44.1 °). The exocyclic, C-4 -C-5 bond orientation is trans (—173.2°). This does not favor intramolecular hydrogen-bonding of 0-5 to N-3 of the syn base. The C=S distance is 166.8 pm. The S atom is involved in a weak, acceptor hydrogen-bond to a water molecule, S H-O(w) = 361 pm. The bases are stacked head-to-tail, with overlap of the C=S bonds and the purine ring, in contrast to the known, related structure l-/ -D-ribofuranosyl-2-thioxo-3ff-benzimidazole,197 where similar head-to-tail stacking of the bases involves overlap of the base rings only. 

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. 

A sequence, in general, is the relative order of base pairs, whether in a fragment of a protein, DNA, a gene, a chromosome, or an entire genome. DNA is composed of two antiparallel strands of deoxynucleotides held together by hydrogen bonds between purine (adenine, A and guanine, G) and pyrimidine (thymidine, T uracil, U and cytosine, C) bases. 

Consistent with the experimental data, mutation of the purine base nitrogens, i.e. N, 3N, 7N and 9N, showed that replacement of N, 3N and 9N with CH had little effect on binding affinity whereas a similar replacement of 7N led to a loss of 2.8 kcal/mol. The 0.6 kcal/mol gain in affinity for the 1-deaza and 3-deaza AMP analogues was consistent with the hydrophobic nature of this portion of the binding site cavity and the absence of hydrogen bond donors in the vicinity of either heteroatom. 

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