A-form double helix

On another way, single-stranded DNA is a poor substrate 15,31) and the Cu(phen)2/H202 system cleaves A, B, and Z forms of DNA at different rates 32). The B structure is the most easily cleaved DNA. A DNA is less efficiently cleaved presumably because of fewer favorable contacts between the complex and the widened minor groove of the A form double helix. The A structure, formed by RNA-DNA hybrids, is cleaved on both strands at roughly one-third of the rate for B DNA under comparable conditions. In contrast, the left-handed Z structure, with its deep narrow minor groove, is completely resistant to Cu(phen)2 degradation. 

RNA motifs refer to the small, finite and natmaUy occurring structmal elements of RNAs that are present abundantly as non-canonical bps in hairpins/loops (loop motifs) and sequences involved in tertiary interactions (tertiary motifs). The most important secondary structural element in RNA is the A-form double helix (A-helix). However, motifs. 

Figure 17 CD of a long (372 nucleotide) naturally occurring mRNA, At 25 °C the RNA is largely that of an A-form double helix at 85 °C there is less chirality In the parts of the molecule being probed—in this case the RNA bases. This is due to there being less base pairing and base stacking at 85 °C. 42eonm = I O at 25 °C. (Source Circular dichroism and linear dichroism, A. Rodger and B. Nord6n, 1997, by permission of Oxford University Press.)...

All multicellular life starts as a single cell. Copies of the DNA in that cell must eventually occupy almost every one of the trillions of cells in a human body. For that to happen, the DNA in the original cell must replicate itself many times. The key to this replication is the famous double helix. When two strands of DNA— let s call them X and Y—separate, each strand can assemble the other. X builds a new Y, forming a fresh double helix. Y does the same thing. This doubles the number of DNA molecules. This mechanism depends on the two strands of DNA being able to hold together under normal conditions, yet unwind easily. That is where hydrogen bonds come in. 

Most of the DNA of animal cells is found in the nucleus, where DNA is the major constituent of the chromosomes. On the other hand, most of the RNA is located in the cytoplasm. Nuclear DNA exists as a thin, double helix only 2 nm wide. The double helix is folded and complexed with protein to form chromosomal strands approxim-ately 100 to 200 nm in diameter. Each chromosome contains a single DNA duplex. The human chromosomes vary in size the smallest contains approximately 4.6 X 10 base pairs of DNA, and the largest 2.4 X 10 base pairs. In contrast, the Escherichia coli chromosome has 4.5 x 106 base pairs. The DNA of die chromosomes is tightly packed and associated with both histone and nonhistone proteins. 

Ladder polysilanes constitute a special case of fused polycyclic silicon macromolecules, in which cyclotetrasilane rings systematically catenate to form a silicon double helix, comprising two multi-linked silicon chains. Work in this area was initiated in this area by Matsumoto in 1987, and now comprises an integral part of the literature on higher-dimensionality polysilanes. 

A DNA molecule is said to be supercoiled when the ends of a DNA double helix join to form a closed circle which then winds back upon itself. 

Sample I, because of quick cooling, did not form a complete double helix. Slow cooling of sample II allowed more complete double-helix formation. 

The most striking conformational variant observed for a DNA double helix with Watson-Crick base pairing is referred to as the Z form. In Z DNA the backbone is twisted in the left-handed (counterclockwise) direction. This structure was first detected by Alex Rich and his co-workers (fig. 25.8). The Z form is a considerably slimmer helix than the B form and contains 12 bp/turn rather than 10. In the Z form, the planes of the base pairs are rotated approximately 180° with respect to the helix axis from their orientation in the B form (fig. 25.9). 

A simple sketch of mutually interacting DNA structures is given in Fig. 12b, in which star-like constructs are formed by the aggregation of four strands, each partially complementary to two other strands. This yields the formation of DNA stars with four arms, each made by a DNA double helix. Moreover, sequences are such that arms terminate with an overhang of a few unpaired bases, chosen so as to stick with the tips of other arms. In this way, structures of unlimited sizes can in principle be generated. 

The structures of RNA molecules consist of a single polymer chain of nucleotides with the same bases as DNA, with the exception of thymine, which is replaced by uracil, which forms a complementary base pair with adenine (Figure 1.33(a)). These chains often form single stranded hairpin loops separated by short sections of a distorted double helix formed by hydrogen bonded complementary base pairs (Figure 1.33(b)). 

RNA molecules consist of a single strand of nucleotides whilst DNA molecules consist of two nucleotide strands in the form of a supercoiled double helix. 

Mitochondria are about the size of bacteria. They have a diameter of 0.2 to 0.5 gm and are 0.5 to 7 p.m long. They are bounded by two lipid bilayers, the inner one being highly folded. These folds are called cristae. The innermost space of the mitochondrion is called the matrix. They have their own DNA in the form of at least one copy of a circular double helix (Chap. 7), about 5 p.m in overall diameter it differs from nuclear DNA in its density and denaturation temperature by virtue of being richer in guanosine and cytosine (Chap. 7). The different density from nuclear DNA allows its separation by isopycnic centrifugation. Mitochondria also have their own type of ribosomes that differ from those in the cytoplasm but are similar to those of bacteria. 

The wobble base pairs are displayed in Fig. 20.4. In comparison with Watson-Crick base pairs, the positions of the glycosyl links differ, but their directions are more or less retained so that the short codon-anticodon double helix is smooth. Pyrimidine-pyrimidine base pairs U - U and U - C, which could also form (Part II, Chap. 16) are considered to be unlikely since their C(l,) -C(r) distances are about 2 A shorter than the 10.5 A in a Watson-Crick base pair. The long A-1 base pair with C(l ) -C(r) distance of about 13.5 A, as actually observed in a comparable crystalline base-pairing complex [678], is too long to be accommodated in a smooth double helix. It has been suggested therefore that inosine in syn form could mimic the Watson-Crick geometry [679]. 

In the homopolymers formed by uridine or 2-thiouridine, base pairs with twofold symmetry are feasible, as described in Part II, Chapter 16 [529, 699]. The situation is more complex, however, because the homopolymer folds back on itself, giving rise to a hairpin-like structure where the polynucleotide strands are necessarily antiparallel and the base pairs are of the form shown in Fig. 20.10. Not surprisingly, a comparable double helix is also observed for polyxanthylic acid poly (X) [700]. The purine base of xanthosine displays the same hydrogen-bonding functional groups as uracil and therefore, the same base pair can be formed, but the purine-purine pair requires a larger separation between the glycosidic links and consequently a wider helix radius. 

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