Polynucleotide biologically formed

A biologically formed protein or polynucleotide, while exhibiting some limited heterogeneity in length or microheterogeneity in the main chain sequence or in pendant prosthetic groups, has an essentially unique sequence. Different forms of a protein or polynucleotide often can be... 

Schuchmann MN, Naumov S, Schuchmann H-P, von Sonntag J, von Sonntag C (2005) 4-Amino-3Ff-pyrimidin-2-one ("isocytosine") is a short-lived non-radical intermediate formed in the pulse radiolysis of cytosine in aqueous solution. Radiat Phys Chem 72 243-250 Schulte-Frohlinde D, Hildenbrand K (1989) Electron spin resonance studies of the reactions of OH and SO4 radicals with DNA, polynucleotides and single base model compounds. In Minisci F (ed) Free radicals in synthesis and biology. Kluwer, Dordrecht, pp 335-359 Schulte-Frohlinde D, Behrens G, Onal A (1986) Lifetime of peroxyl radicals of poly(U), poly(A) and single- and double-stranded DNA and the rate of their reaction with thiols. Int J Radiat Biol 50 103-110... 

One of the most exciting biological discoveries is the recognition of DNA as a double helix (Watson and Crick, 1953) of two antiparallel polynucleotide chains with the base pairings between A and T, and between G and C (Watson and Crick s DNA structure). Thus, the nucleotide sequence in one chain is complementary to, but not identical to, that in the other chain. The diameter of the double helix measured between phosphorus atoms is 2.0 nm. The pitch is 3.4 nm. There are 10 base pairs per turn. Thus the rise per base pair is 0.34 nm, and bases are stacked in the center of the helix. This form (B form), whose base pairs lie almost normal to the helix axis, is stable under high humidity and is thought to approximate the conformation of most DNA in cells. However, the base pairs in another form (A form) of DNA, which likely occurs in complex with histone, are inclined to the helix axis by about 20° with 11 base pairs per turn. While DNA molecules may exist as straight rods, the two ends bacterial DNA are often covalently joined to form circular DNA molecules, which are frequently supercoiled. 

In contrast to RNA, DNA is polymorphic. Under low salt conditions or at high relative humidity, DNA adopts the B-form usually considered to be biologically active. With increasing addition of salt or of polar organic solvents (synonymous with reduced relative humidity or removal of available water of hydration), and with certain types of counterions, DNA and double-stranded synthetic polynucleotides transform from B-DNA to the A-, C-, D-, Z-forms (see Thble 24.1 and Fig. 24.1. Only the A-, B- and Z-DNA structures, which have thus far been determined in detail by single crystal diffraction methods, are of structural interest and they are considered in the following sections. 

Since RNA double helices and most RNA/DNA hybrids have only been observed in conformations similar to the A-form [14-24] whereas studies of the DNA conformation in cells such as salmon sperm have revealed that the resting state of DNA appears to be the B-form [25], it is natural to speculate that the B-form is adopted for DNA replication whereas the A-form is adopted for transcription. Similar considerations apply in the case of synthetic polynucleotides a polynucleotide with a highly repetitive base sequence can be found in the S form under conditions in which a natural DNA with essentially random base sequence would be found in the B form. Highly repetitive sequences flanked on both sides by random sequences are known to exist in natural DNAs and so it is possible that under some ionic conditions the repetitive and random sequences would have different conformations. The potential to exploit such structural differences in control processes mediated by specific DNA-protein recognition mechanisms is clear. Although these speculations have not been confirmed, the fact that conformational transitions may be implicated in such fundamental biological processes is powerful justification for extensive study of the stereochemical pathways of these transitions and the factors which promote and control them. 

From these and many other studies there was by 1950 plenty of evidence pointing to the possible importance of liquid crystals in tissue. Since then the subject has been explored by direct and experimental methods. My purpose is to examine the chemical forms in which liquid crystals occur and to identify more closely their precise structure and integration into protoplasm and biological fluids. This is often a matter of great difficulty for obvious technical reasons. My own work in this respect has been concerned mainly with lipids and lipoproteins, so I shall refer mainly to these though several other important classes of substances, especially certain proteins and polynucleotides, can exist in the liquid crystalline state and may be present as such in living tissue. 

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