Polynucleotides double stranded form

Morphologists postulated for many years that the transfer of information from DNA to protein involves a form of nuclear RNA that migrates from nucleus to cytoplasm. This hypothesis found some concrete support as molecular biology developed. At first, it was found that a small fraction of bacterial RNA has a base composition identical to DNA in bacteria infected with T phage. The synthesis of DNA-depend-ent RNA was demonstrated in bacterial preparations and in mammalian nuclei. Triphosphate ribosides (UTP, GTP, CTP, and ATP) are required precursors for the synthesis of the new polynucleotide. Double-stranded DNA serves as a template in the reaction, and an RNA polymerase catalyzing the polymerization of the ribonucleotide was partially purified from both the bacterial and mammalian systems. 

Watson and Crick showed in 1953, using X-ray diffraction data of hydrated DNA fibres [26], that B-DNA, the most commonly encountered form, corresponds to a right-handed double-stranded helix (Fig. 4). Two polynucleotide... 

The question of energy transfer is introduced also by the fact that polynucleotides frequently exist not only in single-strand forms but also entirely or partially as double-strand helices in which pyrimidine residues on one chain are hydrogen bonded to purine residues on the other chain. The reactivity of the pyrimidine residue can be strongly affected by the presence of its purine partner. An example of this will be found further on. 

A few measmements of direct electrical transport were also performed on single bundles. Other measurements were done on networks formed of either double-stranded DNA [67] or alternative polynucleotides [68]. All the reported measurements showed current flowing through the bundles. We will show a few examples here. 

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... 

For the complexation of double-stranded DNA, a more elaborate polynucleotide morphology has been designed via the introduction of homopolynucleotide sequences on the ends for SPG binding [54]. Poly(dA) 80-mer was introduced at both ends of DNA, forming loops which provide protection from degradation by endonucleases, an approach adopted from viruses. 

Figure 14.11. Construction of biopolymer with HyperChem. Two menus are available for creating 3D structure models in HyperChem. The Build menu provides tools for creating organic molecules. Use the Drawing tool to sketch atoms in a molecule and connect them with covalent bonds. Invoke the Model builder to create a 3D structure from the 2D sketch. The Databases menu offers tools for creating biopolymers from residues with user specified linkages and conformations—that is, polysaccharides from monosaccharides, polypeptides form amino acids, and polynucleotides from nucleotides. A double-stranded DNA chain, for example, is constructed from nucleotide residues in a desired conformation (the inset).

For polynucleotide, choose various options such as either DNA or RNA, Form (a, b, c, d, e, t, or z forms), Build (5 to 3 or 3 to 5 ), single strand/double strand, and conformation of pentofuranose ring. Add bases (pairs) in the specified direction to build polynucleotide chain. 

In DNA, the nucleotides of the bases are linked in a chain-like arrangement, forming a polynucleotide. Two of such chains, associated as a double stranded, uniform helix, constitute a molecule of DNA. 

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. 

Two polynucleotide strands form the double helix of DNA. The backbone of each polymer strand is composed of sugar-phosphate residues. Hydrogen bonding of base pairs (A-T and C-G) holds the two strands of DNA together. 

The analysis obtained with classical polarographic methods corresponds roughly with those reached by the pulse-polarographic technique, but the sensitivity is much lower. The difference between the polarographic behaviour of single-stranded and double-helical form of polynucleotides makes possible the study of the conformation of nucleic acids [81,82,108-113]. Polarography can be utilized also in the study of structural changes of polynucleotides under the influence of the temperature [112,114,115] or irradiation [116]. The photodynamic destabilisation of DNA has been described [117]. 

RNA The secondary structure of RNA consists of a single polynucleotide. RNA can fold so that base pairing occurs between complementary regions. RNA molecules often contain both single- and double-stranded regions. The strands are antiparallel and assume a helical shape. The helices are of the A-form (see above). 

There is a large variability possible in the structures of double stranded DNA due to the fact that (compared to polypeptides) many more bonds can be rotated in the backbone of each monomer (Scheme 14). The most common and physiologically most important structure is the B-DNA helix. It consists of two polynucleotide chains running in opposite direction which coil around a common axis to form a right-handed double helix. In the helix, the phosphate and deoxyribose units of each strand are on the outside, and the purine and pyrimidine bases on the inside. The purine and pyrimidine bases are paired by selective hydrogen bonds adenine is paired with thymine, and guanine with cytosine (Scheme 15). The structure is very flexible and can form a supercoil with itself, or around proteins. It can form a left-handed supercoil around histones to form nucleosomes which assemble in yet another helical structure to form chromatin. ... 

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