Polynucleotide helix

FIGURE 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

In 1953, James Watson and Francis Crick made their classic proposal for the secondary structure of DNA. According to the Watson-Crick model, DNA under physiological conditions consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix like the handrails on a spiral staircase. The two strands are complementary rather than identical and are held together by hydrogen bonds between specific pairs of... 

Molecules of DNA consist of two complementary polynucleotide strands held together by hydrogen bonds between heterocyclic bases on the different strands and coiled into a double helix. Adenine and thymine form hydrogen bonds to each other, as do cytosine and guanine. 

Double helix (Section 28.2) The structure of DNA in which two polynucleotide strands coil around each other. 

The nucleotide bases are flat molecules. Each base pair is parallel to the one below it, with 340 picometers separating the two. There is a rotation of 36° between pairs, giving ten base pairs per complete turn of the helix. The two sugar-phosphate backbone strands wind around these stacked pairs, as shown in Figure 13-29. The two strands of DNA run in opposite directions, with the terminal phosphate end of one polynucleotide matched with the free hydroxyl end of the other. 

The polycondensation of several nucleoside monophosphates gives oligonucleotides (up to 40-50 units). If the chain is even longer, the polymer is referred to as a polynucleotide. Initial experiments on the polycondensation of nucleotides to give longer chains were carried out about ten years after the discovery of the DNA double helix (G. Schramm, Sect. 6.3). 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

Typical examples are the conversion of the neutral form of an amino acid into its zwitterionic form, the helix-coil transitions in polypeptides and polynucleotides, and other conformational changes in biopolymers. Reactions of higher molecularity in which reactants and products have different dipole moments are subject to the same effect (association of the carboxylic acids to form hydrogen-bonded dimers). Equilibrium involving ions are often more sensitive to the application of an electric field ... 

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 protection of a reactive intermediate complex by the DNA double helix versus a neutral oxidising agent in solution, has also been demonstrated by studying a photo-electron transfer process. In this example the intermediate complex is produced photochemically on the DNA, and is examined spectroscopically after a laser pulsed excitation [73]. Thus Ru(TAP)2(HAT) physically bound to nucleic acid is photo-reduced by hydroquinone during the laser pulse. The intermediate [Ru(TAP)2(HAT)] so-produced, detected by its absorption at 480 nm, is reoxidised by benzoquinone purposely added as oxidant to the solution. It is shown that this reoxidation of the mono-reduced complex is slower in the presence of polynucleotide than in its absence, indicating a protection of the transient mono-reduced complex in the DNA grooves. 

As discussed by Pdrschke one can distinguish several basic features of helix-coil transitions in polynucleotides. Formation of a helix from separated complementary... 

Secondary structure of DNA consists of two strands of polynucleotides coiled around each there in the form of double helix. The backbone of each strand is sugar-phosphate unit and the base unit of each strand are pointed into the interior of the helix and are linked through H-bonds. G and C are held by three H-bonds, A and T are held by two bonds. Unlike DNA, RNA has a single strand. 

The absorption coefficients of polynucleotides are different from those calculated from the sum of the mononucleotides in part this reflects the secondary structure. The abrupt increase in the absorption of DNA at the melting point, where the secondary structure changes from the double helix to a random coil, is well known. It is therefore... 

Melting Temperature. The double helix of polynucleotides described above becomes thermodynamically unstable at particular temperatures (with specified conditions of solute concentration, pH, etc.) and is transformed into the open random-coil arrangement. This transformation is rather sharp, and can be measured by the concurrent changes in a number of physical properties of the nucleic acid, such as the optical absorption coefficient. The midpoint of the transition region is called the melting point. 

DNA, a constituent of the cell nucleus, consists of two strands of polynucleotides that are coiled to form a double helix. The strands are held together by H-bonding between the nitrogen bases. The pyrimidines always form H-bonds with a specific purine i.e., cytosine with guanine and thymine with adenine. However, in RNA the pairing is between uracil and adenine. 

N 116 "The Spatial Configuration of Ordered Polynucleotide Chains. I. Helix Formation and Base Stacking"... 

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