Sugar-phosphate backbone

Since sugar radicals are known precursors in mechanisms leading to strand breaks [1, 7], it is of importance to determine the most probable site of hole localization on the DNA backbone following exposure to ionizing radiations and to understand the chemistry that ensues. 

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As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

Polymerization of nucleotides occurs through the sugar and phosphate groups so that the polymers consist of a sugar-phosphate backbone having pendent bases. 

Figure 7.1 Schematic drawing of B-DNA. Each atom of the sugar-phosphate backbones of the double helix is represented as connected circles within ribbons. The two sugar-phosphate backbones are highlighted by orange ribbons. The base pairs that are connected to the backbone are represented as blue planks.

Figure 7.2 Three helical forms of DNA, each containing 22 nucleotide pairs, shown in both side and top views. The sugar-phosphate backbone is dark the paired nucleotide bases are light, (a) B-DNA, which is the most common form in cells, (b) A-DNA, which is obtained under dehydrated nonphysiological conditions. Notice the hole along the helical axis in this form, (c) Z-DNA, which can be formed by certain DNA sequences under special circumstances. (Courtesy of Richard Feldmann.)...

Figure 7.4 The edges of the base pairs in DNA that ate in the major groove are wider than those in the minor groove, due to the asymmetric-attachment of the base pairs to the sugar-phosphate backbone (a). These edges contain different hydrogen bond donors and acceptors for potentially specific interactions with proteins (b).

The sugar-phosphate backbone is represented by connected circles in color and the base pairs as blue planks. Four base pairs are shown from the top of the helix to highlight how the grooves are formed due to the asymmetric connections. The position of the helix axis is marked by a cross. 

The binding model, suggested by Brian Matthews, is shown schematically in (a) with connected circles for the Ca positions, (b) A schematic diagram of the Cro dimer with different colors for the two subunits, (c) A schematic space-filling model of the dimer of Cro bound to a bent B-DNA molecule. The sugar-phosphate backbone of DNA is orange, and the bases ate yellow. Protein atoms are colored red, blue, green, and white, [(a) Adapted from D. Ohlendorf et al., /. Mol. Evol. 19 109-114, 1983. (c) Courtesy of Brian Matthews.]... 

H-bonds between sugar-phosphate backbone and protein help anchor protein to DNA... 

RNA is relatively resistant to the effects of dilute acid, but gentle treatment of DNA with 1 mM HCl leads to hydrolysis of purine glycosidic bonds and the loss of purine bases from the DNA. The glycosidic bonds between pyrimidine bases and 2 -deoxyribose are not affected, and, in this case, the polynucleotide s sugar-phosphate backbone remains intact. The purine-free polynucleotide product is called apurinic acid. 

The base-specific chemical cleavage (or Maxam-Gilbert) method starts with a single-stranded DNA that is labeled at one end with radioactive (Double-stranded DNA can be used if only one strand is labeled at only one of its ends.) The DNA strand is then randomly cleaved by reactions that specifically fragment its sugar-phosphate backbone only where certain bases have been chemically removed. There is no unique reaction for each of the four bases. However,... 

A stereochemical consequence of the way A T and G C base pairs form is that the sugars of the respective nucleotides have opposite orientations, and thus the sugar-phosphate backbones of the two chains run in opposite or... 

Protons bound to heteroatoms in heterocyclic compounds are likely to be very mobile in solution and, where two or more heteroatoms are present in a structure, different isomers (tautomers) may be in equilibrium. As a case in point, consider the nucleotide bases (indicates the point of attachment to the sugar-phosphate backbone). 

DNA consists of two strands of sugar-phosphate backbones wound around each other in a double helix. The two helices are connected by hydrogen bonds between the bases. 

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 structure of DNA. (a) A ball-and-stick model, with the sugar-phosphate backbone colored blue and the bases colored red. b) A space-filling model, showing C atoms in blue, N atoms in dark blue, H atoms in white, O atoms in red, and P atoms in yellow. 

The structures of DNA and RNA are similar in that each has a sugar-phosphate backbone with one organic base bound to each sugar. However, there are four distinct differences between RNA and DNA ... 

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