Deoxyriboses

D-2-deoxyribose, desoxyribose, CjHioO. The sugar isolated by hydrolysis of DNA. Colourless crystals, m.p. 9UC, soluble in water. 

Watson J D and Crick F H C 1953 A structure for deoxyribose nucleic acid Nature 171 737-8... 

The acid treatment in each detritylation step may remove purines from deoxyriboses. Purine residues near the 3 -end will suffer the longest cumulative times of exposure to acid and therefore have the greatest chance for depurination . Thus each acid treatment should be as brief as possible. 

The furanose rings of the deoxyribose units of DNA are conformationally labile. All flexible forms of cyclopentane and related rings are of nearly constant strain and pseudorotations take place by a fast wave-like motion around the ring The flexibility of the furanose rings (M, Levitt, 1978) is presumably responsible for the partial unraveling of the DNA double helix in biological processes. 

Watson and Crick published their work in a pa per entitled A Structure for Deoxyribose Nucleic Acid in the British journal A/ature on April 25 1953 In addition to being one of the most important pa pers of the twentieth century it is also remembered for one brief sentence appearing near the end... 

Any one nucleotide, the basic building block of a nucleic acid, is derived from a molecule of phosphoric acid, a molecule of a sugar (either deoxyribose or ribose), and a molecule of one of five nitrogen compounds (bases) cytosine (C), thymine (T), adenine (A), guanine (G), uracil (U). 

A chain of nucleotides containing only deoxyribose as the sugar is a DNA. Similarly, RNA possesses chains nucleotides having only ribose as the sugar and is therefore a ribonucleic acid. 

The primary stmcture of DNA is based on repeating nucleotide units, where each nucleotide is made up of the sugar, ie, 2 -deoxyribose, a phosphate, and a heterocycHc base, N. The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (Fig. 1). The base, N, is bound at the I -position of the ribose unit through a heterocycHc nitrogen. 

Fig. 1. Elements of DNA stmcture (a) a deoxypolynucleotiide chain, which reads d(ACTG) from 3 — 5 or d(GTCA) from 3 — 5 and (b) and (c) the Watson-Crick purine—pyriinidine base pairs. A—T and G—C, respectively, where — represents attachment to the deoxyribose.

The a-anomeric form of a 2 -deoxyribose, which has the base inverted with respect to the natural P-anomeric form, can be synthesized by using the phosphoramidite method sugar modification renders the derivatives nuclease-resistant. These analogues form parallel duplexes with complementary RNA... 

The sugars are typically ribose (ribonucleic acids, RNA), or 2-deoxyribose (deoxyribonucleic acids, DNA). There are five common bases in nucleic acids adenine (A) thymine (T) uracil (U) cytosine (C) and guanine (G). DNA polymers incorporate the four bases. A, T, C, and G, and RNA, the set A, U, C, and G. 

Cytosine was isolated from hydrolysis of calf thymus in 1894 and by 1903 its structure was known and it had been synthesized from 2-ethylthiopyrimidin-4(3H)-one. The acid hydrolysis of ribonucleic acid gives nucleotides, among which are two cytidylic acids, 2 -and 3 -phosphates of cytidine further hydrolysis gives cytidine itself, i.e. the 1-/3-D-ribofuranoside of cytosine, and thence cytosine. The deoxyribonucleic acids likewise yield deoxyribonucleotides, including cytosine deoxyribose-5 -phosphate, from which the phosphate may be removed to give cytosine deoxyriboside and thence cytosine. 

Watson, J.D., Crick, F.H.C. Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. Nature 171 737-738, 1953. 

DNA (deoxyribonucleic acid) (Section 28.7) A polynucleotide of 2 -deoxyribose present in the nuclei of cells that serves to store and replicate genetic information. Genes are DNA. 

Nucleoside (Section 28.2) The combination of a purine or pyrimidine base and a carbohydrate, usually ribose or 2-deoxyribose. 

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. 

Figure 12.16), can insert between the stacked base pairs of DNA. The bases are forced apart to accommodate these so-called intercalating agents, causing an unwinding of the helix to a more ladderlike structure. The deoxyribose-phosphate backbone is almost fully extended as successive base pairs are displaced 0.7 nm from one another, and the rotational angle about the helix axis between adjacent base pairs is reduced from 36° to 10°. 

As is well-known, nucleic acids consist of a polymeric chain of monotonously reiterating molecules of phosphoric acid and a sugar. In ribonucleic acid, the sugar component is represented by n-ribose, in deoxyribonucleic acid by D-2-deoxyribose. To this chain pyrimidine and purine derivatives are bound at the sugar moieties, these derivatives being conventionally, even if inaccurately, termed as pyrimidine and purine bases. The bases in question are uracil (in ribonucleic acids) or thymine (in deoxyribonucleic acids), cytosine, adenine, guanine, in some cases 5-methylcytosine and 5-hydroxymethylcyto-sine. In addition to these, a number of the so-called odd bases occurring in small amounts in some ribonucleic acid fractions have been isolated. 

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