Sugar-Phosphate Chains

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen parrs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical stnrcture or double helix ). 

Each sugar unit is attached to a phosphate group. The phosphate group on one nucleotide bonds with a hydroxyl group on the sugar of another nucleotide to form a sugar-phosphate chain. 

The two sugar-phosphate chains are aligned in opposite directions. The 50OH linkage is at the top of the one strand and 30OH linkage at the top of the other strand. In the figure the number of dashes between the base symbols indicate the number of H-bonds. S is deoxyribose and P is 0=P—0-. 

Nucleic Acid. A nucleic acid is a natural polynucleotide. It is a sugar-phosphate chain with purine and pyrimidine bases attached to it, as shown in Chart 10. If the sugar is deoxyribose and the pyrimidine bases are cytosine and thymine, the nucleic acid is deoxyribonucleic acid, DNA if the sugar is ribose, and the pyrimidine bases are (mostly) cytosine and uracil, the nucleic acid is ribonucleic acid, RNA. The sequence of bases may appear arbitrary and random, but it constitutes a meaningful code (see Code Word). In double-stranded nucleic acids,... 

As illustrated and defined in Fig. 17.3, torsion angles along the sugar-phosphate chain are denoted in alphabetical order a to [starting with P-0(5 )], those in the furanose ring are called v0 to v4, and the orientation about the glycosidic link C(l )-N is described by X-... 

The sugar-phosphate chains attached to atoms C(l ) are in opposite directions because of the pseudo-twofold axis of the base pairs. The two strands in DNA or RNA double helices with Watson-Crick-type base pairing are therefore always antiparallel. 

The method has been applied to polyene, polyacetylene and polydiacetylene chains, to formamide chains (both hydrogen-bonded and stacked). Applications have been done also to TCNQ and TTF stacks, to (SN) and to periodic DNA models (the four homopolynucleotides), to the sugar phosphate chain of DNA and to different periodic protein models (homopolypeptides). All these systems have relatively broad valence and conduction bands (bandwidths around or larger than 0.5eV) according to our results. 

In Fig. 10-8 the spiraling ribbons represent sugar-phosphate chains and the bars represent pairs of bases H bonding the chains together. Each base is a purine or pyrimidine analogue and contains H bonding acid and base groups such that the pair is held by two or more H bonds (see Fig. 

The type of reaction that forms the sugar-phosphate chains in DNA and... 

Fig. 10. Intercalation Insertion of a planar dye molecule between adjacent base pairs in the DNA double helix. Three combinations are possible insertion between two adenine thymine (AT) or guanine-cytosine (GC) pairs or an AT and a GC base pair sequence 1 sugar-phosphat chain...

One of the most important natural compounds with a helical structure is deoxyribonucleic acid (DNA). It was studied by Watson and Crick based on the X-ray analysis of Franklin and Gossling Two right-handed polynucleotide chains are wound around a central axis. The sugar phosphate chains form an outer screw line, whereas the purine and pyrimidine bases are projecting inside. Their ring planes are... 

In DNA, essentially every base is part of a base pair in RNA only a portion of the bases are paired. Most of the DNA in cells is in the structure known as B-form DNA (Fig. 2.4). B-form DNA is actually a family of similar structures that vary in their detailed conformation depending on the precise sequence of individual bases along the chain. B-form DNA comprises two sugar-phosphate chains with complementary sequences such that when the two chains are wound round one another, in opposite (antiparallel) directions, to form a right-handed double helix,... 

Various self-complementing synthetic deoxyoligomers have been crystallized as a left-hand double helical molecule with Watson-Crick base pairs and an antiparallel organization of the sugar phosphate chains.It differs significantly from right-hand B-DNA. 

Fig. 7.19 Qualitative molecular modelling of the face-on interaction of ZnTMPyP (4) with the major groove. The expanded view (top) reveals the lack of interaction of one of the N-methylpyridinium groups with either of the sugar-phosphate chains.

Poly(alkylene phosphate) chains with bases in the side chains have been synthesised as, for example, in scheme (10.100) [80]. (Sugar phosphate chains devoid of bases are dealt with in Section 10.1.)... 

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