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Structure of components.

Nucleic acids are very long, thread like polymers, made up of a linear array of monomers called nucleotides. Nucleotides are the phophate esters of nucleosides and these are components of both ribonucleic acid and deoxyribonucleic acid. All nucleotides are composed of three components: a nitrogen heterocyclic base, a pentose sugar (2’deoxy ribose for DNA and ribose for RNA), and a phophate residue. The bases are divided into two groups: pirimidines and purines. The major pirimidines are cytosine (C), thymine (T) and uracil (U), the major purines adenine (A) and guanine (G).

            dA dC dG dT structure

Because of some of structural restrictions, conformations available for listed above components play primary role in defining the structure of DNA.

Nucleotides interact with each other via hydrogen bonds forming Watson-Crick base pairs, wobble base pairs, Hoogsteen base pairs.

                                 

Sugar pucker.

The furanose rings are twisted out of plane in order to minimize non-bonded interactions between their substituents. This puckering is described by identifying the major displacement of carbons: 2’ and 3’ from the median plane of C1’-O4’-C4’. Thus, if the endo displacement of C-2’ is greater than the exo displacement of C-3’ the conformation is called C2’-endo, and so on.

Syn-anti conformation

The plane of the base is almost perpendicular to that of the sugars and approximately bisects the O4’-C1’-C2’ angle. This allows the bases to occupy either of two principal orientations. The anti conformer has the smaller H-6 (pirimidine) or H-8 (purine) atom above the sugar ring, while the syn conformer has the larger O-2 (pirimidine) or N-3 (purine) in that position. Pirimidines occupy a narrow range of anti conformations, while purines are found in wider range of anti conformations. There is only one known case where a purine adopts a syn conformation. The unusual form is to find in an even more unusual structure namely left handed Z-DNA. An example of possible interaction between guanosines in syn and anti conformation is shown on a drawing below.

                                

Other restrictions.

Two other bonds which are important for determining the DNA structure are:

  1. the bond between C4’ and C5’ which defines the position of the 5’phosphate relative to the sugar ring (the favoured conformations of this bond are synclinical and antiperiplanar)
  2. C-O and P-O bonds (the former usually appears in antiperiplanar conformation and the latter in gauche conformation.

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