Secondary Structure
Nucleic acid structure consists of the regular, repeating folding pattern (such as a helix and b helix) stabilized by hydrogen bonds between peptide groups close together in sequence. The b form is what is expected in the aqueous environment of the cell. The a form exists under conditions of low humidity. Specific base pairing links the two nucleotide chains. Adenine in one strand is paired with thymine in the other, and guanine is paired to cytosine. They are considered complementary to each other. Hydrogen bonds form between the opposing bases within the pairs. In the structure proposed by Watson and Crick the A:T and G:C base pairs are roughly planer with two H bonds between the A:T pair and three H bonds between G:C pair.
Preferred conformations are those that allow a maximum number of hydrogen bonding. Helical structures formed by single polypeptide chains, as well as sheetlike structures are possible. Helices may be right-handed or left-handed and contain an integral or nonintegral number of residues per turn. The base pairs are stacked on one another with their planes perpendicular to the axis of the helix. Each base pair is rotated 36° to allow for 10 base pairs. The strands complimentary to each other and the bases are internal to the structure, creating a major and minor groove.
Unusual secondary structures of DNA can exit under certain conditions. The Atlas of Structures will contain many different forms with details of DNA Structures, RNA Structures, Unusual Structures, Protein/DNA Complexes, and Protein/RNA Complexes. Left-handed DNA, or Z-DNA is possible when pyrimidines are in their anti form and purines are in their syn form. Hairpin structures occur when single stranded self-complementary molecules fold back on themselves and for a base paired anti parallel helix. Double hairpins or cruciform structures, can form in some DNA sequences and are referred to as palindromes. Certain homopolymers can form triple helices.
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