Polynucleotide Structures

1. B form: Most DNA is in the B form. This so-called B-DNA (see here) is a right-handed helix. It predominates in an aqueous environment like that found in cells.

2. A form: A polynucleotide in the A form is a right-handed helix, too (Figure 4.15d). The A form is found in double-stranded RNA and in DNA-RNA hybrids.

3. Z form: Z-DNA is a left-handed helix found in polynucleotides with alternating purines and pyrimidines in each strand, as in the following:

> `5'CGCGCG3'
> 3'GCGCGC5'`

In polynucleotides, the two most stable orientations of the bases with respect to their deoxyribose rings are called syn and anti (see here). In the syn orientation, the base is situated above the sugar ring. In the anti orientation, the base is turned away from the sugar ring. In B- and A-DNA, both the purine and pyrimidine bases assume the anti orientation. In Z-DNA, however, the pyrimidine bases are anti, but the purine bases are always syn. As a result, the phosphate backbone in Z-DNA forms a zigzag pattern (Figure 4.26), thus giving rise to the name Z-DNA.

4. The presence of self-complementary sequences (called palindromes) within a single strand of polynucleotide can cause the palindromic portion of it to form intramolecular base pairs (Figure 4.27 and Figure 4.28). tRNAs and rRNAs have extensive base pairing of this type, although it can happen in DNA too.

5. Triple helices are unusual forms of DNA (called H-DNA) and RNA (Figure 4.30). Sequences favoring H-DNA include stretches of all pyrimidines on one strand and all purines on the complementary strand. This arrangement makes it possible to form a triple-stranded helix by doubling back. The triple helix of H-DNA consists of bases (e.g., adenine) each forming both a normal Watson-Crick with their complements (e.g., T) as well as an alternate form of base pair called a Hoogsteen pair with another complement (e.g., another thymine). Figure 4.29 shows the base pairing in a T-A-T triplet, but triple helical RNAs of structure poly(U)-poly(A)-poly(U) can form in a similar fashion. Some tRNAs have triple helical regions, too

See also: B-DNA, Primary, Secondary, Tertiary Structure of Nucleic Acids, Palindromes

INTERNET LINKS:

> 1. NDB Atlas of Nucleic Acid-Containing Structures

> 2. IMB-Jena Image Library