Section 23.3.3.5. Allowable RNA helices

So far this discussion has only been concerned with DNA. Which of the three helix types can be adopted by RNA? Fig. 23.3.3.5 shows that addition of a 2′-OH group to a B-DNA helix [part (a)] creates severe steric clash with the phosphate group and sugar ring of the following nucleotide, whereas in an A helix [part (b)], the added hydroxyl group extends radially outward from the helix cylinder and causes no steric problems. Hence, the natural helical form for RNA is the A helix, not the B helix. Table A23.3.1.1 shows several single-crystal analyses of A-RNA and RNA/DNA hybrids; Table A23.3.1.2 shows no B-RNA structures. One RNA/DNA hybrid is known as a Z helix: C-G-c-g-C-G (Z24), in which the two central nucleotides are RNA. If one mentally adds an —OH to each C2′ atom in Fig. 23.3.3.3, on the same side of the ring as O3′, it is apparent that the C2′-OH is not inherently incompatible with the Z helix, as it is with the B helix. At guanine sugars, the C2-OH points out and away from the helix, while at cytosine sugars it points away from the base into the spacious minor groove.

Figure 23.3.3.5| top | pdf | The role of the C2′-OH in RNA helix geometry. (a) Addition of a C2′-OH group (*) to the B-DNA helix leads to close contacts and unallowable steric hindrance with the following O5′ and O4′ atoms and, to a lesser degree, the subsequent base itself. (b) A C2′-OH group added to the A-DNA helix extends outward radially from the helix cylinder surface and produces no steric clashes. Hence, A-RNA is quite possible, whereas B-RNA is disallowed.