6 Torsion Angles in nucleic Acids The structure of nucleic acids are defined by the torsion angles along the phosphoribose backbone (a to z), the torsion angles within the sugar ring( n0 to n4) and the rotation of the nucleobase relative to the sugar (c). Rotation about c places the base either extended from the ribose (anti) or sitting above the ring (syn)
14 A-Form RNA or DNA Most RNA and RNA-DNA duplex in this form Shorter, wider helix than B.Deep, narrow major groove not easily accessible to proteinsWide, shallow minor groove accessible to proteins, but lower information content than major groove.Favored conformation at low water concentrationsBase pairs tilted to helix axis and displaced from axisSugar pucker C3'-endo (in RNA 2'-OH inhibits C2'-endo conformation)
15 B-Form DNA Most common DNA conformation in vivo Narrower, more elongated helix than A.Wide major groove easily accessible to proteinsNarrow minor grooveFavored conformation at high water concentrations (hydration of minor groove seems to favor B-form)Base pairs nearly perpendicular to helix axisSugar pucker C2'-endoLook at this spacefilling view of B-form DNA.
16 Helix has left-handed sense Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure.Narrower, more elongated helix than A or B.Major "groove" not really grooveNarrow minor grooveConformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence.N2-amino of G H-bonds to 5' PO: explains slow exchange of proton, need for G purine.Base pairs nearly perpendicular to helix axis
17 Z-form DNA GpC repeat, not single base-pair P-P distances: vary for GpC and CpGGpC stack: good base overlapCpG: less overlap.Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformationConformations:G; syn, C2'-endoC; anti, C3'-endo