Re: what causes DNA and tRNA to twist

First, the Institute for Molecular Biology, Jena (Germany) supports one of the best sites for images and resources regarding nucleic acid biochemistry I've found, so let me start by directing you to their page on "Nucleic Acids Nomenclature And Structure," which gives complete pictorial descriptions of what I will explain here. Also, some of this has been covered previously by Dr. James Kranz, whose post, "How is DNA better suited than RNA to carry genetic info?" is worth reviewing. Now, on to the question: why are double-stranded nucleic acids helical?

The major consideration in building molecules with covalent bonding is bond angles, since they limit the shapes and conformations that the molecule can assume. While bond angles are usually fixed, rotation around these bonds is often free, unless prevented by the nature of the molecule around the bonds. In the case of nucleic acids, the bonds that make up their backbones are contained within and between the phosphate and ribose molecules. The bonds in ribose that constitute the backbone involve the third fourth and fifth carbons (C3', C4', and C5', respectively) and the oxygens attached to them. Because ribose is cyclical, the C5'-C4', C4'-C3', and C3'-O3' bonds are drastically limited in how they can be arranged in space. Similarly, the orientation of these bonds compared to the basepairs in a double-stranded nucleic acid is limited by the shape of the ribose. Confounding matters further, the negatively-charged phosphates of the backbone repel each other, such that they will favor any conformation that keeps them as far apart as possible; whereas, the basepairs prefer to interact with each other through stacking, such that a more uniform "ladder" of flat, stackable basepairs is more favorable. The result of all of these considerations is that the C5'-C4'-C3'-O3' ribose bonds are limited to three known conformations. Each of these conformations allows for a nearly linear, though jagged, repeating arrangement of ribose-phosphates, but none of them allow the axis of the backbone to be perpendicular to the plane of the basepairs. Since the backbones are not perpendicular and run in opposite directions, they cannot be parallel and the angle away from perpendicular determines the extent to which they must twist to maintain basepairing. These three possible conformations of ribose result in the three known nucleic acid helices: A-DNA, B-DNA, and Z-DNA.

To sum up: double-stranded nucleic acids twist because their ribose-phosphate backbones cannot run perpendicular to their basepairs, because their conformations are limited by the properties of their chemical bonds.