Introduction

The effect of a solvent and the buffer it carries on the behavior of a biopolymer is hardly negligible. A good solvent is able to take up large quantities of polymer, a poor solvent not. The molecular weight at which a polymer precipitates is governed by polymer-solvent interactions. However, solvation is hardly the most profound effect; it is the global structure of such polymers that are strongly under the influence of solvent as well.

Biopolymers characteristically have varying degrees of amphiphilic behavior that complicates predicting their overall interactions. Hydrophobic parts of the molecule tend to repel water away, yet at the same time, functional groups composed of nitrogen or oxygen tend to attract charged ions and the water that carries them. This effect is no more obvious than in the case of nucleic acids that have aromatic rings on the base but a negatively charged phosphate on the sugar. An atmosphere of positively charged ions form a cloud around the nucleic acids, balancing the large negative charge.

Nucleic acids are affected by the quantity of salt and the type of salt. This effect is referred to as the ionic strength. The Mg-water complex ([Mg(H$_2$O)$_6$]$^{2+})$, although poor at forming specific binding sites, is excellent at stabilizing RNA and large clouds of charged Mg$^{2+}$ ions are known to surround the group I intron (T. thermophilus) and in the measured tRNA there also appears to be a similar cloud of ions. The stabilizing effect is strong enough that the biopolymer can end up balling up into a small globule that is much smaller than the size of a Gaussian polymer chain (GPC). Denaturing agents may also play a role in swelling the biopolymer in the process of denaturing.

So the net effect of divalent counter ions is not in specific interactions with the RNA, rather it is the weak interactions of the polymer with the solvent and possible counter ions that have a long range impact on the global structure of RNA causing it to be globular in some cases or swelled in others. It is in these initial conditions where the polymer folds into its final structure after transcription by RNA-polymerase.

Thus, although these effects are non-specific, solvent interactions have a profound effect on folding. It is here that we now introduce Flory's polymer swelling model and apply it in the program to calculate RNA structure.

This discussion contains many equations not because I like to write equation, or because I enjoy rambling about thermodynamics and decorating my work with symbols. Thinking about these problems requires looking for ways to understand why we are right. Merely throwing equations around without considering whether what one writes makes sense is just as bad as ignoring the importance of equations in summarizing our understanding. Nature, although opaque in many ways, is also something that should yield to our examination, and the equations presented here is my attempt to help cut a pathway through the thick jungle of confusion and uncertainty.