Structural Analyses of the Ribosome by Chemical Modification Methods - Biophysical Approaches to Translational Control of Gene Expression - page 68

Chapter 4
Structural Analyses of the Ribosome
by Chemical Modi fi cation Methods

Jonathan A. Leshin , Arturas Meskauskas, and Jonathan D. Dinman

4.1 Introduction

4.1.1 What Is Chemical Modi fi cation and Why Is It Useful?

Imagine the following puzzle. Your “Sensei” tied a simple knot in a rope, dipped the
knot in paint, allowed the paint to dry, and then untied it. Your challenge is to retie
the knot based solely on the paint patterns. In essence this is a topological problem
of dimensional reduction, in this case one in which the information about the three-
dimensional structure of the knot is reduced to the two-dimensional linear rope that
bears markings pertaining to its prior three-dimensional topology. The solution to
this type of problem is based on the understanding that only those regions of the
rope that lay on the surface were exposed to paint, while those that had been buried
in its interior were not. In the case of a simple knot, a clever child should be able to
solve this problem using the paint markings as guides to work through a set of possible
solutions. While solving the structure of a ball of yarn that had been similarly pro-
cessed would be much more challenging, the solution would lie in taking the same
approach. It would merely require more time and computational power.
Nucleic acids are polymers of nucleic acid bases attached to ribose sugars that are
in turn linked together by phosphodiester bonds. Each of these moieties, the bases,
the sugars, and the phosphate groups, contains specific chemical groups that can be
modified by specific chemicals. Referring back to the analogy above, the nucleic acid
polymer is the rope, while the specific modifying chemicals constitute the palette of
available paints. While double-stranded DNA tends to assume rigid linear topologies