ABSTRACT
The Crick wobble hypothesis attributes the phenomenon of codon degeneracy to a certain impreciseness of pairing between the third base of the codon and the first base of the anticodon. This theoretical study investigates the pairing properties of some wobble bases, including both, observed and unobserved pairs. Some wobble base-pairs are predicted to follow the Watson-Crick pairs in configuration and pairing facility, while others deviate from this norm. The observed U:V pair is unique in that a pairing configuration may be suggested for it wherein the hydrogen-bonding involves the exocyclic 5-carboxymethoxy group of V. By comparing the theoretical data on the configurations of these pairs with the evidence for their existence/non-existence in nature, some guidelines emerge for differentiating between observed and unobserved base pairs on the basis of the pairing configuration.
Subject(s)
Adenine/chemistry , Anticodon , Base Pairing , Codon , Computer Simulation , Cytosine/chemistry , DNA/chemistry , Guanine/chemistry , Hydrogen Bonding , Inosine/chemistry , Models, Chemical , Nitrogen/chemistry , Nucleic Acid Conformation , Uracil/chemistryABSTRACT
Loss of Watson–Crick protons following DNA base alkylation has been proposed as a key event which confers mutation-inducing properties on to alkylated DNA bases. In this theoretical study, the promutagenic O6-guanine and O4-thymine sites are clearly distinguished from the nonmutagenic N7-guanine site on the basis of calculated values of mechanistic indicators for Watson–Crick proton acidity following alkylation at these respective sites. The degree of acidity predicted for these protons for each type of alkylated base accords well with the presence or absence of mutagenicity observed experimentally in each case.