Premium
Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNA Phe
Author(s) -
Marky Nancy L.,
Olson Wilma K.
Publication year - 1987
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360260309
Subject(s) - chemistry , polynucleotide , transfer rna , loop (graph theory) , oligonucleotide , molecular dynamics , genetic code , rna , stereochemistry , crystallography , dna , computational chemistry , biochemistry , mathematics , combinatorics , gene
The flexibility of hairpin loops containing n bases (residues) has been examined using a theoretical model [N. L. Marky and W. K. Olson (1982), Biopolymers , 21 , 2329–2344] of oligonucleotide loop closure. The study is based on correlated probabilities of chain separation and terminal residue orientation as outlined previously. The probabilities are calculated using standard statistical mechanical methods as functions of local conformational changes of the chain backbone. Our results for an RNA chain of 9 residues suggest that the anticodon loop is a dynamic structure capable of assuming a variety of different spatial conformations. Free energy values related to the various conformations span a narrow range of values (2–4 kcal/mole) and compare well with experimental observations in aqueous solution. Conformational transitions between the loop conformations are within less than 0.5 kcal/mole in free energy. The different spatial loop conformations and the likely pathways between them may have potential relevance to the molecular translation of the genetic code.