title: Favored and less favored codon-anticodon duplexes arising from the GC codon family box encoding for alanine: some computational perspectives.
abstract: Alanine is encoded by the four codons of the GC box (GCA, GCG, GCU, and GCC). Known alanine anticodons include the UGC, IGC, and VGC triplets (I = inosine; V = uridine-5-oxyacetic acid). The energy-minimized structures of all possible codon-anticodon combinations involving all the alanine codons GCA, GCG, GCU, and GCC with the alanine anticodons UGC, IGC, and VGC are studied using the AMBER software. Fifteen H-bonded duplex structures arising out of these combinations are studied here, all having Watson-Crick-type base pairs at the first and second codon positions, and a variety of base pairing possibilities at the third (or wobble) position. Structural and stability considerations suggest that some codon-anticodon duplexes would be more favored than others for accommodation during the translation process. The UGC anticodon is predicted to favor the GCA codon for reading, while the GCC codon is least favored. The IGC anticodon would prefer to read the GCC codon, the GCG codon being least favored, while a syn conformer for A in the GCA codon could allow for it to be read. For the VGC anticodon, the GCA codon is predicted to be read most favorably, and the GCC codon least favorably, while a syn conformer for V in the anticodon would allow for the codon GCU to be read through a wobble pair which involves the exocyclic 5-oxyacetate group of V in H-bonding.
authors.affiliation: a Department of Chemistry , North-Eastern Hill University , Shillong 793022 , India.
authors.forename: Martina
authors.initials: M
authors.lastname: Devi
authors.affiliation: a Department of Chemistry , North-Eastern Hill University , Shillong 793022 , India.
authors.forename: R H Duncan
authors.initials: RHD
authors.lastname: Lyngdoh
mesh_terms: D000409:Alanine / Q000737:chemistry* / Q000235:genetics; D000926:Anticodon / Q000737:chemistry / Q000235:genetics*; D020029:Base Pairing; D003062:Codon / Q000737:chemistry / Q000235:genetics*; D019295:Computational Biology; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation
chemical_list: D000926:Anticodon; D003062:Codon; D000409:Alanine
keywords: Alanine GC codon box; alanine anticodons; codon–anticodon duplex stability; favored codons; wobble base pair configuration