Anticodons, frameshifts, and hidden periodicities in tRNA sequences.
Fourier analysis of the short-range periodicities for the complete set of sequences coding for tRNA genes in genome of Bacillus subtilis proves that periodicities with periods p = 2, 3, 4, and 6 sites are the inherent properties of tRNAs. The related periodicities should be understood in a broad statistical sense and their identifying needs the elaborate statistical methods. To improve the statistics, the analysis of significant periodicities was performed for the binary R-Y, S-W, and K-M sequences. Generally, such short-range periodicities are produced via biased positioning of particular nucleotides rather than via the tandem multiplication and subsequent modifications of repeats, though the latter mechanism may also be realized. Quasi-coherently piercing long segments of tRNA, the short-range periodicities create the effective long-range structural coupling between the acceptor stem and the anticodon loop and may participate in the mechanisms of molecular recognition. The periodicities with p = 2 and 4 provide the natural ground for the translation with spontaneous or programmed frameshifting and are present in tRNAs decoding the most frameshift-prone codons. The observation of short-range periodicities suggests that the mechanisms of amino-acylation of tRNAs and codon-anticodon pairing are not independent. Their study may also provide the important information related to the origin and evolution of the genetic code.
Chechetkin
V R
VR
Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Theoretical Department of Division for Perspective Investigations, 142190 Troitsk, Moscow Region, Russia. chechet@biochip.ru
Lobzin
V V
VV
D000926:Anticodon / Q000235:genetics* / Q000378:metabolism; D001412:Bacillus subtilis / Q000235:genetics; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
D000926:Anticodon; D012343:RNA, Transfer