Silent DNA: speaking RNA language?
The sequence of silent DNA in the human genome (intergenic spacers, introns and synonymous codon positions of protein-coding genes) was found here to have the higher thermostability of corresponding RNA/RNA and RNA/DNA duplexes as compared with randomized sequence. This difference increased with elevation of GC content. The revealed effect was not due to correlation of RNA/RNA and RNA/DNA thermostabilities with thermostability of the DNA/DNA duplex, which, on the contrary, was lower than in the randomized sequence and lagged behind the elevation of GC content. The same picture was observed in the genomes of other warm-blooded vertebrates but not in the lower organisms. This finding suggests that RNA-RNA and RNA-DNA interactions could be involved in the putative function of silent DNA.
Vinogradov
Alexander E
AE
Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St Petersburg 194064, Russia. aevin@mail.cytspb.rssi.ru
D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000737:chemistry / Q000235:genetics; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D020862:GC Rich Sequence / Q000235:genetics*; D020868:Gene Silencing; D015894:Genome, Human; D006801:Humans; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D020125:Mutation, Missense / Q000235:genetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D013329:Structure-Activity Relationship; D013696:Temperature
D003062:Codon; D012313:RNA; D004247:DNA