title: Stability of mRNA/DNA and DNA/DNA duplexes affects mRNA transcription.
abstract: Nucleic acids, due to their structural and chemical properties, can form double-stranded secondary structures that assist the transfer of genetic information and can modulate gene expression. However, the nucleotide sequence alone is insufficient in explaining phenomena like intron-exon recognition during RNA processing. This raises the question whether nucleic acids are endowed with other attributes that can contribute to their biological functions. In this work, we present a calculation of thermodynamic stability of DNA/DNA and mRNA/DNA duplexes across the genomes of four species in the genus Saccharomyces by nearest-neighbor method. The results show that coding regions are more thermodynamically stable than introns, 3'-untranslated regions and intergenic sequences. Furthermore, open reading frames have more stable sense mRNA/DNA duplexes than the potential antisense duplexes, a property that can aid gene discovery. The lower stability of the DNA/DNA and mRNA/DNA duplexes of 3'-untranslated regions and the higher stability of genes correlates with increased mRNA level. These results suggest that the thermodynamic stability of DNA/DNA and mRNA/DNA duplexes affects mRNA transcription.
authors.affiliation: Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
authors.forename: Rayna I
authors.initials: RI
authors.lastname: Kraeva
authors.forename: Dragomir B
authors.initials: DB
authors.lastname: Krastev
authors.forename: Assen
authors.initials: A
authors.lastname: Roguev
authors.forename: Anna
authors.initials: A
authors.lastname: Ivanova
authors.forename: Marina N
authors.initials: MN
authors.lastname: Nedelcheva-Veleva
authors.forename: Stoyno S
authors.initials: SS
authors.lastname: Stoynov
mesh_terms: D015825:Chromosomes, Fungal / Q000235:genetics; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D004355:Drug Stability; D007438:Introns / Q000235:genetics; D016366:Open Reading Frames; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics*; D012440:Saccharomyces / Q000235:genetics*; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D012331:RNA, Fungal; D012333:RNA, Messenger; D004247:DNA