{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["2(3)"],"submitter":["Kraeva RI"],"pubmed_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."],"journal":["PloS one"],"pagination":["e290"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC1808433"],"repository":["biostudies-literature"],"pubmed_title":["Stability of mRNA/DNA and DNA/DNA duplexes affects mRNA transcription."],"pmcid":["PMC1808433"],"pubmed_authors":["Krastev DB","Kraeva RI","Ivanova A","Roguev A","Stoynov SS","Nedelcheva-Veleva MN"],"additional_accession":[]},"is_claimable":false,"name":"Stability of mRNA/DNA and DNA/DNA duplexes affects mRNA transcription.","description":"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.","dates":{"release":"2007-01-01T00:00:00Z","publication":"2007 Mar","modification":"2025-04-05T10:03:50.728Z","creation":"2019-03-26T23:01:13Z"},"accession":"S-EPMC1808433","cross_references":{"pubmed":["17356699"],"doi":["10.1371/journal.pone.0000290"]}}