title: Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.
abstract: Thermodynamic parameters for bulge loops of one to three nucleotides in oligoribonucleotide duplexes have been measured by optical melting. The results indicate bulges Bn of An and Un have similar stabilities in the duplexes, GCGBmGCG + CGCCGC. The stability increment for a bulge depends on more than its adjacent base pairs. For example, the stability increment for a bulge is affected more than 1 kcal/mol by changing two nonadjacent base pairs or by adding terminal unpaired nucleotides (dangling ends) three base pairs away. Thus a nearest-neighbor approximation for helixes with bulges is oversimplified. Many of the non-self-complementary strands used in this study were observed to form homoduplexes. Such duplexes with GA mismatches were particularly stable.
authors.affiliation: Department of Chemistry, University of Rochester, New York 14627.
authors.forename: C E
authors.initials: CE
authors.lastname: Longfellow
authors.forename: R
authors.initials: R
authors.lastname: Kierzek
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides; D009843:Oligoribonucleotides; D013053:Spectrophotometry; D013816:Thermodynamics
chemical_list: D009711:Nucleotides; D009843:Oligoribonucleotides