title: Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs.
abstract: Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl(2) or 1 M KCl. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47-2.06 kcal/mol more favorable for the RNA bulge loops. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.
authors.affiliation: Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Strom
authors.affiliation: Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA.
authors.forename: Evgenia
authors.initials: E
authors.lastname: Shiskova
authors.affiliation: Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA.
authors.forename: Yaeeun
authors.initials: Y
authors.lastname: Hahm
authors.affiliation: Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA NGrover@ColoradoCollege.edu.
authors.forename: Neena
authors.initials: N
authors.lastname: Grover
mesh_terms: D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011687:Purines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011687:Purines; D012313:RNA; D004247:DNA
keywords: DNA bulge loops; RNA thermodynamics; magnesium binding to RNA; metal–RNA interactions; purine bulge loops