Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate.
C IVS is the cyclized form of the intron from the RNA precursor of the Tetrahymena thermophila large subunit (LSU) ribosomal RNA. C IVS was mapped by chemical modification in 1 M Na+, 0.05 M Na+ and 10 mM Mg2+ (Na+/Mg2+), and Na+/Mg2+ with CUCU substrate. The results suggest the secondary structure is similar for all three conditions. Optical melting curves were also measured for C IVS in 1 M Na+ and Na+/Mg2+ and indicate the secondary structures have similar stabilities under both conditions. Computer predictions of secondary structure and stability are in good agreement with observations. The results suggest that many of the approximations used for computer prediction of secondary structure by free energy minimization are reasonable.
Jaeger
J A
JA
Department of Chemistry, University of Rochester, New York 14627.
Zuker
M
M
Turner
D H
DH
D000447:Aldehydes / Q000494:pharmacology; D000818:Animals; D001483:Base Sequence; D002074:Butanones; D003028:CME-Carbodiimide / Q000031:analogs & derivatives*; D002234:Carbodiimides / Q000494:pharmacology; D003198:Computer Simulation; D003432:Cross-Linking Reagents / Q000494:pharmacology; D004047:Diethyl Pyrocarbonate / Q000494:pharmacology; D007438:Introns / Q000187:drug effects; D008274:Magnesium / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012326:RNA Splicing; D016337:RNA, Catalytic / Q000187:drug effects / Q000378:metabolism*; D012964:Sodium / Q000494:pharmacology; D013463:Sulfuric Acid Esters / Q000494:pharmacology; D013768:Tetrahymena / Q000235:genetics
D000447:Aldehydes; D002074:Butanones; D002234:Carbodiimides; D003432:Cross-Linking Reagents; D016337:RNA, Catalytic; D013463:Sulfuric Acid Esters; C060331:1-cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide; D003028:CME-Carbodiimide; D012964:Sodium; C005135:kethoxal; D008274:Magnesium; C007482:dimethyl sulfate; D004047:Diethyl Pyrocarbonate