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.

Jaeger JA; Zuker M; Turner DH

Department of Chemistry, University of Rochester, New York 14627.

Biochemistry 29: 10147-58 (1990)

Abstract
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.

Mesh Headings

Aldehydes

Animal

Base Sequence

Carbodiimides

Comparative Study

Computer Simulation

Cross-Linking Reagents

Diethyl Pyrocarbonate

Introns*

Magnesium

Molecular Sequence Data

Nucleic Acid Conformation

Nucleic Acid Denaturation

RNA Splicing*

RNA, Catalytic*

Sodium

Sulfuric Acid Esters

Support, Non-U.S. Gov't

Support, U.S. Gov't, P.H.S.

Tetrahymena

Unique Identifier: 91104932

Chemical Identifiers (Names)

15580-20-8 (1-cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide)

1609-47-8 (Diethyl Pyrocarbonate)

27762-78-3 (kethoxal)

7439-95-4 (Magnesium)

7440-23-5 (Sodium)

77-78-1 (dimethyl sulfate)