Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

Walter AE; Turner DH; Kim J; Lyttle MH; Muller P; Mathews DH; Zuker M

Department of Chemistry, University of Rochester, NY 14627-0216.

Proc Natl Acad Sci U S A 91: 9218-22 (1994)

Abstract
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 1 kcal/mol (1 cal = 4.184J). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.

Mesh Headings

Animal

Base Sequence

Calorimetry

Comparative Study

Introns

Molecular Sequence Data

Nucleic Acid Conformation*

Oligoribonucleotides*

Phylogeny

Rats

RNA*

RNA, Bacterial

RNA, Fungal

Structure-Activity Relationship

Support, Non-U.S. Gov't

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

Unique Identifier: 95023882

Chemical Identifiers (Names)

(Oligoribonucleotides)

(RNA)

(RNA, Fungal)

9010-74-6 (RNA, Bacterial)