The NMR structure of a kissing complex of two RNA hairpins

Conference · Wed Dec 31 04:00:00 EST 1997

OSTI ID:560019

Chang, K Y; Pelton, J; Comolli, L; Tinoco, I Jr ^[1]

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1. Lawrence Berkeley National Lab., CA (United States)

We have used nuclear magnetic resonance to obtain the solution structure of an RNA {open_quotes}kissing{close_quotes} hairpin complex formed between the HIV TAR hairpin loop and a hairpin with a complementary loop. The loops of the hairpins base pair to produce an A-form helix with six Watson-Crick base pairs that stack between the two helices of the hair-pin stems. The loop-loop-interaction helix has a compressed major groove with an alternating overtwist and undertwist pattern for each adjacent base pair. This alternating helical twist is reminiscent of the sequence-dependent {open_quotes}alternating-B{close_quotes} DNA structure, however, the formation of this {open_quotes}alternating-A{close_quotes} RNA seems to be sequence-independent. The alternating-A RNA has a set of minor groove AH2-H1{prime} intrastrand and cross-strand NOEs with a unique intensity pattern that can be used to distinguish it from a normal A-form RNA helix. The ROM protein is a four-helix bundle protein that specifically recognizes kissing hairpin complexes. We are currently investigating the correlation between ROM-protein binding and alternating helical twist within the kissing hairpins.

• OSTI ID: 560019
• Report Number(s): CONF-970443--
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
66 PHYSICS
HELICAL CONFIGURATION
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
RNA