Determinants of RNA Hairpin Loop-Loop Complex Stability

Gregorian, Razmic S.; Crothers, Donald M.

doi:10.1006/jmbi.1995.0275

Cited by 80 publications

(77 citation statements)

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“…The role of magnesium ions in the stability and structure of RNA is well-known. The stabilizing role of magnesium ions in natural or artificial kissing complexes has been characterized (Eguchi and Tomizawa 1991;Gregorian and Crothers 1995;Ducongé et al 2000). One magnesium ion would bind at the center of a pocket made by the two phosphate clusters at the stem-loop junctions (Chang and Tinoco 1997;Lee and Crothers 1998;Jossinet et al 1999;Reblova et al 2003).…”

Section: Discussionmentioning

confidence: 99%

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

Palau

Masante

Ventura

et al. 2013

RNA

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Surface plasmon resonance was used to investigate two previously described interactions analyzed by reverse genetics and complementation mutation experiments, involving 5BSL3.2, a stem-loop located in the NS5B coding region of HCV. 5BSL3.2 was immobilized on a sensor chip by streptavidin-biotin coupling, and its interaction either with the SL2 stem-loop of the 3 ′ end or with an upstream sequence centered on nucleotide 9110 (referred to as Seq9110) was monitored in real-time. In contrast with previous results obtained by NMR assays with the same short RNA sequences that we used or SHAPE analysis with longer RNAs, we demonstrate that recognition between 5BSL3.2 and SL2 can occur in solution through a kissing-loop interaction. We show that recognition between Seq9110 and the internal loop of 5BSL3.2 does not prevent binding of SL2 on the apical loop of 5BSL3.2 and does not influence the rate constants of the SL2-5BSL3.2 complex. Therefore, the two binding sites of 5BSL3.2, the apical and internal loops, are structurally independent and both interactions can coexist. We finally show that the stem-loop SL2 is a highly dynamic RNA motif that fluctuates between at least two conformations: One is able to hybridize with 5BSL3.2 through loop-loop interaction, and the other one is capable of self-associating in the absence of protein, reinforcing the hypothesis of SL2 being a dimerization sequence. This result suggests also that the conformational dynamics of SL2 could play a crucial role for controlling the destiny of the genomic RNA.

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Section: Discussionmentioning

confidence: 99%

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

Palau

Masante

Ventura

et al. 2013

RNA

View full text Add to dashboard Cite

show abstract

“…This validates the choice of shorter RNAs to investigate the role of the GA loop-closing bases of the aptamer. Despite the importance of Mg 2ϩ ions for the stability of kissing complexes (27), the interaction is still strong enough to enable a high-resolution NMR study in the absence of magnesium (K d Ϸ0.5 M). The addition of five equivalents of magnesium ions does not significantly change the NMR spectra, as described for a similar kissing complex (14).…”

Section: Minimal Functional System Suitable For High-resolution Nmr Smentioning

confidence: 99%

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

Melckebeke

Devany

Primo

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…To determine the free-energy change for formation of the bimolecular oligomer-oligomer structure, the algorithm of Zuker (Zuker & Stiegler, 1981;Zuker, 1989a) was modified to predict bimolecular secondary structures+ This is done by predicting secondary structure for two sequences joined by a virtual linker composed of nucleotides that cannot pair+ For the loop region occupied by the linker, the algorithm applies the free energy of intermolecular initiation rather than a loop penalty+ This method allows many conformations of intermolecular structure, but it cannot predict those that mimic a pseudoknot, most notably the kissing hairpin motif (Chang & Tinoco, 1994Gregorian & Crothers, 1995;Comolli et al+, 1998)+ In the future, however, this method for bimolecular structure prediction could be combined with recent work in dynamic programming (Rivas & Eddy, 1999) to predict kissing hairpins+…”

Section: Bimolecular Secondary Structure Predictionmentioning

confidence: 99%