Spectroscopic evidence for an intramolecular RNA triple helix

Klinck, Roscoe; Guittet, Éric; Liquier, J.; Taillandier, E.; Gouyette, Catherine; Huynh‐Dinh, Tam

doi:10.1016/0014-5793(94)01228-8

Cited by 18 publications

(15 citation statements)

References 25 publications

(9 reference statements)

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“…The possibility of poly(C) forming a higher order structure at low pH in the presence of a polyamine cannot be dismissed. Cations are known to stabilize higher order, acid-pH-dependent triple-stranded RNA structures (Klinck et al, 1994) and polyamines can induce conformational changes when bound to nucleic acids (Manning, 1978). Our argument is reinforced by the observation that chemical modification of C residues within TYMV RNA results in loss of binding by coat protein .…”

Section: Requirement Of Low Ph and Poly(c) For Virus Assemblysupporting

confidence: 60%

Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly?

Rohozinski

Hancock²

1996

Journal of General Virology

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Turnip yellow mosaic virus (TYMV) induces gross morphological and biochemical changes in the chloroplasts of infected cells. Viral RNA is synthesized in vesicles formed by invagination of the outer chloroplast bilayer. Virion assembly occurs at the neck of these vesicles and requires illumination. Data collected over the last three decades are consistent with the hypothesis that light-induced generation of a low pH drives TYMV assembly within the intermembrane space of chloroplasts. In a low-pH environment, poly(C) regions within the genomic RNA of TYMV may interact to form tertiary structures, and the recognition of these structures by TYMV coat protein initiates virion assembly.

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Section: Requirement Of Low Ph and Poly(c) For Virus Assemblysupporting

confidence: 60%

Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly?

Rohozinski

Hancock²

1996

Journal of General Virology

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“…Assignment of exchangeable protons. Assignments of the exchangeable protons involved in the base triples have been described elsewhere (Klinck et al. 1994) and are included in Table 1 .…”

Section: Resultsmentioning

confidence: 99%

“…RNA synthesis and purification. The 29-nucleotide oligomer was chemically synthesized as described previously (Klinck et al. 1994).…”

Section: Methodsmentioning

confidence: 99%

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Structural Characterization of an Intramolecular RNA Triple Helix by NMR Spectroscopy

Klinck¹,

Liquier²,

Taillandier³

et al. 1995

European Journal of Biochemistry

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A chemically synthesized 29-base RNA oligomer, designed to fold to form an intramolecular triple helix at acid pH, has been studied by NMR spectroscopy. The molecule consisted of seven U . A . U or C ' . G . C base triples joined by two pyrimidine tetra-loops. The fold was such that the third strand was Hoogsteen base-paired in the major groove of a Watson-Crick paired double helix. The nature and size of the molecule required the use of an assignment strategy using two-and three-dimensional homonuclear methods, complemented by a natural abundance ' ' C correlation experiment. The assignment of the majority of the exchangeable and non-exchangeable resonances is presented. The data suggest a C3'-mdo sugar puckering for all the nucleotides involved in base triples. A preliminary structural model consistent with the NMR data is presented.K~yworzls: RNA structure; NMR; triple helix.The important relationship between RNA structure and function is now well established with examples including tertiary-folding-dependent molecular recognition, translation and catalytic activity. Yet to date relatively little structural data is available compared to the ever increasing amount of information related to RNA function. Recent advances in NMR instrumentation and techniques are helping to narrow this gap, but there are still many structural aspects of RNA that remain to be investigated in detail.RNA has been known to form base triples since 1957 (Felsenfeld et al., 1957). Early X-ray fiber diffraction studies of poly(U) . poly(A) . poly(U) triple helices (Arnott and Bond, 1973) characterized sugar puckers and helical parameters. The discovery of catalytic RNA (Kruger et al., 1982; GuerrierTakada et al., 1983) has renewed interest in triple base interactions. Base triples have been proposed to form in the catalytic core of the Trtrcihyrr~enu group I intron (Michel et al.. 1990), in both the major and minor grooves formed by base-pairs. RNA oligomers modelled after this catalytic core which form minor groove base triples have recently been studied by NMR Tinoco Jr, 1992, 1993).To further investigate the structure of RNA base triples, we have chemically synthesized a 29-base RNA oligomer designed to form an intramolecular triple helix with the third strand in the major groove of a Watson-Crick double helix. The sequence, shown in Fig. 1, was based on the 28-base DNA triplex studied by SklenBr and Feigon (1990), with an additional loop nucleoCorrr.vf~orzrfi,nc,r to E. Guittet, Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique. F-91198 Gifsur-Yvette, France Fast +33 1 69 07 72 17. Abbrevintions. HMQC, heteronuclear multiple quantum correlation: HOHAHA, homonuclear Hartmann-Hahn: NOESY, nuclear Overhauser enhancement spectroscopy ; P. COSY, purged correlation spectroscopy ; TPPI. time proportional phase increment: ID, 2D and 3D, one-, two-, and three-dimensional. In this paper we report the assignment of the non-exchangeable resonances, obtained using multidimensional homo-and hetero-nuclear...

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“…Therefore, molecules having the ability to recognize, bind and stabilize specific sequences of triple helical nucleic acid structures are of particular interest in antigene therapy. Recently several biophysical studies on the properties of DNA triple helices [2], [3], [26], [27] and many small molecules that can enhance the stability of triplexes have been described [28]–[31]. But most of these are limited to DNA triplexes and studies on the stabilization of RNA triplexes and correlating thermodynamic factors to the structural aspects that actually account for the observed differences in stability are scarce.…”

Section: Introductionmentioning

confidence: 99%

Biophysical Characterization of the Strong Stabilization of the RNA Triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) Alkyl Ether Berberine Analogs

et al. 2012

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BackgroundBinding of two 9-O-(ω-amino) alkyl ether berberine analogs BC1 and BC2 to the RNA triplex poly(U)•poly(A)*poly(U) was studied by various biophysical techniques.Methodology/Principal FindingsBerberine analogs bind to the RNA triplex non-cooperatively. The affinity of binding was remarkably high by about 5 and 15 times, respectively, for BC1 and BC2 compared to berberine. The site size for the binding was around 4.3 for all. Based on ferrocyanide quenching, fluorescence polarization, quantum yield values and viscosity results a strong intercalative binding of BC1 and BC2 to the RNA triplex has been demonstrated. BC1 and BC2 stabilized the Hoogsteen base paired third strand by about 18.1 and 20.5°C compared to a 17.5°C stabilization by berberine. The binding was entropy driven compared to the enthalpy driven binding of berbeine, most likely due to additional contacts within the grooves of the triplex and disruption of the water structure by the alkyl side chain.Conclusions/SignificanceRemarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine. The length of the alkyl side chain influence in the triplex stabilization phenomena.

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Spectroscopic evidence for an intramolecular RNA triple helix

Cited by 18 publications

References 25 publications

Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly?

Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly?

Structural Characterization of an Intramolecular RNA Triple Helix by NMR Spectroscopy

Biophysical Characterization of the Strong Stabilization of the RNA Triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) Alkyl Ether Berberine Analogs

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