The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

Hilbers, C. W.; Heus, Hans A.; Dongen, M.J.P. van; Wijmenga, Sybren S.

doi:10.1007/978-3-642-78666-2_4

Cited by 48 publications

(43 citation statements)

References 84 publications

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“…The shortest sequential distances, 0.447 nm and 0.378 nm, were found for T(c)C4'-T(d)C4' in T4 and T(c)C4'-G(5)C4' in T3, respectively. Similar phosphodiester conformations were found for the turning phosphate of several other three-membered and four-membered loop models reviewed by Hilbers et al (1994) Conformation of the stem. The complementary stems of the T4 and T3 hairpin models showed no significant differences.…”

Section: (B)ch-t(a)h4' (B) T(b)h3'-t(c)ch (C) T(b)h6-t(c)ch3 and supporting

confidence: 75%

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Kuklenyik

Yao

Marzillï

1996

European Journal of Biochemistry

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"P signals of the two hairpins have been nearly completely assigned by means of two-dimensional NMR spectroscopy in D,O (NOESY (two-dimensional nuclear Overhauser effect and exchange spectroscopy) at mixing times of 5, 50, 100, 300 and 500 ms, double-quantum-filtered correlation spectroscopy (DQF-COSY) and 'H-"P reverse chemical shift correlation (RCSC), and one-dime,nsional NOE spectra in 90% H,O. Conformational analysis using distance geometry (DG), molecular mechanics (MM) and molecular dynamics (MD) gave model conformations, which were evaluated by comparison of experimental and simulated 2D NOESY spectra. For the T, sequence in T4, both NMR data and modeling indicated a T(a) . (5) of T3] has a gauche', gauche' <,a conformation with a trans y angle for the second residue in both. These or similar features appear to be present in most of the few other hairpins studied previously by conformational methods. Thus, we believe that the conformations of the loops in T, and T, hairpins have greater similarities than previously recognized.

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Section: (B)ch-t(a)h4' (B) T(b)h3'-t(c)ch (C) T(b)h6-t(c)ch3 and supporting

confidence: 75%

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Kuklenyik

Yao

Marzillï

1996

European Journal of Biochemistry

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“…Minihairpins with a UUCG loop closed by a C-G base pair, considered to be the classical unusually stable RNA loop, show high T m 's of 75.2°C and 76.2°C, and the UUCG loop destabilizes the hairpin by only 1-1.2 kcal/mol. Hairpins with down to 7°C lower T m 's and destabilizing DG 37°u p to 2 kcal/mol have been classified as unusually stable as well Hilbers et al 1994;Proctor et al 2002). The poliovirus UGCG and novel GCUA loops, closed by a U-G base pair, clearly fall outside this range, exhibiting much lower T m 's and higher destabilizing DG 37°.…”

Section: Thermodynamic Studiesmentioning

confidence: 99%

“…Starting with a 6-nt random RNA hairpin loop library, the already known cUNCGg and gCUUGc sequences were selected, but others were also found, i.e., cUNAGg, cCNCGg, and cCNAGg, with almost the same stability as the cUNCGg hairpin loops. Stable tetraloops with GNRA sequences were not detected, presumably because, as suggested by the investigators, the DNA GNRA tetraloops (contrary to the DNA TNCG tetraloops) can be exceptionally stable as well Hilbers et al 1994), and might have interfered with the PCR reaction used in SELEX. A reevaluation of a more recent 16S and 23S rRNA database revealed that the cUNAGg, cCNCGg, and cCNAGg hairpin sequences are at least as abundant as the gCUUGc sequence (Proctor et al 2002).…”

Section: Introductionmentioning

confidence: 95%

“…Since then, tetraloops were recognized as frequent and important elements in many other RNAs as well (Poritz et al 1988;Pace et al 1989;Michel and Westhof 1990). Thermodynamic studies revealed that hairpins with these tetraloops are also very stable , and because the majority of the UNCG and GNRA loops are closed by a C-G base pair, which also contributes to a higher stability (reversing the closing base pair of a UUCG loop to G-C destabilizes tetraloop formation by a D(DG 37°) of 2.3 kcal/mol Hilbers et al 1994]), the sequences of the two families were subsequently refined to cUNCGg and cGNRAg (the lowercase letters represent the base pair closing the loop).…”

Section: Introductionmentioning

confidence: 99%

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A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA

Melchers

Zoll²,

Tessari³

et al. 2006

RNA

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The cloverleaf structure in the 59-untranslated region of enterovirus RNA that regulates viral RNA replication contains an evolutionarily conserved YNMG tetraloop closed by a Y-G base pair. This loop is believed to interact specifically with the viral protease 3C. To further characterize the specificity of this interaction, the tetraloop and two flanking base pairs of the poliovirus RNA were randomized, and viable viral clones were obtained using in vivo SELEX. Among many different mutants with the canonical YNMG sequences to be described elsewhere, a large-plaque-forming clone contained a deviating uGCUAg sequence. The NMR structure of a small hairpin capped with uGCUAg that we present here shows that the GCUA tetraloop adopts a novel fold, which is highly similar to that of the YNMG tetraloop with common stacking properties and hydrogen-bond interactions including an unusual syn conformation of the adenosine. Thermodynamic studies show moderate stabilities of hairpins with canonical YNMG and the novel GCUA loops, which, together with the similarity of spatial structures, illustrates that the tetraloop structure itself is crucial for the RNA-protein interaction required for the viral replication. A re-evaluation of the ribosomal secondary structure database reveals a hairpin containing a GCUA loop, which covaries with YNMG and is involved in a tertiary interaction, and in the 50S ribosomal subunit from Haloarcula marismortui the structurally comparable apex of stem-loop 35a is a recognition site for protein L2. These observations show a more general occurrence and importance of the so-far unrecognized GYYA hairpin loops.

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“…A detailed comparison of the accumulated thermodynamic and structural data, presented by Hilbers et al (1994), shows that the loops of stable and unusually stable DNA and RNA hairpins consist of two to four residues (for a definition see Hilbers et al, 1994), and fold into a limited number of well-defined, compact conformations. Less stable loops, on the other hand, show considerable internal mobility.…”

Section: Introductionmentioning

confidence: 99%

The Transition from a Neutral-pH Double Helix to a Low-pH Triple Helix Induces a Conformational Switch in the CCCG Tetraloop Closing a Watson-Crick Stem

Dongen¹,

Wijmenga

Marel

et al. 1996

Journal of Molecular Biology

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The CCCG-loop in a DNA fragment, which is capable of forming an Structure, Design, and intramolecular triple helix as well as a hairpin structure, was investigated Synthesis, Laboratory of by NMR and molecular modeling studies. We used molecular modeling to lay the foundations for understanding 2300 RA Leiden the observed conformational switch. A lower amount of strain, related to The Netherlands the short C1'-C1' of the base-pair, and protonation effects of the structure comprising the Hoogsteen base-pair turn out to outweigh the effects of a more stable base-pair, improved stacking and more favorable interactions in the minor groove of the structure comprising the Watson-Crick C·G base-pair. The models also provide an explanation for the general preference of loops meeting the consensus sequence -d(CYNG)-to fold into a type II conformation, i.e. with the base of second loop residue turned into the minor groove.

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The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

Cited by 48 publications

References 84 publications

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA

The Transition from a Neutral-pH Double Helix to a Low-pH Triple Helix Induces a Conformational Switch in the CCCG Tetraloop Closing a Watson-Crick Stem

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