Regular ArticleRNA Structure and Stability
References (70)
- et al.
Kinking of RNA helices by bulged bases and the structure of the human immunodeficiency virus trans-activator responce element
J. Mol. Biol.
(1992) - et al.
Bulge-induced bends in RNA: Quantification by transient electric birefringence
J. Mol. Biol.
(1995) Codon–anticodon pairing: The wobble hypothesis
J. Mol. Biol.
(1966)- et al.
Structure of the P1 helix from group I self-splicing introns
J. Mol. Biol.
(1995) - et al.
A major family of motifs involving G · A mismatches in ribosomal RNA
J. Mol. Biol.
(1994) - et al.
Molecular recognition in the FMN–RNA aptamer complex
J. Mol. Biol.
(1996) - et al.
The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein
J. Mol. Biol.
(1995) - et al.
Crystal structure of yeast phenylalanine transfer RNAII structural features and functional implications
J. Mol. Biol.
(1978) - et al.
On the conformation of the anticodon loops of initiator and elongator methionine tRNAs
J. Mol. Biol.
(1997) - et al.
The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for the RNA catalytic cleavage
Cell
(1995)
Conformation of an RNA pseudoknot
J. Mol. Biol.
The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus
J. Mol. Biol.
Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus
J. Mol. Biol.
A characteristic bent conformation of RNA pseudoknots causes minus-one frameshifting during translation of retroviral RNA
J. Mol. Biol.
Dissecting RNA–protein interactions: RNA–RNA recognition by Rop
Cell
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
J. Mol. Biol.
Stability of ribonucleic acid double-stranded helices
J. Mol. Biol.
Principles of Nucleic Acid Structure
Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: evidence that A-tracts do not generate curvature in RNA
Biochemistry
Major groove accessibility of RNA
Science
Proton NMR and structural features of a 24-nucleotide RNA hairpin
Biochemistry
Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG)(CCGCCCAG) A model-building and NMR study
Nucleic Acids Res.
Sequence effects on RNA bulge-induced helix bending and a conserved five-nucleotide bulge from the group I introns
Biochemistry
The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide
Proc. Natl. Acad. Sci. USA
Conformation of the TAR RNA–arginine complex by NMR spectroscopy
Science
The RNA World
The conformation of loop E of eukaryotic 5S ribosomal RNA
Biochemistry
Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite
Biochemistry
Solution structure of an ATP-binding RNA aptamer reveals a novel fold
RNA
Crystal structure of an RNA double helix incorporating a track of non-Watson–Crick base pairs
Nature
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics
Biochemistry
Bend and helical twist associated with a symmetric internal loop from 5S ribosomal RNA
Biochemistry
Alpha helix–RNA major groove recognition in an HIV-1 rev peptide–RRE RNA complex
Science
Structure of the A Site ofEscherichia coli
Science
Cited by (51)
Structural basis for water modulating RNA duplex formation in the CUG repeats of myotonic dystrophy type 1
2023, Journal of Biological ChemistryThe molecular memory code and synaptic plasticity: A synthesis
2023, BioSystemsConformational Effects of a Cancer-Linked Mutation in Pri-miR-30c RNA
2022, Journal of Molecular BiologyCitation Excerpt :We thus considered the presence of additional base-pair formation as a result of dimerization. Inspection of the primary sequence of the TSLWT RNA shows that the nucleotide sequence between U26 and A33 is self-complementary and thus capable of forming a duplex or kissing stem-loop interaction (Figure 2(c) and (d)).46 With this arrangement, U26 is base-paired with A33* (the asterisk denotes the base is from another RNA molecule), G27 is base-paired with C32*, G29 is base-paired with C30*, and U31 forms the last U-A base-pair with A28*.
Towards SINEUP-based therapeutics: Design of an in vitro synthesized SINEUP RNA
2022, Molecular Therapy Nucleic AcidsCitation Excerpt :The apparent melting temperature (Tm) was determined by following the variation of the CD intensity at 270 nm as a function of temperature.39 In accordance with literature, we found that the two miniSINEUPs displaying a spectrum similar to B-form conformation of DNA showed improved stability compared with the unmodified RNA sequence and increased the Tm by about 15°C.40 Of the remaining SINEUP versions, Am + m6A RNA sequences had an apparent Tm comparable with the unmodified one, while the RNA with m6A displayed a Tm increment of 5°C.
SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration
2024, Algorithms for Molecular Biology