Chemical and Computer Probing of RNA Structure

Overview

Journal Prog Nucleic Acid Res Mol Biol

Specialties Biochemistry
Molecular Biology

Date 1996 Jan 1

PMID 8650302

Citations 7

Authors

N A Kolchanov

I I Titov

I E Vlassova

V V Vlassov

Affiliations

Soon will be listed here.

Citing Articles

V, 2.Ribosomal frameshifting in astroviruses.

Brierley I, Vidakovic M Perspect Med Virol. 2020; 9:587-606.

PMID: 32287603 PMC: 7133818. DOI: 10.1016/S0168-7069(03)09035-9.

An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs.

Ray D, White K J Virol. 2002; 77(1):245-57.

PMID: 12477830 PMC: 140596. DOI: 10.1128/jvi.77.1.245-257.2003.

Evidence for an RNA pseudoknot loop-helix interaction essential for efficient -1 ribosomal frameshifting.

Liphardt J, Napthine S, Kontos H, Brierley I J Mol Biol. 1999; 288(3):321-35.

PMID: 10329145 PMC: 7141562. DOI: 10.1006/jmbi.1999.2689.

The role of RNA pseudoknot stem 1 length in the promotion of efficient -1 ribosomal frameshifting.

Napthine S, Liphardt J, Bloys A, Routledge S, Brierley I J Mol Biol. 1999; 288(3):305-20.

PMID: 10329144 PMC: 7126229. DOI: 10.1006/jmbi.1999.2688.

Secondary structure and mutational analysis of the ribosomal frameshift signal of rous sarcoma virus.

Marczinke B, Fisher R, Vidakovic M, Bloys A, Brierley I J Mol Biol. 1998; 284(2):205-25.

PMID: 9813113 PMC: 7126186. DOI: 10.1006/jmbi.1998.2186.

References

Jacobson A, Good L, Simonetti J, Zuker M . Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res. 1984; 12(1 Pt 1):45-52. PMC: 320982. DOI: 10.1093/nar/12.1part1.45. View

Wetlaufer D . Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci U S A. 1973; 70(3):697-701. PMC: 433338. DOI: 10.1073/pnas.70.3.697. View

Abrahams J, van den Berg M, van Batenburg E, Pleij C . Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 1990; 18(10):3035-44. PMC: 330835. DOI: 10.1093/nar/18.10.3035. View

Steger G, Hofmann H, Fortsch J, Gross H, Randles J, Sanger H . Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. J Biomol Struct Dyn. 1984; 2(3):543-71. DOI: 10.1080/07391102.1984.10507591. View

Davies R, Waring R, Ray J, Brown T, Scazzocchio C . Making ends meet: a model for RNA splicing in fungal mitochondria. Nature. 1982; 300(5894):719-24. DOI: 10.1038/300719a0. View

Ehresmann C, Baudin F, Mougel M, Romby P, Ebel J, Ehresmann B . Probing the structure of RNAs in solution. Nucleic Acids Res. 1987; 15(22):9109-28. PMC: 306456. DOI: 10.1093/nar/15.22.9109. View

Christiansen J . The 9S RNA precursor of Escherichia coli 5S RNA has three structural domains: implications for processing. Nucleic Acids Res. 1988; 16(15):7457-76. PMC: 338420. DOI: 10.1093/nar/16.15.7457. View

Celander D, Cech T . Visualizing the higher order folding of a catalytic RNA molecule. Science. 1991; 251(4992):401-7. DOI: 10.1126/science.1989074. View

Fresco J, Alberts B, Doty P . Some molecular details of the secondary structure of ribonucleic acid. Nature. 1960; 188:98-101. DOI: 10.1038/188098a0. View

10.

Ciesiolka J, Hardt W, Schlegl J, Erdmann V, Hartmann R . Lead-ion-induced cleavage of RNase P RNA. Eur J Biochem. 1994; 219(1-2):49-56. DOI: 10.1111/j.1432-1033.1994.tb19913.x. View

11.

Ciesiolka J, Lorenz S, Erdmann V . Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA--ribosomal-protein complexes by means of Pb(II)-induced hydrolysis. Eur J Biochem. 1992; 204(2):575-81. DOI: 10.1111/j.1432-1033.1992.tb16670.x. View

12.

Vlassov V, Giege R, Ebel J . The tertiary structure of yeast tRNAPhe in solution studied by phosphodiester bond modification with ethylnitrosourea. FEBS Lett. 1980; 120(1):12-6. DOI: 10.1016/0014-5793(80)81034-9. View

13.

Tullius T, Dombroski B . Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science. 1985; 230(4726):679-81. DOI: 10.1126/science.2996145. View

14.

Boguski M, Hieter P, Levy C . Identification of a cytidine-specific ribonuclease from chicken liver. J Biol Chem. 1980; 255(5):2160-3. View

15.

Pleij C . Pseudoknots: a new motif in the RNA game. Trends Biochem Sci. 1990; 15(4):143-7. DOI: 10.1016/0968-0004(90)90214-v. View

16.

Wyatt J, Puglisi J, Tinoco Jr I . RNA pseudoknots. Stability and loop size requirements. J Mol Biol. 1990; 214(2):455-70. DOI: 10.1016/0022-2836(90)90193-P. View

17.

Williams Jr A, Tinoco Jr I . A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res. 1986; 14(1):299-315. PMC: 339410. DOI: 10.1093/nar/14.1.299. View

18.

Martinez H . Detecting pseudoknots and other local base-pairing structures in RNA sequences. Methods Enzymol. 1990; 183:306-17. DOI: 10.1016/0076-6879(90)83020-a. View

19.

Fontana , STADLER , Griesmacher , Hofacker , Tacker , Tarazona . RNA folding and combinatory landscapes. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993; 47(3):2083-2099. DOI: 10.1103/physreve.47.2083. View

20.

Vlassov V, Giege R, Ebel J . Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur J Biochem. 1981; 119(1):51-9. DOI: 10.1111/j.1432-1033.1981.tb05575.x. View