RNA Accessibility Prediction: a Theoretical Approach is Consistent with Experimental Studies in Cell Extracts

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2000 Jun 28

PMID 10871393

Citations 24

Authors

M Scherr

J J Rossi

G Sczakiel

V Patzel

Affiliations

Soon will be listed here.

Abstract

The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specifically suppress gene expression is simple in concept and relies on efficient binding of the antisense strand to the target RNA. Although the identification of target sites accessible to base pairing is gradually being overcome by different techniques, it remains a major problem in the antisense and ribozyme approaches. In this study we have investigated the potential of a recent experimental and theoretical approach to predict the local accessibility of murine DNA-methyltransferase (MTase) mRNA in a comparative way. The accessibility of the native target RNA was probed with antisense ODN in cellular extracts. The results strongly correlated with the theoretically predicted target accessibility. This work suggests an effective two-step procedure for predicting RNA accessibility: first, computer-aided selection of ODN binding sites defined by an accessibility score followed by a more detailed experimental procedure to derive information about target accessibility at the single nucleotide level.

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References

Sczakiel G, Nedbal W . The potential of ribozymes as antiviral agents. Trends Microbiol. 1995; 3(6):213-7. DOI: 10.1016/s0966-842x(00)88927-1. View

Nedbal W, Frey M, Willemann B, Zentgraf H, Sczakiel G . Mechanistic insights into p53-promoted RNA-RNA annealing. J Mol Biol. 1997; 266(4):677-87. DOI: 10.1006/jmbi.1996.0813. View

Rossi J . Controlled, targeted, intracellular expression of ribozymes: progress and problems. Trends Biotechnol. 1995; 13(8):301-6. DOI: 10.1016/S0167-7799(00)88969-6. View

Scherr M, Rossi J . Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts. Nucleic Acids Res. 1998; 26(22):5079-85. PMC: 147980. DOI: 10.1093/nar/26.22.5079. View

Birikh K, Berlin Y, Soreq H, Eckstein F . Probing accessible sites for ribozymes on human acetylcholinesterase RNA. RNA. 1997; 3(4):429-37. PMC: 1369494. View

Scherr M, Grez M, Ganser A, Engels J . Specific hammerhead ribozyme-mediated cleavage of mutant N-ras mRNA in vitro and ex vivo. Oligoribonucleotides as therapeutic agents. J Biol Chem. 1997; 272(22):14304-13. DOI: 10.1074/jbc.272.22.14304. View

Peyman A, Helsberg M, Kretzschmar G, Mag M, Grabley S, Uhlmann E . Inhibition of viral growth by antisense oligonucleotides directed against the IE110 and the UL30 mRNA of herpes simplex virus type-1. Biol Chem Hoppe Seyler. 1995; 376(3):195-8. DOI: 10.1515/bchm3.1995.376.3.195. View

Matveeva O, Felden B, Audlin S, GESTELAND R, Atkins J . A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures. Nucleic Acids Res. 1998; 25(24):5010-6. PMC: 147128. DOI: 10.1093/nar/25.24.5010. View

Homann M, Nedbal W, Sczakiel G . Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications. Nucleic Acids Res. 1996; 24(22):4395-400. PMC: 146270. DOI: 10.1093/nar/24.22.4395. View

10.

Eckstein F, Aurup H, Benseler F, Heidenreich O, Marschall P, Ng M . Design of hammerhead ribozymes for the inhibition of gene expression ex vivo by exogenous application. Nucleic Acids Symp Ser. 1993; (29):115. View

11.

Monia B, Johnston J, Geiger T, Muller M, Fabbro D . Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase. Nat Med. 1996; 2(6):668-75. DOI: 10.1038/nm0696-668. View

12.

Subirana J, Doty P . Kinetics of Renaturation of Denatured DNA. I. Spectrophotometric results. Biopolymers. 1966; 4(2):171-87. DOI: 10.1002/bip.1966.360040204. View

13.

Lieber A, Strauss M . Selection of efficient cleavage sites in target RNAs by using a ribozyme expression library. Mol Cell Biol. 1995; 15(1):540-51. PMC: 232008. DOI: 10.1128/MCB.15.1.540. View

14.

Lima W, Brown-Driver V, Fox M, Hanecak R, Bruice T . Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity. J Biol Chem. 1997; 272(1):626-38. View

15.

Milner N, Mir K, Southern E . Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol. 1997; 15(6):537-41. DOI: 10.1038/nbt0697-537. View

16.

Tsuchihashi Z, Khosla M, Herschlag D . Protein enhancement of hammerhead ribozyme catalysis. Science. 1993; 262(5130):99-102. DOI: 10.1126/science.7692597. View

17.

Patzel V, Sczakiel G . Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat Biotechnol. 1998; 16(1):64-8. DOI: 10.1038/nbt0198-64. View

18.

Wagner R . Gene inhibition using antisense oligodeoxynucleotides. Nature. 1994; 372(6504):333-5. DOI: 10.1038/372333a0. View

19.

Ho S, Bao Y, Lesher T, Malhotra R, Ma L, Fluharty S . Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol. 1998; 16(1):59-63. DOI: 10.1038/nbt0198-59. View

20.

Wetmur J, Davidson N . Kinetics of renaturation of DNA. J Mol Biol. 1968; 31(3):349-70. DOI: 10.1016/0022-2836(68)90414-2. View