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Nucleic Acids Research, 2000, Vol. 28, No. 13 2455-2461
© 2000 Oxford University Press

RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts

Michaela Scherr1,2, John J. Rossi2, Georg Sczakiel3,4 and Volker Patzel3,*

1Abteilung für Hämatologie und Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany, 2Department of Molecular Biology, Beckman Research Institute, City of Hope, 1450 East Duarte Road, Duarte, CA 91010-3011, USA, 3Deutsches Krebsforschungszentrum, F0200, Im Neuenheimer Feld 242, D-69120 Heidelberg, Germany and 4Medizinische Universität zu Lübeck, Institut für Molekulare Medizin, Ratzeburger Allee 160, D-23538 Lübeck, Germany

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.

* To whom correspondence should be addressed. Tel: +49 6221 424938; Fax: +49 6221 424932; Email: patzel@dkfz-heidelberg.de


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