Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (554K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (69)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Scherr, M.
Right arrow Articles by Patzel, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Scherr, M.
Right arrow Articles by Patzel, V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 JNMHome page
M. Liu, R. F. Wang, C. L. Zhang, P. Yan, M. M. Yu, L. J. Di, H. J. Liu, and F. Q. Guo
Noninvasive Imaging of Human Telomerase Reverse Transcriptase (hTERT) Messenger RNA with 99mTc-Radiolabeled Antisense Probes in Malignant Tumors
J. Nucl. Med., December 1, 2007; 48(12): 2028 - 2036.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. V. Matveeva, D. H. Mathews, A. D. Tsodikov, S. A. Shabalina, R. F. Gesteland, J. F. Atkins, and S. M. Freier
Thermodynamic criteria for high hit rate antisense oligonucleotide design
Nucleic Acids Res., September 1, 2003; 31(17): 4989 - 4994.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Boden, O. Pusch, F. Lee, L. Tucker, P. R. Shank, and B. Ramratnam
Promoter choice affects the potency of HIV-1 specific RNA interference
Nucleic Acids Res., September 1, 2003; 31(17): 5033 - 5038.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
K. Kraemer, S. Fuessel, U. Schmidt, M. Kotzsch, B. Schwenzer, M. P. Wirth, and A. Meye
Antisense-mediated hTERT Inhibition Specifically Reduces the Growth of Human Bladder Cancer Cells
Clin. Cancer Res., September 1, 2003; 9(10): 3794 - 3800.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Kretschmer-Kazemi Far and G. Sczakiel
The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides
Nucleic Acids Res., August 1, 2003; 31(15): 4417 - 4424.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. J. Bergeron and J.-P. Perreault
Development and comparison of procedures for the selection of delta ribozyme cleavage sites within the hepatitis B virus
Nucleic Acids Res., November 1, 2002; 30(21): 4682 - 4691.
[Abstract] [Full Text] [PDF]

Home page
 Molecular Cancer TherapeuticsHome page
N. Dias and C. A. Stein
Antisense Oligonucleotides: Basic Concepts and Mechanisms
Mol. Cancer Ther., March 1, 2002; 1(5): 347 - 355.
[Full Text] [PDF]

Home page
 BloodHome page
S. M. Luger, S. G. O'Brien, J. Ratajczak, M. Z. Ratajczak, R. Mick, E. A. Stadtmauer, P. C. Nowell, J. M. Goldman, and A. M. Gewirtz
Oligodeoxynucleotide-mediated inhibition of c-myb gene expression in autografted bone marrow: a pilot study
Blood, February 15, 2002; 99(4): 1150 - 1158.
[Abstract] [Full Text] [PDF]

Home page
 FASEB J.Home page
N. S. LEE, B. SUN, R. WILLIAMSON, N. GUNKEL, P. M. SALVATERRA, and J. J. ROSSI
Functional colocalization of ribozymes and target mRNAs in Drosophila oocytes
FASEB J, November 1, 2001; 15(13): 2390 - 2400.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Bramlage, E. Luzi, and F. Eckstein
HIV-1 LTR as a target for synthetic ribozyme-mediated inhibition of gene expression: site selection and inhibition in cell culture
Nucleic Acids Res., November 1, 2000; 28(21): 4059 - 4067.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Amarzguioui, G. Brede, E. Babaie, M. Grotli, B. Sproat, and H. Prydz
Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes
Nucleic Acids Res., November 1, 2000; 28(21): 4113 - 4124.
[Abstract] [Full Text] [PDF]

Home page
 Stem CellsHome page
K.-Y. Jen and A. M. Gewirtz
Suppression of Gene Expression by Targeted Disruption of Messenger RNA: Available Options and Current Strategies
Stem Cells, September 1, 2000; 18(5): 307 - 319.
[Abstract] [Full Text]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.