Selection of target sites for antisense attack of RNA

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C435S004000, C435S006120, C702S020000, C702S027000

Reexamination Certificate

active

10478049

ABSTRACT:
Nucleic acid hybridization under steady-state conditions is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. An expression was derived that relates nucleic acid secondary structure to the rate of oligonucleotide-RNA hybridization. The model allows the calculation of a rate factor that is proportional to the rate constant for hybridization between complementary nucleic acids and is generally applicable to any RNA molecule with potential utility for rapid identification of sites for antisense attack of mRNA.

REFERENCES:
patent: 1 103910 (2001-05-01), None
Birikh, K. R., Y. A. Berlin, H. Soreq, and F. Eckstein. (1997) Probing accessible sites for ribozymes on human acetylcholinesterase RNA.RNA3: 429-437.
Christofferson, R. E., J. McSwiggen, and D. Konings. (1994) Application of computational technologies to ribozyme biotechnology products.Journal of Molecular Structure(Theochem)311: 273-284.
Ding, Y., and C. E. Lawrence. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.Nucleic Acids Res29: 1034-46.
Kushon, Stuart A. et al., (2001) Effect of Secondayr Structure on the Thermodynamics and Kinetics of PNA Hybridization to DNA Hairpins.J. Am. Chem. Soc.123; 10805-10813.
Luebke, K. J., R. P. Balog, and H. R. Garner. (2003) Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts.Nucleic Acids Res31: 750-8.
Mathews, D. H., M. E. Burkard, S. M. Freier, J. R. Wyatt, and D. H. Turner. (1999) Predicting oligonucleotide affinity to nucleic acid target.RNA5: 1458-1469.
Matveeva, O. V., A. D. Tsodikov, M. Giddings, S. M. Freier, J. R. Wyatt, A. N. Spiridonov, S. A. Shabalina, R. F. Gesteland, and J. F. Atkins (2000) Identification of sequence motifs in olionucleotides whose presence is correlated with antisense activity.Nucleic Acids Res28: 2862-2865.
Patzel, V. et al. (2000) In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells.Nucleic Acids Res28; 2462-2466.
Patzel, V., and G. Sczakiel. (2000) In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells.Nucleic Acids Res28: 2462-2466.
Scherr, M., J. J. Rossi, G. Sczakiel, and V. Patzel. (2000) RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts.Nucleic Acids Res28:2455-2461.
Stull, R. A., L. A. Taylor, and J. Francis C. Szoka. (1992) Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices.Nucleic Acids Research20: 3501-3508.
Tu, G. C., Q. N. Cao, F. Zhou, and Y. Israel. (1998) Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design.J Biol Chem273: 25125-31.
Walton, S. P., G. N. Stephanopoulos, M. L. Yarmush, and C. M. Roth. (1999) Prediction of antisense oligonucleotide binding affinity to a structured RNA target.Biotechnology and Bioengineering65: 1-9.
Walton, S.P., et al. (2002) Thermodynamic and Kinetic Characterization of Antisense Oligodeoxynucleotide Binding to a Structured mRNA.Biophysical Journal82; 366-377.
Wang, J.-Y., and K. Drlica. (2003) Modeling hybridization kinetics.Mathematical Biosciences183: 37-47.
Patzel, V., and G. Sczakiel. (1999) Length Dependence of RNA-RNA Annealing. J. Mol. Biol. (1999) 294, 1127-1134.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Selection of target sites for antisense attack of RNA does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Selection of target sites for antisense attack of RNA, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Selection of target sites for antisense attack of RNA will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3895588

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.