Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA

Biophysical Journal

Volumn 82, Issue 1, 2002, Pages 366-377

  Patrick Walton, S ^a,b   Stephanopoulos, Gregory N ^b   Yarmush, Martin L ^a   Roth, Charles M ^a,c  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGODEOXYNUCLEOTIDE; BETA GLOBIN; MESSENGER RNA;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; DISSOCIATION CONSTANT; ENERGY; GENE DISRUPTION; GENE EXPRESSION; HYBRIDIZATION; RABBIT; RNA BINDING; RNA STRUCTURE; RNA TRANSLATION; TEMPERATURE; THERMODYNAMICS;

ORYCTOLAGUS CUNICULUS;

EID: 0036217930     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0006-3495(02)75401-5     Document Type: Article

References (40)

1. Antisense treatment directed against mutated Ki-ras in human colorectal adenocarcinoma
2. Thermodynamic parameters for DNA sequences with dangling ends
3. Enzymatic amplification of translation inhibition of rabbit beta-globin mRNA mediated by antimessenger oligodeoxynucleotides covalently linked to intercalating agents
4. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
5. Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1
6. Inhibition of rabbit beta-globin synthesis by complementary oligonucleotides: Identification of mRNA sites sensitive to inhibition
7. Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate
8. Specific regulation of gene expression by antisense, sense and antigene nucleic acids
9. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries
10. Improved predictions of secondary structures for RNA
11. Rational selection and quantitative evaluation of antisense oligonucleotides
12. RNA secondary structure prediction based on free energy and phylogenetic analysis
13. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity
14. Implication of RNA structure on antisense oligonucleotide hybridization kinetics
15. Predicting oligonucleotide affinity to nucleic acid targets
16. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
17. A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: Correlation with an intracellular pattern and known RNA structures
18. Prediction of antisense oligonucleotide efficacy by in vitro methods
19. Selecting effective antisense reagents on combinatorial oligonucleotide arrays
20. Determining the influence of structure on hybridization using oligonucleotide arrays
21. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
22. Theoretical and experimental selection parameters for HBV-directed antisense RNA are related to increased RNA-RNA annealing
23. A dynamic programming algorithm for RNA structure prediction including pseudoknots
24. Nucleic acid biotechnology
25. Improved nearest-neighbor parameters for predicting DNA duplex stability
26. RNA accessibility prediction: A theoretical approach is consistent with experimental studies in cell extracts
27. Quantitative hybridization kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation analysis
28. Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1
29. Rational selection of antisense oligonucleotide sequences
30. Two problems in antisense biotechnology: In vitro delivery and the design of antisense experiments
31. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
32. An RNA folding method capable of identifying pseudoknots and base triples
33. Effects of RNA secondary structure on cellular antisense activity
34. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
35. Antisense technology
36. Prediction of antisense oligonucleotide binding affinity to a structured RNA target
37. RNA folding causes secondary structure rearrangement
38. On finding all suboptimal foldings of an RNA molecule
39. "Well-determined" regions in RNA secondary structure prediction: Analysis of small subunit ribosomal RNA
40. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison