Rational selection and quantitative evaluation of antisense oligonucleotides

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1520, Issue 2, 2001, Pages 105-114

  Jayaraman, Arul ^a,b   Walton, S Patrick ^a,b   Yarmush, Martin L ^a,b   Roth, Charles M ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b SHRINERS HOSPITALS FOR CHILDREN   (United States)

Author keywords

Antisense; Hybridization; MRNA dynamics; Quantitative polymerase chain reaction

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; GLYCOPROTEIN GP 130; HAPTOGLOBIN; INTERLEUKIN 6; LACTATE DEHYDROGENASE; MESSENGER RNA; OLIGONUCLEOTIDE; OLIGONUCLEOTIDE PHOSPHODIESTER; OLIGONUCLEOTIDE PHOSPHOROTHIOATE; RIBONUCLEASE H; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING AFFINITY; CELL CULTURE; CELL TYPE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG ACTIVITY; DRUG EFFICACY; ENZYME ACTIVITY; ENZYME INHIBITION; FETUS; GENE EXPRESSION REGULATION; GENE TARGETING; HEPATOMA CELL; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN SECRETION; QUANTITATIVE ASSAY; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; ANTIGENS, CD; CELL LINE; CYTOKINE RECEPTOR GP130; GENE EXPRESSION; HUMANS; L-LACTATE DEHYDROGENASE; MEMBRANE GLYCOPROTEINS; OLIGONUCLEOTIDES, ANTISENSE; POLYMERASE CHAIN REACTION; RATS; RNA, MESSENGER; THERMODYNAMICS; TRANSCRIPTION, GENETIC; TUMOR CELLS, CULTURED;

EID: 0035975193     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4781(01)00229-9     Document Type: Article

References (38)

1. Nucleic acid biotechnology
2. Antisense technology
3. Nucleic acid therapeutics: State of the art and future prospects
4. Sensible use of antisense: How to use oligonucleotides as research tools
5. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity
6. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries
7. Targeting of antisense DNA: Comparison of activity of anti-rabbit beta-globin oligodeoxyribonucleoside phosphorothioates with computer predictions of mRNA folding
8. A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: Correlation with an intracellular pattern and known RNA structures
9. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
10. RNA accessibility prediction: A theoretical approach is consistent with experimental studies in cell extracts
11. Effects of RNA secondary structure on cellular antisense activity
12. Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design
13. Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity
14. Prediction of antisense oligonucleotide binding affinity to a structured RNA target
15. Predicting oligonucleotide affinity to nucleic acid targets
16. Prediction of antisense oligonucleotide efficacy by in vitro methods
17. Rat liver transcript profiling in normal and disease states using a kinetic polymerase chain reaction assay
18. Real-time quantitative RT-PCR after laser-assisted cell picking
19. Quantitative RT-PCR: Pitfalls and potential
20. Stimulation of hepatic acute phase response by cytokines and glucocorticoids
21. Smooth muscle differentiation in cultured human breast gland stromal cells
22. On finding all suboptimal foldings of an RNA molecule
23. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
24. Improved nearest-neighbor parameters for predicting DNA duplex stability
25. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
26. Covalent protein-oligonucleotide conjugates for efficient delivery of antisense molecules
27. Analysis of antisense oligonucleotides
28. Signaling pathways for cardiac hypertrophy and failure
29. Interleukin-6 family of cytokines and gp130
30. Biosynthesis and half-life of the interleukin-6 receptor and its signal transducer gp130
31. Epidermal growth factor or serum stimulation of rat fibroblasts induces an elevation in mRNA levels for lactate dehydrogenase and other glycolytic enzymes
32. Dynamics of gene expression in rat hepatocytes under stress
33. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia
34. Serum albumin
35. Novel mechanisms for antisense-mediated regulation of gene expression
36. Physicochemical properties of phosphorothioate oligodeoxynucleotides
37. RNA folding causes secondary structure rearrangement
38. New insights into the resistance of alpha-oligonucleotides to nucleases