Prediction of antisense oligonucleotide binding affinity to a structured RNA target

Biotechnology and Bioengineering

Volumn 65, Issue 1, 1999, Pages 1-9

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

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b USA   (United States)

Author keywords

Affinity; Antisense; Hybridization; RNA folding

Indexed keywords

ALGORITHMS; BINDING ENERGY; BIOASSAY; CHEMICAL BONDS; COST EFFECTIVENESS; ENGINEERING RESEARCH; MATHEMATICAL MODELS; MEDICAL APPLICATIONS; RNA; THERMAL CYCLING;

ANTISENSE EFFICACY; BINDING AFFINITY; HYBRIDIZATION; OLIGONUCLEOTIDE; RNA FOLDING;

DNA SEQUENCES;

ANTISENSE OLIGONUCLEOTIDE; BETA GLOBIN; MESSENGER RNA; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; BINDING AFFINITY; DNA RNA HYBRIDIZATION; NUCLEOTIDE SEQUENCE; RNA STRUCTURE; THERMODYNAMICS;

ANIMALS; BASE SEQUENCE; GLOBINS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES, ANTISENSE; RABBITS; RNA, MESSENGER; THERMODYNAMICS; TUMOR NECROSIS FACTOR-ALPHA;

ORYCTOLAGUS CUNICULUS;

EID: 0033527352     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0290(19991005)65:1<1::AID-BIT1>3.0.CO;2-F     Document Type: Article

References (27)

1. Agrawal S, Jiang Z, Zhao Q, Shaw D, Cai Q, Roskey A, Channavajjala L, Saxinger C, Zhang R. 1997. Mixed-backbone oligonucleotides as second generation antisense oligonucleotides: in vitro and in vivo studies. Proc Natl Acad Sci USA 94:2620-2625.
2. Gewirtz AM, Sokol DL, Ratajczak MZ. 1998. Nucleic acid therapeutics: state of the art and future prospects. Blood 92:712-736.
3. Goodchild J, Agrawal S, Civeira MP, Sarin PS, Sun D, Zamecnik PC. 1988. Inhibition of human immunodeficiency virus replication by antisense oligodeoxynucleotides. Proc Natl Acad Sci USA 85:5507-5511.
4. Hines WW, Montgomery DC. 1990. Probability and statistics in engineering and management science. New York: John Wiley & Sons.
5. Ho SP, Bao Y, Lesher T, Malhotra R, Ma LY, Fluharty SJ, Sakai RR. 1998. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol 16:59-63.
6. Jaroszewski JW, Syi JL, Ghosh M, Ghosh K, Cohen JS. 1993. Targeting of antisense DNA: comparison of activity of anti-rabbit beta-globin oligodeoxyribonucleoside phosphorothioates with computer predictions of mRNA folding. Antisense Res Dev 3:339-348.
7. Laptev AV, Lu Z, Colige A, Prockop DJ. 1994. Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA. Biochemistry 33:11033-11039.
8. Lefebvre d'Hellencourt C, Diaw L, Cornillet P, Guenounou M. 1996. Inhibition of human TNFα and LT in cell-free extracts and in cell culture by antisense oligonucleotides. Biochim Biophys Acta 1317: 168-174.
9. Lima WF, Brown-Driver V, Fox M, Hanecak R, Bruice TW. 1997. Combinatorial screening and rational optimization for hybridization to folded hepatitis C virus RNA of oligonucleotides with biological antisense activity. J Biol Chem 272:626-638.
10. Matveeva O, Felden B, Tsodikov A, Johnston J, Monia BP, Atkins JF, Gesteland RF, Freier SM. 1998. Prediction of antisense oligonucleotide efficacy by in vitro methods. Nat Biotechnol 16:1374-1375.
11. Milner N, Mir KU, Southern EM. 1997. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 15: 537-541.
12. Mologni L, leCoutre P, Nielsen PE, Gambacorti-Passerini C. 1998. Additive antisense effects of different PNAs on the in vitro translation of the PML/RAR-a gene. Nucleic Acids Res 26:1934-1938.
13. Peyman A, Helsberg M, Kretzschmar G, Mag M, Grabley S, Uhlmann E. 1995. Inhibition of viral growth by antisense oligonucleotides directed against the IE110 and the UL30 mRNA of herpes simplex virus type-1. Biol Chem Hoppe Seyler 376:195-198.
14. Prati E, Scheidegger P, Sburlati A, Bailey J. 1998. Antisense strategies for glycosylation engineering of Chinese hamster ovary (CHO) cells. Biotechnol Bioeng 59:445-450.
15. Ramsay G. 1998. DNA chips: state-of-the art. Nat Biotechnol 16:40-44.
16. SantaLucia J, Allawi HT, Seneviratne PA. 1996. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555-3562.
17. Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA. 1998. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279:1940-1943.
18. Sczakiel G, Homann M, Rittner K. 1993. Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1. Antisense Res Dev 3:45-52.
19. Stein CA. 1998. How to design an antisense oligodeoxynucleotide experiment: a consensus approach. Antisense Nucleic Acid Drug Dev 8: 129-132.
20. Stull RA, Zon G, Szoka FC Jr. 1996. An in vitro messenger RNA binding assay as a tool for identifying hybridization-competent antisense oligonucleotides. Antisense Nucleic Acid Drug Dev 6:221-228.
21. Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M, Sasaki M. 1995. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34:11211-11216.
22. Tsiang M, Gibbs CS, Griffin LC, Dunn KE, Leung LL. 1995. Selection of a suppressor mutation that restores affinity of an oligonucleotide inhibitor for thrombin using in vitro genetics. J Biol Chem 270: 19370-19376.
23. Wakita T, Wands JR. 1994. Specific inhibition of hepatitis C virus expression by antisense oligodeoxynucleotides. In vitro model for selection of target sequence. J Biol Chem 269:14205-14210.
24. Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 91:9218-9222.
25. Wu M, Tinoco I Jr. 1998. RNA folding causes secondary structure rearrangement. Proc Natl Acad Sci USA 95:11555-11560.
26. Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.
27. Zuker M, Jacobson AB. 1995. "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucleic Acids Res 23:2791-2798.