Structural effect of complete [Rp]-phosphorothioate and phosphorodithioate substitutions in the DNA strand of a model antisense inhibitor-target RNA complex

Journal of Molecular Biology

Volumn 285, Issue 4, 1999, Pages 1609-1622

  Furrer, Patrick ^a   Billeci, Todd M ^a   Donati, Alessandro ^a   Kojima, Chojiro ^a   Karwowski, Boleslaw ^b   Sierzchala, Agnieszka ^b   Stec, Wojciech ^b   James, Thomas L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CENTRE OF MOLECULAR AND MACROMOLECULAR STUDIES   (Poland)

Author keywords

Antisense; Phosphorodithioate; Phosphorothioate; RNase H; RNA DNA hybrid structure

Indexed keywords

COMPLEMENTARY DNA; DEOXYRIBOSE; OLIGONUCLEOTIDE; PHOSPHORODITHIOIC ACID DERIVATIVE; PHOSPHOROTHIOIC ACID; PROTON; RIBONUCLEASE H;

ARTICLE; COMPUTER PROGRAM; DNA RNA HYBRIDIZATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; R FACTOR;

EID: 0033613999     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2305     Document Type: Article

References (25)

1. Bachelin M., Hessler G., Kurz G., Hacia J. Structure of a stereoregular phosphorothioate DNA/RNA duplex. Nature Struct. Biol. 5:1998;271-276.
2. Cummins L., Graff D., Beaton G., Marshall W. S., Caruthers M. H. Biochemical and physicochemical properties of phosphorodithioate DNA. Biochemistry. 35:1996;8734-8741.
3. Delaglio F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J., Bax A. NMRPipe: a multi dimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6:1995;227-293.
4. Fedoroff O. Y., Salazar M., Reid B. R. Structure of a DNA·RNA hybrid duplex: Why RNase H does not cleave pure DNA. J. Mol. Biol. 233:1993;509-523.
5. Freier S. M., Altman K.-H. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA·RNA duplexes. Nucl. Acids Res. 25:1997;4429-4443.
6. Ghosh M. K., Ghosh K., Dahl O., Cohen J. S. Evaluation of some properties of a phosphorodithioate oligodeoxyribonucleotide for antisense application. Nucl. Acids Res. 21:1993;5761-5766.
7. González C., Stec W., Kobylanska A., Hogrefe R. I., Reynolds M., James T. L. Structural study of a DNA·RNA hybrid duplex with a chiral phosphorothioate moiety by NMR: extraction of distance and torsion angle constraints and imino proton exchange rates. Biochemistry. 33:1994;11062-11072.
8. González C., Stec W., Reynolds M., James T. L. Structure and dynamics of a DNA·RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints. Biochemistry. 34:1995;4969-4982.
9. James T. L. Relaxation matrix analysis of 2D NOE spectra to obtain accurate biomolecular structural constraints and to assess structural quality. Curr. Opin. Struct. Biol. 1:1991;1042-1053.
10. Jaroszewski J. W., Clausen V., Cohen J. S., Dahl O. NMR investigations of duplex stability of phosphorothioate and phosphorodithioate DNA analogues modified in both strands. Nucl. Acids Res. 24:1996;829-834.
11. Koziolkiewicz M., Krakowiak A., Kwinkowski M., Boczkowska M., Stec W. J. Stereodifferentiation - the effect of chirality of oligonucleoside phosphorothioates on the activity of bacterial RNase H. Nucl. Acids Res. 23:1995;5000-5005.
12. Lane A., Ebel S., Brown T. NMR assignments and solution conformation of the DNA·RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC). Eur. J. Biochem. 215:1993;297-306.
13. Lesser D. R., Grajkowski A., Kurpiewski M. R., Koziolkiewicz M., Stec W. J., Jen-Jacobson L. Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex. J. Biol. Chem. 267:1992;24810-24818.
14. Lingbeck J., Kubinec M. G., Miller J., Reid B. R., Drobny G. P., Kennedy M. A. Effect of adenine methylation on the structure and dynamics of TA steps in DNA-NMR structure determination of [d(CGAGGTTTAAACCTCG)](2) and its A9-methylated derivative at 750 MHZ. Biochemistry. 35:1996;719-734.
15. Liu H., Thomas P. D., James T. L. Averaging of cross-relaxation rates and distances for methyl, methylene and aromatic ring protons due to motion or overlap: extraction of accurate distances iteratively via relaxation matrix analysis of 2D NOE spectra. J. Magn. Reson. 98:1992;163-175.
16. Liu H., Spielmann H. P., Ulyanov N. B., Wemmer D. E., James T. L. Interproton distance bounds from 2D NOE intensities: effect of experimental noise and peak integration errors. Biomol. NMR. 6:1995;390-402.
17. Matteuci M. Structural modifications toward improved antisense oligonucleotides. Persp. Drug Disc. Des. 4:1996;1-16.
18. Mujeeb A., Reynolds M. A., James T. L. High-resolution NMR of an antisense DNA·RNA hybrid containing alternating chirally pure R(p) methylphosphonates in the DNA backbone. Biochemistry. 36:1997;2371-2379.
19. Okruszek A., Sierzchala A., Fearon K. L., Stec W. J. Synthesis of oligodeoxyribonucleoside phosphorodithioates by the dithiaphospholane approach. J. Org. Chem. 60:1995;6998-7005.
20. Pearlman D. A., Case D. A., Caldwell J. C., Seibel G. L., Singh U. C., Weiner P., Kollman P. A. AMBER 4.0. 1991;University of California, San Francisco.
21. Scaringe S. A., Francklyn C., Usman N. Chemical synthesis of biologically active oligoribonucleotides using beta-cyanoethyl protected ribonucleoside phosphoramidates. Nucl. Acids Res. 18:1990;5433-5441.
22. Schmitz U., Sethson I., Egan W. M., James T. L. Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from 2D NMR spectral fitting. J. Mol. Biol. 227:1992;510-531.
23. Spitzer S., Eckstein F. Inhibition of deoxyribonucleases by phosphorothioate groups in oligoribonucleotides. Nucl. Acids Res. 16:1988;11691-11704.
24. Stec W. J., Grajkowski A., Karwowski B., Kobylanska A., Koziolkiewicz M., Misiura K., Okruszek A., Wilk A., Guga P., Boczkowska M. Diastereomers of nucleoside 3′- O -(2-thio-1,3,2-oxathia(selena)phospholanes) - building blocks for stereocontrolled synthesis of oligonucleoside phosphorothioates. J. Am. Chem. Soc. 117:1995;12019-12029.
25. 2via complete relaxation matrix analysis of 2D NOE spectra and molecular mechanics calculations: evidence for a hydration tunnel. Biochemistry. 25:1986;6854-6865.