A novel thymidine phosphoramidite synthon for incorporation of internucleoside phosphate linkers during automated oligodeoxynucleotide synthesis

Nucleosides, Nucleotides and Nucleic Acids

Volumn 27, Issue 2, 2008, Pages 157-172

  Tabatadze, David ^a   Zamecnik, Paul ^a   Yanachkov, Ivan ^b   Wright, George ^b   Pierson, Katherine ^a   Zhang, Surong ^c   Bogdanov Jr , Alexei ^c   Metelev, Valeri ^c,d  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b GLSYNTHESIS INC   (United States)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Multiple ligands; Reporter molecules; Sequence specific attachment; Single ligand; Thymidine phosphoramidite synthon

Indexed keywords

2 [2 (2 AMINOETHOXY)ETHOXY]ETHANOL; 5' O DIMETHOXYTRITYLTHYMIDINE 3' O [2[2(2 TRIFLUOROACETAMIDOETHOXY)ETHOXY]ETHYL] N,N DIISOPROPYLPHOSPHORAMIDITE; CARBOCYANINE; NUCLEOSIDE MONOPHOSPHATE KINASE; OLIGONUCLEOTIDE; THYMIDINE PHOSPHORAMIDITE SYNTHON; TRIFLUORO N [2 [2 (2 HYDROXYETHOXY)ETHOXY]ETHYL]ACETAMIDE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CONJUGATION; COVALENT BOND; DNA SYNTHESIS; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN STABILITY;

BASE PAIRING; CARBOCYANINES; OLIGODEOXYRIBONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; THYMIDINE;

EID: 38349121967     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770701795938     Document Type: Article

References (36)

1. Padmapriya, A.A.; Tang, J.Y.; Agrawal, S. Large-scale synthesis, purification, and analysis of oligodeoxynucleotide phosphorothioates. Antisense Res. Dev. 1994, 4, 185-199.
2. Reddy, M.P.; Farooqui, F.; Hanna, N.B. Elimination of transamination side product by the use of dCAc methylphosphonamidite in the synthesis of oligonucleoside methylphosphonates. Tetrahedron Lett 1996, 37, 8691-8694.
3. Shaw, B.R.; Madison, J.; Sood, A.; Spielvogel, B.F. Oligonucleoside boranophosphate (borane phosphonate). Methods Mol. Biol. 1993, 20, 225-243.
4. Samstag, W.; Eisenhardt, S.; Offensperger, W.B.; Engels, J.W. Synthesis and properties of new antisense oligodeoxynucleotides containing benzylphosphonate linkages. Antisense Nucleic Acids Drug Dev. 1996, 6, 153-156.
5. Kurreck, J.; Wyszko, E.; Gillen, C.; Erdmann, V. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res. 2002, 30, 1911-1918.
6. Crinelli, R.; Bianchi, M.; Gentilini, L.; Magnani, M. Design and characterization of decoy oligonucleotides containing locked nucleic acids. Nucleic Acids Res. 2002, 30, 2435-2443.
7. Egholm, M.; Buchardt, O.; Christensen, L.; Behrens, C.; Freier, S.; Driver, D.; Berg, R.; Kim, S.; Norden, B.; Nielsen, P. PNA hybridizes to complementary oligonucleotides obeying the watson-crick hydrogen-bonding rules. Nature 1993, 365, 566-568. (article)
8. Stirchak, E.P.; Summerton, J.E.; Weller, D.D. Uncharged stereoregular nucleic acid analogs: 2. Morpholino nucleoside oligomers with carbamate internucleoside linkages. Nucleic Acids Res. 1989, 17, 6129-6141.
9. Sinha, N.D.; Biernat, J.; McManus, J.; Koster, H. Polymer support oligonucleotide synthesis XVIII: Use of beta-cyanoethyl-n,n-dialkylamino-/n- morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984, 12, 4539-4557.
10. Shchepinov, M.S.; Udalova, I.A.; Bridgman, A.J.; Southern, E.M. Oligonucleotide dendrimers: Synthesis and use as polylabelled DNA probes. Nucleic Acids Res. 1997, 25, 4447-4454.
11. Shchepinov, M.S.; Mir, K.U.; Elder, J.K.; Frank-Kamenetskii, M.D.; Southern, E.M. Oligonucleotide dendrimers: Stable nanostructure. Nucleic Acids Res. 1999, 27, 3035-3041.
12. Horn, T.; Chang, C.A.; Urdea, M.S. Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucleic Acids Res. 1997, 25, 4842-4849.
13. Guzaev, A.; Salo, H.; Azhayev, A.; Lonnberg, H. New approach for chemical phosphorylation of oligonucleotides at the 5′-terminus. Tetrahedron 1995, 51, 9375-9384.
14. Monteith, D.K.; Levin, A.A. Synthetic Oligonucleotides: The development of antisense therapeutics. Toxicol. Pathol. 1999, 27, 8-13.
15. Ma, D.D.; Rede, T.; Naqvi, N.A.; Cook, P.D. Synthetic oligonucleotides as therapeutics: the coming of age. Biotechnol. Annu. Rev. 2000, 5, 155-196.
16. Wilson, J.A.; Richardson, C.D. Future promise of siRNA and other nucleic acid based therapeutics for the treatment of chronic HCV. Infect. Disord. Drug Targets 2006, 6, 43-56.
17. Landegren, U.; Kaiser, R.; Caskey, C.T.; Hood, L. DNA diagnostics - Molecular techniques and automation. Science 1988, 242, 229-237.
18. Goodchild, J. Conjugates of oligonucleotides and modified oligonucleotides: a review of their synthesis and properties. Bioconj. Chem. 1990, 1, 165-187.
19. Da Ros, T.; Spalluto, G.; Prato, M. Oligonucleotides and oligonucleotide conjugates: A new approach for cancer treatment. Current Med. Chem. 2005, 12, 71-88.
20. Boutorine, A.S.; Grimm, G.N.; Héléne, C. Methods of attaching unprotected oligonucleotides to DNA-binding, fluorescent, or reactive ligands for synthesis of antisense or gene-directed agents and probes. Mol. Biol. 2000, 34, 804-813.
21. Urban, E.; Noe, R.C. Structural modifications of antisense oligonucleotides. Il Farmaco 2003, 58, 243-258.
22. Silverman, A.P.; Kool, E.T. Detecting RNA and DNA with templated chemical reactions. Chem. Rev. 2006, 106, 3775-3789.
23. Tang, J.Y.; Agrawal, S. Incorporation of multiple reporter groups on synthetic oligonucleotides. Nucleic Acids Res. 1990, 18, 6461.
24. Agrawal, S.; Zamecnik, P.C. Site specific functionalization of oligonucleotides for attaching two different reporter groups. Nucleic Acids Res. 1990, 18, 5419-5423.
25. Agrawal, S.; Christodoulou, Ch.; Gait, M.J. Efficient methods for attaching non-radioactive labels to the 5′ ends of synthetic oligodeoxyribonucleotides. Nucleic Acids Res. 1986, 14, 6227-6245.
26. Kachalova, A.V.; Stetsenko, D.A.; Romanova, E.A.; Tashlitsky, V.N.; Gait, M.J.; Oretskaya, T.S. A new and efficient method for synthesis of 5-conjugates of oligonucleotides through amide-bond formation on solid phase. Helv. Chim. Acta 2002, 85, 2409-2417.
27. Markiewicz, W.T.; Gröger, G.; Rösch, R.; Zebrowska, A.; Markiewicz, M.; Klotz, M.; Hinz, M.; Godzina, P.; Seliger, H. A new method of synthesis of fluorescently labelled oligonucleotides and their application in DNA sequencing. Nucl. Acids Res. 1997, 25, 3672-3680.
28. Wenninger, D.; Hinz, M.; Hahner, S.; Hillenkamp, F.; Seliger, H. Enzymatic and hybridization properties of oligonucleotide analogues containing novel phosphotriester internucleotide linkage. Nucleos. Nucleot. 1998, 17, 2117-2125.
29. Awad, A.M.; Sobkowski, M.; Seliger, H. Enzymatic and hybridization properties of oligonucleotide analogs containing novel phosphoramidate internucleotide linkages. Nucleosides, Nucleotides and Nucl. Acids 2004, 23, 777-787.
30. Seliger, H.; Krist, B.; Berner, S. Specific intrachain introduction of reporter groups into oligonucleotides as substituents at internucleotidic linkages. Nucleos. Nucleot. 1991, 10, 303-306.
31. Wilk, A.; Grajkowski, A.; Phillips, L.R.; Beaucage, S.L. The 4-[N-methyl-N-(2,2,2-trifluoroacetyl)amino]butyl group as an Alternative to the 2-cyanoethyl group for phosphate protection in the synthesis of oligodeoxyribonucleotides. J. Org. Chem. 1999, 64, 7515-7522.
32. Winnik, M. Cyclization and the conformation of hydrocarbon chains. Chem. Rev. 1981, 81, 491-524.
33. Greenwald, R.B.; Conover, Ch.D.; Choe, Y.H. Poly(ethylene glycol) conjugated drugs and prodrugs: A comprehensive review. Critical Rev. Ther. Drug Carrier Systems 2000, 17, 101-161.
34. Zalipsky, S. Functionalized Poly(ethylene glycol) for preparation of biologically relevant conjugates. Bioconjugate Chem. 1995, 6, 150-165.
35. Caruthers, M.H.; Barone, A.D.; Beaucage, S.L.; Dodds, D.R.; Fisher, E.F.; McBride, L.J.; Matteucci, M.; Stabinsky, Z.; Tang, J.Y. Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods Enzymol. 1987, 154, 287-313.
36. Bannon, P.; Verly, W. Alkylation of phosphates and stability of phosphate triesters in DNA. Eur. J. Biochem. 1972, 31, 103-111.