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. 1998 Jun 1;26(11):2665–2671. doi: 10.1093/nar/26.11.2665

Triple helices containing arabinonucleotides in the third (Hoogsteen) strand: effects of inverted stereochemistry at the 2'-position of the sugar moiety.

A Noronha 1, M J Damha 1
PMCID: PMC147614  PMID: 9592152

Abstract

Arabinonucleic acid, the 2'-stereoisomer of RNA, was tested for its ability to recognize double-helical DNA, double-helical RNA and RNA-DNA hybrids. A pyrimidine oligoarabinonucleotide (ANA) was shown to form triple-helical complexes only with duplex DNA and hybrid DNA (Pu):RNA (Py) with an affinity that was slightly lower relative to the corresponding pyrimidine oligodeoxynucleotide (DNA) third strand. Neither the ANA nor DNA third strands were able to bind to duplex RNA or hybrid RNA (Pu):DNA (Py). In contrast, an RNA third strand recognized all four possible duplexes (DD, DR, RD and RR), as previously demonstrated. Such an understanding can be applied to the design of sequence-selective oligonucleotides which interact with double-stranded nucleic acids and emphasizes the role of the 2'-OH group as a general recognition and binding determinant of RNA.

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Selected References

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  1. Alvarado-Urbina G., Sathe G. M., Liu W. C., Gillen M. F., Duck P. D., Bender R., Ogilvie K. K. Automated synthesis of gene fragments. Science. 1981 Oct 16;214(4518):270–274. doi: 10.1126/science.6169150. [DOI] [PubMed] [Google Scholar]
  2. Chwang A. K., Sundaralingam M. Intramolecular hydrogen bonding in 1- -D-arabinofuranosylcytosine (ara-C). Nat New Biol. 1973 May 16;243(124):78–80. [PubMed] [Google Scholar]
  3. Dagneaux C., Liquier J., Taillandier E. Sugar conformations in DNA and RNA-DNA triple helices determined by FTIR spectroscopy: role of backbone composition. Biochemistry. 1995 Dec 26;34(51):16618–16623. doi: 10.1021/bi00051a009. [DOI] [PubMed] [Google Scholar]
  4. Damha M. J., Giannaris P. A., Zabarylo S. V. An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis. Nucleic Acids Res. 1990 Jul 11;18(13):3813–3821. doi: 10.1093/nar/18.13.3813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Damha M. J., Ogilvie K. K. Oligoribonucleotide synthesis. The silyl-phosphoramidite method. Methods Mol Biol. 1993;20:81–114. doi: 10.1385/0-89603-281-7:81. [DOI] [PubMed] [Google Scholar]
  6. Escudé C., François J. C., Sun J. S., Ott G., Sprinzl M., Garestier T., Hélène C. Stability of triple helices containing RNA and DNA strands: experimental and molecular modeling studies. Nucleic Acids Res. 1993 Dec 11;21(24):5547–5553. doi: 10.1093/nar/21.24.5547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Frank-Kamenetskii M. D., Mirkin S. M. Triplex DNA structures. Annu Rev Biochem. 1995;64:65–95. doi: 10.1146/annurev.bi.64.070195.000433. [DOI] [PubMed] [Google Scholar]
  8. Gao Y. G., van der Marel G. A., van Boom J. H., Wang A. H. Molecular structure of a DNA decamber containing an anticancer nucleoside arabinosylcytosine: conformational perturbation by arabinosylcytosine in B-DNA. Biochemistry. 1991 Oct 15;30(41):9922–9931. doi: 10.1021/bi00105a016. [DOI] [PubMed] [Google Scholar]
  9. Giovannangeli C., Perrouault L., Escudé C., Nguyen T., Hélène C. Specific inhibition of in vitro transcription elongation by triplex-forming oligonucleotide-intercalator conjugates targeted to HIV proviral DNA. Biochemistry. 1996 Aug 13;35(32):10539–10548. doi: 10.1021/bi952993x. [DOI] [PubMed] [Google Scholar]
  10. Gotfredsen C. H., Spielmann H. P., Wengel J., Jacobsen J. P. Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Bioconjug Chem. 1996 Nov-Dec;7(6):680–688. doi: 10.1021/bc960061f. [DOI] [PubMed] [Google Scholar]
  11. Han H., Dervan P. B. Different conformational families of pyrimidine.purine.pyrimidine triple helices depending on backbone composition. Nucleic Acids Res. 1994 Jul 25;22(14):2837–2844. doi: 10.1093/nar/22.14.2837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Han H., Dervan P. B. Sequence-specific recognition of double helical RNA and RNA.DNA by triple helix formation. Proc Natl Acad Sci U S A. 1993 May 1;90(9):3806–3810. doi: 10.1073/pnas.90.9.3806. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ito T., Smith C. L., Cantor C. R. Sequence-specific DNA purification by triplex affinity capture. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):495–498. doi: 10.1073/pnas.89.2.495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kanehara H., Mizuguchi M., Tajima K., Kanaori K., Makino K. Spectroscopic evidence for the formation of four-stranded solution structure of oligodeoxycytidine phosphorothioate. Biochemistry. 1997 Feb 18;36(7):1790–1797. doi: 10.1021/bi961528c. [DOI] [PubMed] [Google Scholar]
  15. Le Doan T., Perrouault L., Praseuth D., Habhoub N., Decout J. L., Thuong N. T., Lhomme J., Hélène C. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 1987 Oct 12;15(19):7749–7760. doi: 10.1093/nar/15.19.7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Letsinger R. L., Lunsford W. B. Synthesis of thymidine oligonucleotides by phosphite triester intermediates. J Am Chem Soc. 1976 Jun 9;98(12):3655–3661. doi: 10.1021/ja00428a045. [DOI] [PubMed] [Google Scholar]
  17. Maher L. J., 3rd DNA triple-helix formation: an approach to artificial gene repressors? Bioessays. 1992 Dec;14(12):807–815. doi: 10.1002/bies.950141204. [DOI] [PubMed] [Google Scholar]
  18. Manzini G., Yathindra N., Xodo L. E. Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences. Nucleic Acids Res. 1994 Nov 11;22(22):4634–4640. doi: 10.1093/nar/22.22.4634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moser H. E., Dervan P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987 Oct 30;238(4827):645–650. doi: 10.1126/science.3118463. [DOI] [PubMed] [Google Scholar]
  20. Neidle S. Recent developments in triple-helix regulation of gene expression. Anticancer Drug Des. 1997 Jul;12(5):433–442. [PubMed] [Google Scholar]
  21. Puglisi J. D., Tinoco I., Jr Absorbance melting curves of RNA. Methods Enzymol. 1989;180:304–325. doi: 10.1016/0076-6879(89)80108-9. [DOI] [PubMed] [Google Scholar]
  22. Roberts R. W., Crothers D. M. Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science. 1992 Nov 27;258(5087):1463–1466. doi: 10.1126/science.1279808. [DOI] [PubMed] [Google Scholar]
  23. Robidoux S., Damha M. J. D-2-deoxyribose and D-arabinose, but not D-ribose, stabilize the cytosine tetrad (i-DNA) structure. J Biomol Struct Dyn. 1997 Dec;15(3):529–535. doi: 10.1080/07391102.1997.10508963. [DOI] [PubMed] [Google Scholar]
  24. Schweitzer B. I., Mikita T., Kellogg G. W., Gardner K. H., Beardsley G. P. Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Biochemistry. 1994 Sep 27;33(38):11460–11475. [PubMed] [Google Scholar]
  25. Semerad C. L., Maher L. J., 3rd Exclusion of RNA strands from a purine motif triple helix. Nucleic Acids Res. 1994 Dec 11;22(24):5321–5325. doi: 10.1093/nar/22.24.5321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Shimizu M., Konishi A., Shimada Y., Inoue H., Ohtsuka E. Oligo(2'-O-methyl)ribonucleotides. Effective probes for duplex DNA. FEBS Lett. 1992 May 11;302(2):155–158. doi: 10.1016/0014-5793(92)80428-j. [DOI] [PubMed] [Google Scholar]
  27. Singh S., Patel P. K., Hosur R. V. Structural polymorphism and dynamism in the DNA segment GATCTTCCCCCCGGAA: NMR investigations of hairpin, dumbbell, nicked duplex, parallel strands, and i-motif. Biochemistry. 1997 Oct 28;36(43):13214–13222. doi: 10.1021/bi970819y. [DOI] [PubMed] [Google Scholar]
  28. Skoog J. U., Maher L. J., 3rd Repression of bacteriophage promoters by DNA and RNA oligonucleotides. Nucleic Acids Res. 1993 May 11;21(9):2131–2138. doi: 10.1093/nar/21.9.2131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Strobel S. A., Doucette-Stamm L. A., Riba L., Housman D. E., Dervan P. B. Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. Science. 1991 Dec 13;254(5038):1639–1642. doi: 10.1126/science.1836279. [DOI] [PubMed] [Google Scholar]
  30. Teng M. K., Liaw Y. C., van der Marel G. A., van Boom J. H., Wang A. H. Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]. Biochemistry. 1989 Jun 13;28(12):4923–4928. doi: 10.1021/bi00438a001. [DOI] [PubMed] [Google Scholar]
  31. Uddin A. H., Piunno P. A., Hudson R. H., Damha M. J., Krull U. J. A fiber optic biosensor for fluorimetric detection of triple-helical DNA. Nucleic Acids Res. 1997 Oct 15;25(20):4139–4146. doi: 10.1093/nar/25.20.4139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wang S., Friedman A. E., Kool E. T. Origins of high sequence selectivity: a stopped-flow kinetics study of DNA/RNA hybridization by duplex- and triplex-forming oligonucleotides. Biochemistry. 1995 Aug 1;34(30):9774–9784. doi: 10.1021/bi00030a015. [DOI] [PubMed] [Google Scholar]
  33. Wang S., Kool E. T. Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties, and a comparison with circular DNAs. Nucleic Acids Res. 1994 Jun 25;22(12):2326–2333. doi: 10.1093/nar/22.12.2326. [DOI] [PMC free article] [PubMed] [Google Scholar]

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