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. 1990 Jun 11;18(11):3347–3352. doi: 10.1093/nar/18.11.3347

Enzymatic and NMR analysis of oligoribonucleotides synthesized with 2'-tert-butyldimethylsilyl protected cyanoethylphosphoramidite monomers.

Y Y Wang 1, M H Lyttle 1, P N Borer 1
PMCID: PMC330943  PMID: 2356125

Abstract

The regioisomeric integrity of the internucleotide phosphate linkage in synthetic RNA using 2'-tert-butyldimethylsilyl protection was examined using enzymatic and NMR techniques. Two sets of DNA-RNA hybrid nonamers, T3XT5 and T5XT3 (where X = rA, rC, rG and U) and the tetramer AGCU were analyzed. Enzyme catalyzed hydrolysis of the nonamers with ribonuclease T2 showed that the linkage at the ribonucleotide was the desired 3'-5'. A control nonamer with a 2'-5' linkage was subjected to the enzyme, and showed no cleavage. High-resolution proton NMR of the tetramer also gave a favorable comparison with the same molecule obtained by non-chemical means.

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Selected References

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  1. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  2. Borer P. N., Kan L. S., Ts'o P. O. Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU. Biochemistry. 1975 Nov 4;14(22):4847–4863. doi: 10.1021/bi00693a012. [DOI] [PubMed] [Google Scholar]
  3. Bubienko E., Uniack M. A., Borer P. N. Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2. Biochemistry. 1981 Nov 24;20(24):6987–6994. doi: 10.1021/bi00527a032. [DOI] [PubMed] [Google Scholar]
  4. Carey J., Lowary P. T., Uhlenbeck O. C. Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site. Biochemistry. 1983 Sep 27;22(20):4723–4730. doi: 10.1021/bi00289a017. [DOI] [PubMed] [Google Scholar]
  5. Chou S. H., Flynn P., Reid B. Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG). Biochemistry. 1989 Mar 21;28(6):2422–2435. doi: 10.1021/bi00432a013. [DOI] [PubMed] [Google Scholar]
  6. Kan L. S., Borer P. N., Ts'o P. O. Conformation and interaction of short nucleic acid double-stranded helices. II. Proton magnetic resonance studies on the hydrogen-bonded NH-N protons of ribosyl ApApGpCpUpU helix. Biochemistry. 1975 Nov 4;14(22):4864–4869. doi: 10.1021/bi00693a013. [DOI] [PubMed] [Google Scholar]
  7. Kempe T., Chow F., Sundquist W. I., Nardi T. J., Paulson B., Peterson S. M. Selective 2'-benzoylation at the cis 2',3'-diols of protected ribonucleosides. New solid phase synthesis of RNA and DNA-RNA mixtures. Nucleic Acids Res. 1982 Nov 11;10(21):6695–6714. doi: 10.1093/nar/10.21.6695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kierzek R., Caruthers M. H., Longfellow C. E., Swinton D., Turner D. H., Freier S. M. Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry. 1986 Dec 2;25(24):7840–7846. doi: 10.1021/bi00372a009. [DOI] [PubMed] [Google Scholar]
  9. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Reese C. B., Skone P. A. Action of acid on oligoribonucleotide phosphotriester intermediates. Effect of released vicinal hydroxy functions. Nucleic Acids Res. 1985 Jul 25;13(14):5215–5231. doi: 10.1093/nar/13.14.5215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Sinha N. D., Biernat J., McManus J., Köster 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 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Stawinski J., Strömberg R., Thelin M., Westman E. Studies on the t-butyldimethylsilyl group as 2'-O-protection in oligoribonucleotide synthesis via the H-phosphonate approach. Nucleic Acids Res. 1988 Oct 11;16(19):9285–9298. doi: 10.1093/nar/16.19.9285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Tanaka T., Tamatsukuri S., Ikehara M. Solid phase synthesis of oligoribonucleotides using o-nitrobenzyl protection of 2'-hydroxyl via a phosphite triester approach. Nucleic Acids Res. 1986 Aug 11;14(15):6265–6279. doi: 10.1093/nar/14.15.6265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  15. de Vroom E., Fidder A., Marugg J. E., van der Marel G. A., van Boom J. H. Use of a 1-hydroxybenzotriazole activated phosphorylating reagent towards the synthesis of short RNA fragments in solution. Nucleic Acids Res. 1986 Jul 25;14(14):5885–5900. doi: 10.1093/nar/14.14.5885. [DOI] [PMC free article] [PubMed] [Google Scholar]

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