Introduction to the Synthesis and Purification of Oligonucleotides

Andrew Ellington1, Jack D. Pollard2

1 University of Texas, Austin, Texas, 2 Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Appendix 3C
DOI:  10.1002/0471142700.nca03cs00
Online Posting Date:  May, 2001
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Modern nucleic acid synthesizers utilize phosphite triester chemistries that employ stable phosphoramidite monomers to build a growing polymer. These robust reactions allow easy generation of specific oligodeoxyribo‐ and oligoribonucleotides with a variety of labels, modified linkages, and nonstandard bases. Strategies are given for the maximization of synthetic yield, the generation of sequences containing site‐specific modifications, and the isolation of synthetic oligonucleotides. Protocols describe monitoring the progress of synthesis via the trityl assay and methods for deprotection.

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Table of Contents

  • Introduction to Chemical Nucleic Acid Synthesis
  • Strategies for Nucleic Acid Synthesis
  • Strategies for Oligonucleotide Purification
  • Basic Protocol 1: Monitoring DNA Synthesis Using the Trityl Assay
  • Support Protocol 1: Using the Trityl Assay for Troubleshooting
  • Basic Protocol 2: Deprotection of DNA Oligonucleotides
  • Basic Protocol 3: Deprotection of RNA Oligonucleotides
  • Reagents and Solutions
  • Commentary
  • Figures
  • Tables
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Basic Protocol 1: Monitoring DNA Synthesis Using the Trityl Assay

  • 0.1 M para‐toluene sulfonic acid (TSA; monohydrate) in acetonitrile (see recipe for dry acetonitrile)
  • 15‐ml glass tubes (graduated, if possible)

Support Protocol 1: Using the Trityl Assay for Troubleshooting

  • Concentrated (14.8 N) ammonium hydroxide (see recipe)
  • Triethylamine
  • 3:1 (v/v) concentrated ammonium hydroxide/ethanol
  • n‐Butanol
  • Screw‐cap plastic vial (preferably fitted with rubber O ring)
  • Heat block or oven, 55° to 60°C
  • 0.2‐µm filter

Basic Protocol 2: Deprotection of DNA Oligonucleotides

  • 100% ethanol
  • 3:1 (v/v) recipeconcentrated (14.8 N) ammonium hydroxide/ethanol
  • 3 M sodium acetate, pH 5.2 ( appendix 2A)
  • Triethylamine trihydrofluoride
  • Screw‐cap plastic vial (preferably fitted with rubber O ring)
  • Heat block or oven, 55° to 60°C
  • 0.2‐µm filter
  • Sephadex G‐25 column (Amersham Pharmacia Biotech)
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Literature Cited

Literature Cited
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   Ciccarelli, R.B., Gunyuzlu, P., Huang, J., Scott, C., and Oakes, F.T. 1991. Construction of synthetic genes using PCR after automated DNA synthesis of their entire top and bottom strands. Nucl. Acids Res. 19:6007‐6013.
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   Eadie, J.S., McBride, L.J., Efcavitch, J.W., Hoff, L.B., and Cathcart, R. 1987. High‐performance liquid chromatographic analysis of oligodeoxyribonucleotide base composition. Anal. Biochem. 165:442‐447.
   Farrance, I.K., Eadie, J.S., and Ivarie, R. 1989. Improved chemistry for oligodeoxyribonucleotide synthesis substantially improves restriction enzyme cleavage of a synthetic 35mer. Nucl. Acids Res. 17:1231‐1245.
   Gait, M.J. (ed.). 1984. Oligonucleotide Synthesis: A Practical Approach. IRL Press, Washington, D.C.
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   Kinoshita, Y., Nishigaki, K., and Husimi, Y. 1997. Fluorescence‐, isotope‐ or biotin‐labeling of the 5′‐end of single‐stranded DNA/RNA using T4 RNA ligase. Nucl. Acids Res. 25:3747‐3748.
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   Pharmacia. 1989. Analects Vol. 17, no. 2. Pharmacia Biotech, Piscataway, NJ.
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   Reddy, M.P., Hanna, N.B., and Farooqui, F. 1994. Fast cleavage and deprotection of oligonucleotides. Tetrahedron Lett. 35:4311‐4314.
   Reddy, M.P., Farooqui, F., Hanna, N.B. 1995. Methylamine deprotection provides increased yield of oligoribonucleotides. Tetrahedron Lett. 36:8929‐8932.
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   Schulhof, J.C., Molko, D., and Teoule, R. 1987. The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base‐protecting groups. Nucl. Acids Res. 15:397.
   Song, Q. and Jones, R.A. 1999. Use of silyl‐ethers as fluoride scavengers in RNA synthesis. Tetrahedron Lett. 40:4653‐4654.
   Sproat, B., Colonna, F., Mullah, B., Tsou, D., Andrus, A., Hampel, A., and Vinayak, R. 1995. An efficient method for the isolation and purification of oligoribonucleotides. Nucleosides Nucleotides 14:255‐273.
   Szostak, J. 1992. In vitro genetics. Trends Biochem. Sci. 17:89‐93.
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   Usman, N., Ogilvie, K.K., Jiang, M.Y., and Cederagren, R.J. 1987. Automated chemical synthesis of long oligoribonucleotides using 2′‐O‐silylated ribonucleotide 3′‐O‐phosphoramidites on a controlled‐pore glass support: Synthesis of a 43‐nucleotide sequence similar to the 3′ half molecule of an E. coli formylmethionine tRNA. J. Am. Chem. Soc. 109:7845‐7854.
   Vargeese, C., Carter, J., Yegge, J., Karivjansky, S., Settle, A., Kropp, E., Peterson, K., and Peiken, W. 1998. Efficient activation of nucleoside phosphoramidites with 4,5‐dicyanoimidazole during oligonucleotide synthesis. Nucl. Acids Res. 26:1046‐1050.
   Warren, W.J. and Vella, G. 1994. Analysis and purification of synthetic oligonucleotides by high‐performance liquid chromatography. Methods Mol. Biol. 233‐264.
   Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., and Usman, N. 1995. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucl. Acids Res. 23:2677‐2684.
   Zhu, Y., He, L., Srinivasan, R., and Lubman, D. 1997. Improved resolution in the detection of oligonucleotides up to 60‐mers in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry using pulsed‐delayed extraction with a simple high voltage transistor switch. Rapid Commun. Mass Spectrom. 11:987‐992.
   Zon, G., Gallo, K.A., Samson, C.J., Shao, K., Summers, M.F., and Byrd, R.A. 1985. Analytical studies of “mixed sequence” oligodeoxyribonucleotides synthesized by competitive coupling of either methyl or β‐cyanoethyl‐N,N‐diisopropylamino phosphoramidite reagents, including 2′‐deoxyinosine. Nucl. Acids Res. 13:8181‐8196.
Key References
   Applied Biosystems, 1988. See above.
  A well‐organized overview of synthetic oligonucleotide synthesis, purification, and quantitation.
   Bretherick, L. 1986. Hazards in the Chemical Laboratory, 4th ed. Alden Press, Oxford.
  A guide to hazardous chemical handling.
   Gait, 1984. See above.
  The seminal text on synthetic oligonucleotide synthesis that provides critical insight.
Internet Resources
  Web site detailing synthesis chemistries, procedures, and reagents for solid‐phase oligonucleotide chemistry.
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