Syntheses of DNA Duplexes That Contain a N4C‐Alkyl‐N4C Interstrand Cross‐Link

Paul S. Miller1

1 Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 5.10
DOI:  10.1002/0471142700.nc0510s44
Online Posting Date:  March, 2011
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Abstract

This unit describes a simple procedure for preparing short DNA duplexes that contain a single N4C‐alkyl‐N4C interstrand cross‐link. The synthesis is carried out on an automated DNA synthesizer using standard phosphoramidite chemistry. The cross‐link is introduced during the synthesis of the duplex. The method can be used to prepare milligram quantities of cross‐linked duplexes suitable for physical studies and for the preparation of larger DNA molecules that can be used as substrates to study DNA repair in whole cell extracts and in living cells in culture. Curr. Protoc. Nucleic Acid Chem. 44:5.10.1‐5.10.9. © 2011 by John Wiley & Sons, Inc.

Keywords: oligonucleotide; interstrand cross‐link; DNA duplex; synthesis

     
 
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Table of Contents

  • Preparing Short DNA Duplexes that Contain a Single N4C‐Alkyl‐N4C Interstrand Cross‐Link
  • Basic Protocol 1: Synthesis of an N4C‐Ethyl‐N4C Cross‐Linked Duplex
  • Basic Protocol 2: Purification of the Cross‐Linked Duplex
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Synthesis of an N4C‐Ethyl‐N4C Cross‐Linked Duplex

  Materials
  • Nucleoside derivatized polystyrene support (PS; Applied Biosystems)
  • Protected 5′‐O‐dimethoxytrityldexoyribonucleoside‐3′‐O‐cyanoethylphosphoramidites (Glen Research) including:
    • 5′‐dimethyoxytrityl‐O4‐triazole‐deoxyuridine‐ 3′‐O‐cyanoethylphosphoramidite
  • Anhydrous acetonitrile (ACN)
  • 95% Ethanol (C 2H 5OH, EtOH)
  • Concentrated ammonium hydroxide solution (NH 4OH)
  • SAX buffer A: 100 mM Tris⋅Cl, pH 7.8, containing 10% (v/v) acetonitrile
  • SAX buffer B: 0.5 M NaCl in 100 mM Tris⋅Cl, pH 7.8, containing 10% (v/v) acetonitrile
  • C‐18 buffer A: 50 mM sodium phosphate (pH 5.8) containing 2% (v/v) acetonitrile
  • C‐18 buffer B: 50 mM sodium phosphate (pH 5.8) containing 50% (v/v) acetonitrile
  • 5′‐O‐dimethyoxytrityl‐3′‐Ot‐butyldimethylsilyl‐N4‐alkyl‐deoxycytidine ( S.5a; see Noll et al., )
  • Anhydrous pyridine
  • Protected 3′‐O‐dimethoxytrityldexoyribonucleoside‐5′‐O‐cyanoethylphosphoramidites (Glen Research)
  • Anhydrous triethylamine (Et 3N, TEA)
  • Triethylamine trihydrofluoride
  • 50% aqueous acetonitrile
  • Empty DNA synthesis column (Glen Research)
  • DNA synthesizer (Applied Biosystems, model #3400)
  • 4‐mL autosampler vial fitted with a Teflon‐lined cap
  • Vacuum centrifuge (SpeedVac; Savant Instruments)
  • Analytical strong anion‐exchange (SAX) HPLC column (Dionex)
  • Analytical C‐18 reversed‐phase HPLC column (Varian)
  • 1‐mL and 10‐mL disposable syringes
  • Additional reagents and equipment for anion‐exchange HPLC and reversed‐phase HPLC (unit 10.5)
CAUTION: Acetonitrile, pyridine, triethylamine, triethylamine trihydrofluoride, and ammonium hydroxide are toxic. All procedures and reactions employing these materials should be carried out in a fume hood.

Basic Protocol 2: Purification of the Cross‐Linked Duplex

  Materials
  • Cross‐linked duplex (see protocol 1)
  • SAX buffer A: 100 mM Tris⋅Cl, pH 7.8, containing 10% (v/v) acetonitrile
  • SAX buffer B: 0.5 M NaCl in 100 mM Tris⋅Cl, pH 7.8, containing 10% (v/v) acetonitrile
  • C‐18 buffer A: 50 mM sodium phosphate (pH 5.8) containing 2% (v/v) acetonitrile
  • Acetonitrile
  • 50% (v/v) aqueous acetonitrile
  • Deionized water
  • Analytical strong anion‐exchange (SAX) HPLC column (Dionex)
  • C‐18 reversed‐phase desalting column or cartridge (Phenomenex)
  • Vacuum centrifuge (SpeedVac)
  • UV spectrophotometer
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Figures

Videos

Literature Cited

Literature Cited
   Guainazzi, A. and Scharer, O.D. 2010. Using synthetic DNA interstrand crosslinks to elucidate repair pathways and identify new therapeutic targets for cancer chemotherapy. Cell Mol. Life Sci. 67:3683‐3689.
   Hlavin, E.M., Smeaton, M.B. and Miller, P.S. 2010a. Initiation of DNA interstrand cross‐link repair in mammalian cells. Environ. Mol. Mutagen. 51:604‐624.
   Hlavin, E.M., Smeaton, M.B., Noronha, A.M., Wilds, C.J., and Miller, P.S. 2010b. Cross‐link structure affects replication‐independent DNA interstrand cross‐link repair in mammalian cells. Biochemistry 49:3977‐3988.
   Muniandy, P.A., Liu, J., Majumdar, A., Liu, S.T. and Seidman, M.M. 2010. DNA interstrand crosslink repair in mammalian cells: Step by step. Crit. Rev. Biochem. Mol. Biol. 45:23‐49.
   Noll, D.M., Noronha, A.M. and Miller, P.S. 2001. Synthesis and characterization of DNA duplexes containing an N(4)C‐ethyl‐N(4)C interstrand cross‐link. J. Am. Chem. Soc. 123:3405‐3411.
   Noll, D.M., Noronha, A.M., Wilds, C.J., and Miller, P.S. 2004. Preparation of interstrand cross‐linked DNA oligonucleotide duplexes. Front Biosci. 9:421‐437.
   Noll, D.M., Webba da Silva, M., Noronha, A.M., Wilds, C.J., Colvin, O.M., Gamcsik, M.P., and Miller, P.S. 2005. Structure, flexibility, and repair of two different orientations of the same alkyl interstrand DNA cross‐link. Biochemistry 44:6764‐6775.
   Noll, D.M., Mason, T.M. and Miller, P.S. 2006. Formation and repair of interstrand cross‐links in DNA. Chem. Rev. 106:277‐301.
   Noronha, A.M., Noll, D.M., Wilds, C.J., and Miller, P.S. 2002a. N(4)C‐ethyl‐N(4)C cross‐linked DNA: Synthesis and characterization of duplexes with interstrand cross‐links of different orientations. Biochemistry 41:760‐771.
   Noronha, A.M., Wilds, C.J., and Miller, P.S. 2002b. N(4)C‐alkyl‐N(4)C cross‐linked DNA: Bending deformations in duplexes that contain a ‐CNG‐ interstrand cross‐link. Biochemistry 41:8605‐8612.
   Rajski, S.R. and Williams, R.M. 1998. DNA cross‐linking agents as antitumor drugs. Chem. Rev. 98:2723‐2796.
   Smeaton, M.B., Hlavin, E.M., McGregor Mason, T., Noronha, A.M., Wilds, C.J., and Miller, P.S. 2008. Distortion‐dependent unhooking of interstrand cross‐links in mammalian cell extracts. Biochemistry 47:9920‐9930.
   Smeaton, M.B., Hlavin, E.M., Noronha, A.M., Murphy, S.P., Wilds, C.J. and Miller, P.S. 2009. Effect of cross‐link structure on DNA interstrand cross‐link repair synthesis. Chem. Res. Toxicol. 22:1285‐1297.
   Swenson, M.C., Paranawithana, S.R., Miller, P.S., and Kielkopf, C.L. 2007. Structure of a DNA repair substrate containing an alkyl interstrand cross‐link at 1.65 A resolution. Biochemistry 46:4545‐4553.
   Webba da Silva, M., Noronha, A.M., Noll, D.M., Miller, P.S., Colvin, O.M., and Gamcsik, M.P. 2002. Solution structure of a DNA duplex containing mispair‐aligned N4C‐ethyl‐N4C interstrand cross‐linked cytosines. Biochemistry 41:15181‐15188.
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