3,4‐Diaminobenzophenone Matrix for Analysis of Oligonucleotides by MALDI‐TOF Mass Spectrometry

Yu Fu1, Songyun Xu1, Chensong Pan1, Mingliang Ye1, Hanfa Zou1

1 National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Dalian, China
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 10.12
DOI:  10.1002/0471142700.nc1012s31
Online Posting Date:  December, 2007
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Abstract

This unit contains procedures for analysis of oligonucleotides by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry with 3,4‐diaminobenzophenone (DABP) as a matrix. This new matrix has demonstrated advantages in the analysis of oligonucleotides. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation, and fewer alkali‐metal ion adducts compared with results obtained using conventional matrices. Minimal fragmentation and fewer alkali‐metal ion adducts were seen even at low oligonucleotide concentrations. It was also found that samples prepared with DABP are highly homogenous, therefore reducing the need to find “sweet spots” in MALDI. Finally, excellent shot‐to‐shot reproducibility, resolution, and signal‐to‐noise ratio are observed using the DABP matrix. Curr. Protoc. Nucleic Acid Chem. 31:10.12.1‐10.12.6. © 2007 by John Wiley & Sons, Inc.

Keywords: diaminobenzophenone; DABP; DNA; oligonucleotide; MALDI; mass spectrometry; matrix

     
 
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Table of Contents

  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1:

  Materials
  • Oligonucleotide (HPLC‐grade; e.g., TaKaRa Biotechnology)
  • TE buffer, pH 7.75 ( appendix 2A)
  • 3,4‐Diaminobenzophenone (DABP; 99% pure; Acros Organics)
  • Methanol (HPLC‐grade)
  • 12 M hydrochloric acid (HCl; guaranteed reagent)
  • Ethanol (guaranteed reagent)
  • Target, MTP 384 matt steel
  • Autoflex time‐of‐flight mass spectrometer (Bruker), equipped with a nitrogen‐pulsed 337‐nm laser
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Figures

Videos

Literature Cited

Literature Cited
   Chen, W.Y. and Chen, Y.C. 2003. Reducing the alkali cation adductions of oligonucleotides using sol‐gel‐assisted laser desorption/ionization mass spectrometry. Anal. Chem. 75:4223‐4228.
   Distler, A.M. and Allison, J. 2001. 5‐Methoxysalicylic acid and spermine: A new matrix for the matrix‐assisted laser desorption/ionization mass spectrometry analysis of oligonucleotides. J. Am. Soc. Mass Spectrom. 12:456‐462.
   Distler, A.M. and Allison, J. 2002. Additives for the stabilization of double‐stranded DNA in UV‐MALDI MS. J. Am. Soc. Mass Spectrom. 13:1129‐1137.
   Fu, Y., Xu, S.Y., Pan, C.S., Ye, M.L., Zou, H.F., and Guo, B.C. 2006. A matrix of 3,4‐diaminobenzophenone for the analysis of oligonucleotides by matrix assisted laser desorption ionization time of flight mass spectrometry. Nucl. Acids Res. 34:e94.
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