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

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

¹National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Dalian, China, People's Republic of 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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Basic Protocol
Commentary
Literature Cited
Figures
Tables

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Materials

Basic Protocol

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

Figure 10.12.1

MALDI mass spectra of d(T)₆ obtained using matrices of (A) DABP, (B) 3-HPA, and (C) 2,4,6-THAP. The quantity of d(T)₆ loaded was 1.4 pmol, and no NaCl was added to the sample solution. From Fu et al. (2006).

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Figure 10.12.2

MALDI mass spectra of 12.5 fmol of two 12-mers. From Fu et al. (2006).

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Figure 10.12.3

MALDI mass spectra of an oligonucleotide using matrices of (A) DABP, (B) 2,4,6-THAP, and (C) 3-HPA. The quantity of each oligonucleotide loaded was 500 fmol. From Fu et al. (2006).

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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.
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	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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