MALDI oligonucleotides

Li, Y. Tang, K. Little, D. P. Koster, H. Hunter, R. L. Mclver, R. T. High-resolution MALDI Fourier transform mass spectrometry of oligonucleotides. Anal. Chem. 1996, 68, 2090-2096. 

E. Nordhoff, M. Schurenberg, G. Thiele, C. Lubbert, K.-D. Kloeppel, D. Theiss, H. Lehrach, and J. Gobom. Sample Preparation Protocols for MALDI-MS of Peptides and Oligonucleotides Using Prestructured Sample Supports. Int. J. Mass Spectrom., 226(2003) 163-180. 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

Fig. 10.7. Negative-ion MALDI spectra of the oligonucleotide pd[T]g (a) 5 pmol, (b) same as (a) after addition of 5-10 cation exchange beads to the sample preparation. Adapted from Ref [24] by permission. John Wiley Sons, 1992.

Due to their numerous acidic hydrogens, oligonucleotides require desalting prior to MALDI analysis, e.g. by using cation exchange resins (Chap. 10.4.2). [24]... 

Meyer, A. Spinedi, N. Imbach, J.-L. Vasseur, J.-J. Analysis of SoUd-Supported Oligonucleotides by MALDI-TOF-MS. Rapid Commun. Mass Spectrom. 2000,14, 234-242. 

Tire MALDI method is especially useful for complex mixtures of peptides and can be utilized in peptide sequencing. The technique is also appropriate for studying mixtures of glycoproteins. Negative-ion MALDI can be applied to oligonucleotide mixtures. Further improvements in resolution in both MALDI... 

Another very sensitive MS technique is MALDI-TOF. Its high-resolution mass spectra allowed, for example, the identification of the 8-oxo-G lesion by its 416-Da mass shift in a oligonucleotide heptamer at picomol level (Bartolini and Johnston 2000). 

Figure 2 Oligonucleotide artifacts detectable on MALDI-TOF MS. The spectrum shows a typical example of an oligonucleotide of poor quality. The presence of a sodium adduct peak is depicted (Na adduct) and evidence of depurination potentially at G nucleobases (Depurinated). The oligonucleotide sequence used was 5 OH-TAGGCCTGGGAAGCAGCA-OH 3. ...

Molin L, Cristoni S, Crotti S, Bemardi L, Seraglia R, Traldi P (2008) Sieve-based device for MALDI sample preparation. I. Influence of sample deposition conditions in oligonucleotide... 

This was introduced in 1988 principally by Karas and Hillenkamp [19-21], It has since become a widespread and powerful source for the production of intact gas-phase ions from a broad range of large, non-volatile and thermally labile compounds such as proteins, oligonucleotides, synthetic polymers and large inorganic compounds. The use of a MALDI matrix, which provides for both desorption and ionization, is the crucial factor for the success of this ionization method. The method is characterized by easy sample preparation and has a large tolerance to contaminantion by salts, buffers, detergents, and so on [22,23],... 

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