Nucleotides, mass spectrometry

A last problem in nucleotide mass spectrometry is related to the dinucleotides. Hunt and Hignite tried to prepare a matrix of several ribodinucleo-tides (silylated) for further application to the sequential analysis of oligonucleotides. The fact that common enzymatic and/or chemically induced hydrolyses do not stop at the nucleotide level, but rather continue until they become nucleosides, does not reduce the merit of their work. That work, as well as that of Biemann, enable one to identify any dinucleotide pair of the type B,pB2, where p stands for phosphate. This information is of very limited use, however, because from any given RNA, for instance, one obtains practically any possible B1PB2 combination of dinucleotides. 

A modified nucleotide found in RNA sequencing could either be a new nucleotide of unknown chemical structure or it could correspond to an already known modified nucleotide (up to now about 90 different modified nucleotides have been identified in RNA). Keith [124] proposed preparative purifications of major and modified ribonucleotides on cellulose plates, allowing for their further analysis by UV or mass spectrometry. Separation was realized by two-dimensional elution using the following mobile phases (1) isobutyric acid-25% ammonia-water (50 1.1 28.9,... 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Krahmer, M. T. Johnson, Y. A. Walters, J. J. Fox, K. F. Fox, A. Nagpal, M. Electrospray quadrupole mass spectrometry analysis of model oligonucleotides and polymerase chain reaction products determination of base substitutions, nucleotide additions/deletions, and chemical modifications. Anal. Chem. 1999, 71, 2893-2900. 

Walters, J. Muhammad, W. Fox, K. F. Fox, A. Xi, R. D. Creek, C. Pirisi, L. Geno-typing single nucleotide polymorphisms using intact PCR products by electrospray quadrupole mass spectrometry. Rapid Comm. Mass Spectrom. 2001,15,1752-1759. 

Z. Zhao, J.H. Wahl, H.R. Udseth, S.A. Hofstadler, A.F. Fuciarelli and R.D. Smith, Online capillary electrophoresis-electrospray ionization mass spectrometry of nucleotides, Electrophoresis, 16 (1995) 389-395. 

Misra A, Hong JY, Kim S (2007) Multiplex genotyping of cytochrome p450 single-nucleotide polymorphisms by use of MALDI-TOF mass spectrometry. Clin Chem 53 933-939 Moon YJ, Zhang S, Brazeau DA, Morris ME (2007) Effects of the flavonoid biochanin A on gene expression in primary human hepatocytes and human intestinal cells. Mol Nutr Food Res 51 317-323... 

Sauer, S. Typing of single nucleotide polymorphisms by MALDI mass spectrometry Principles and... 

Andersen M.D., Shaffer J., Jennings P.A., Adams J.A. Structural characterization of protein kinase A as a function of nucleotide binding. Hydrogen-deuterium exchange studies using matrix-assisted laser desorption ionization-time of flight mass spectrometry detection. J. Biol. Chem. 2001, 276, 14204-14211. 

Buetow, K.H., Edmondson, M., MacDonald, R., Clifford, R., Yip, P., Kelley, ]., Little, D.P, Strausberg, R., Koester, H., Cantor, C.R., and Braun, A., High-throughput development and characterization of a genome-wide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Proc. Natl. Acad. Sci. USA, 98, 581-584, 2001. 

Electrospray (ESI) is an atmospheric pressure ionization source in which the sample is ionized at an ambient pressure and then transferred into the MS. It was first developed by John Fenn in the late 1980s [1] and rapidly became one of the most widely used ionization techniques in mass spectrometry due to its high sensitivity and versatility. It is a soft ionization technique for analytes present in solution therefore, it can easily be coupled with separation methods such as LC and capillary electrophoresis (CE). The development of ESI has a wide field of applications, from small polar molecules to high molecular weight compounds such as protein and nucleotides. In 2002, the Nobel Prize was awarded to John Fenn following his studies on electrospray, for the development of soft desorption ionization methods for mass spectrometric analyses of biological macromolecules. ... 

Guanosine nucleotide, redox pathways, 43 129 Guided-ion-beam mass spectrometry, metal-0X0 systems, 44 323 Gutmann donor number, 34 174 Gypsum... 

Prinz, H. Lavie, A. Scheidig, A.J. Spangenberg, O. Konrad, M. Binding of nucleotides to guanylate kinase, p21(ras), and nucleoside-diphosphate kinase studied by nano-electrospray mass spectrometry. J. Biol. Chem., 274, 35337-35342 (1999)... 

Diepoxybutane also reacts with nucleosides, nucleotides and DNA. Adducts at N of adenine were identified in incubations (pH 7) containing deoxyadenosine, deoxyadenosine monophosphate or poly(dA-dT)(dA-dT), as determined by mass spectrometry, or calf tliymus DNA as determined by a high-performance liquid chromatography/ 32P-postlabelling method (Leuratti et al., 1994). By the latter method, the authors demonstrated adduct formation to N of adenine in DNA from Chinese hamster ovary cells incubated with diepoxybutane at 37°C. 

We hydrolyzed ATP and ADP in 1 N and 0.1 N HC1 and in buffered solutions at pH 4j nd 8 in which the hydrolysis medium was variously enriched in °0 to either 10% or 20%. To assess the isotopic enrichment of each such solution for use in the nucleotide hydrolysis experiments, we hydrolyzed PCI, in the solution, esterified the resultant phosphoric acid/inorganic phosphate (P.) by reaction with diazomethane, and determined the isotopic distribution of the trimethyl phosphate (TMPO) by mass spectrometry. The 1 N and 0.1 N HC1 hydrolyses were allowed to proceed for 45 min and 10 hr, respectively, at 70, insuring complete conversion of ATP into AMP + 2P. The pH 8 hydrolyses were allowed to proceed for 36 hr at 70 to a point (20-25% completion) at which the ratio of ADP to AMP established that 96% and 4%, respectively, of the P. released had arisen by the primary and secondary hydrolysis steps, namely, ATP ADP + P. and ADP " AMP + P. 0The pH 4 hydrolyses were allowed to proceed for 24 hr, also at 70, to 40% completion. 

Haff LA, Smirnov IP. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res 1997 7 378-388. 

Ross P, Hall L, Haff LA. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 2000 29 620-626, 628-629. 

Jardine, I., and Weidner, M. M. (1980). Approach to the quantitative analysis of nucleotides by gas chromatography-mass spectrometry. J. Chromatogr. 182, 395-401. 

There are no reports currently available of an on-line application of the very powerful MALDI technique (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). However, this technique has become increasingly important for the analysis of complex molecules and quality control, for example, for glycosylated material [177] or peptides [104] or nucleotides [324],... 

Although the determination of HA or HB selectivity is relatively straightforward the techniques for isolation of pyridine nucleotides from the reaction mixtures are tedious and time consuming. Two more recent techniques use either proton magnetic resonance or electron impact and field desorption mass spectrometry. The technique of Kaplan and colleagues requires a 220 MHz nuclear magnetic resonance spectrometer interfaced with a Fourier transform system [104], It allows the elimination of extensive purification of the pyridine nucleotide, is able to monitor the precise oxidoreduction site at position 4, can be used with crude extracts, and can be scaled down to /nmole quantities of coenzyme. The method can distinguish between [4-2H]NAD+ (no resonance at 8.95 8) and NAD+ (resonance at 8.95—which is preferred) or between [4A-2H]NADH (resonance at 2.67 8, 75 4B = 3.8 Hz) and [4B-2H]NADH (resonance at 2.77 8, J5 4A = 3.1 Hz). 

For many years, mass spectrometry has had an important role in the analysis of nucleic acids. However, older work was limited to the analysis of nucleotides because the El and Cl methods did not allow oligonucleotide analysis. With the advent of FAB and PD, small oligonucleotides comprising up to about 10 bases have been analysed. 

Another important advantage of mass spectrometry is its capacity to verify the incorporation of modified nucleotides. Figure 8.31 displays the mass spectrum of a synthetic oligonucleotide whose theoretical mass is 5838 Da. In addition to the desired nucleotide, other compounds are present. The mass difference between the peaks (111-151 Da) corresponds to the masses of the nucleic bases. This suggests that depurination reactions have occurred during the synthesis. 

Other methods (described in Figure 8.40) based on mass spectrometry, such as gas chro-matography/mass spectrometry (GC/MS) [211] or high-performance liquid chromatogra-phy/mass spectrometry (HPLC/MS), [212-215] also allow one to detect and identify the modified constituents of oligonucleotides. These methods are good for small sample quantities of around 1 og, and allow the detection of a modified nucleotide within a mixture of 107 nucleotides. 

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