Nucleic acids mass spectrometry

Nomenclature of heterocycles, 20, 175 Nuclear magnetic resonance spectroscopy, application to indoles, IS, 277 Nucleic acids, mass spectrometry of, 39, 79 Nucleophiles, bifunctional, cyclisations and ring transformations on reaction of azines with, 43, 301... 

See also Electrophoresis Nucleic Acids. Mass Spectrometry Peptides and Proteins. 

E. Nordhoff, F. Kirpekar, and P. Roepstorff, Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15, 67-138 (1996). 

The difficulty with protein arrays is that proteins do not behave as uniformly as nucleic acid. Protein function is dependent on a precise, and fragile, three-dimensional structure that may be difficult to maintain in an array format. In addition, the strength and stability of interactions between proteins are not nearly as standardized as nucleic acid hybridization. Each protein-protein interaction is unique and could assume a wide range of affinities. Currently, protein expression mapping is performed almost exclusively by two-dimensional electrophoresis and mass spectrometry. The development of protein arrays, however, could provide another powerful... 

Nordhoff, E. Ingendoh, A. Cramer, R. Overberg, A. Stahl, B. Karas, M. Hillenkamp, F. Crain, P. F. Matrix-assisted laser desorption/ionization mass spectrometry of nucleic acids with wavelengths in the UV and IR. Rapid Comm. Mass Spectrom. 1992, 6,771-776. 

This chapter will address the applications of protein-based bioinformatics to analysis of microorganisms introduced intact into the instrumental system for rapid processing and analysis. Strategies that require offline extraction and fractionation of proteins will not be discussed. Although the amplification of nucleic acids is a powerful approach, especially coupled with mass spectrometry,15 it requires extraction and processing, and thus is not included. 

Tandem mass spectrometry has become an important tool for determining the sequence of amino acids in protonated peptides98 and the sequence of bases in deprotonated nucleic acids such as DNA.99 Despite the importance and widespread use of CID-MS to sequence peptides and nucleic acids, the mechanistic details of the dissociation processes are poorly understood. A better understanding of the... 

LeDuc, R.D., Taylor, G.K., Kim, Y.B., Januszyk, T.E., Bynum, L.H., Sola, J.V., Garavelli, J.S., Kelleher, N.L. (2004). ProSight PTM an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 32, W340-W345. 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

Willems, A. V., Deforce, D. L., Van Peteghem, C. H., and Van Bocxlaer, J. E. (2005). Analysis of nucleic acid constituents by on-line capillary electrophoresis-mass spectrometry. Electrophoresis 26, 1221-1253. 

Hanson, C. L., Robinson, C. V. Protein-nucleic acid interactions and the expanding role of mass spectrometry. J Biol Chem 2004, 279, 24907-24910. 

Polymeric stationary phases have many advantages when polymerized in capillaries (diameter < 0.5 mm) as rods in the presence of porogens to yield channels for mobile phase transport. They are frequently used in the analysis of peptides, proteins, and nucleic acids when directly coupled to electro spray mass spectrometry. 

Premstaller, A., Oberacher, H., and Huber, C. G., High-performance liquid chromatography-electrospray ionization mass spectrometry of single- and double-stranded nucleic acids using monolithic capillary columns, A a/yft ca/ Chemistry 72(18), 4386 393, 2000. 

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