Nucleosides and nucleotides part 24 Investigation of ribo- and deoxyribonucleosides and -nucleotides by fast- atom-bombardment mass spectrometry

On the interaction of bare and hydrated aluminum ion with nucleic acid bases (U, T, C, A, G) and monophosphate nucleotides (UMP, dTMP, dCMP, dAMP, dGMP)

The B3LYP/6-311+G(2df,2p) density functional approach was used to study the interaction that aluminum trication, in the bare and hydrated forms, establishes with the nucleic acid bases and the corresponding monophosphate nucleotides. In this investigation, we determine equilibrium geometry of all possible complexes resulting from the attachment of the ion on the different binding sites selected on each ligand. The relative energies of complexes and metal ion affinities are also given. The most meaningful aspect was found to lie in the energetics of this interaction that underlines a very high affinity of aluminum ion for the examined biological systems.

Negative ion FAB mass spectroscopy of some ribose alkylated 5'-UMP derivatives

Characteristic fragment ions obtained in Fast atom bombardment (FAB) mass spectroscopy of ribose alkylated Uridine 5'-monophosphate (5'-UMP) derivatives in negative ion mode are described. All the compounds examined exhibited either [M]- or quasimolecular ion [M - H]- the fragmentations can be used to characterize these nucleotides.

Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase

Gas-phase metal affinities of DNA and RNA bases for the Na(+) and K(+) ions were determined at density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of nucleic acid bases and the alkali ions on the different binding sites, were considered. Structural features of the sodium and potassium complexes were found to be similar except in some uracil and thymine compounds in which the tendency of potassium ion toward monocoordination appeared evident. B3LYP bond energies for both metal ions were in agreement with the available experimental results in the cases of uracil and thymine for which the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base. For adenine, although the interaction of the ions with the most stable free tautomer generated the least stable molecular complex, the best agreement with experiment was found in just this case. For the remaining cytosine and guanine bases, our calculations indicated that the metal ion affinity value closest to experiment should be determined taking into account the role played by the different tautomers of the free bases with similar energy and all the possible complexes obtained by them.

Molecular recognition and supramolecular chemistry in the gas phase

Supramolecular chemistry, in particular, the fields of molecular recognition and self-assembly, profit much from the development of soft ionization techniques and advanced methods for mass analysis and gas-phase chemistry. Vice versa, weakly bonded architectures and host-guest complexes represent a veritable challenge for the mass spectrometrist, leading to further development of methods and techniques. This review describes the state-of-the-art in this field, and includes topics such as the effects of solvation on meta binding to crown ethers, chiral discrimination of guests by chiral hosts, the elucidation of the secondary structure of self assembled complexes, and the mechanistic pathways of self assembly or the fragmentations of supramolecular complexes in the gas phase.

Mass spectrometry of nucleic acids

The present article is a survey of ESI and MALDI mass spectrometric analysis of nucleic acid oligomers and polymers. In order to limit the extent of the review, mass spectrometry of mononucleotides is generally not considered, except where such data are important for an understanding of the analysis of larger nucleic acids. The first part of the review is a condensed description of the structure and the acid-base properties of nucleic acids. The remaining part is divided into three main sections, dealing with the practical aspects of the two ionization techniques, fragmentation, and applications, respectively. The first section includes an extensive discussion of experimental parameters and problems, which are important for the analysis of different types of nucleic acid samples, including noncovalent complexes and mixtures. At the end of this section, as well as the following one, a comparison between MALDI and ESI as ionization techniques for nucleic acid is given. In addition to a detailed discussion of ion fragmentation, the fragmentation section includes an overview of the direct mass spectrometric sequencing of nucleic acids performed with either technique. The fragmentation reactions occurring upon MALDI and ESI are compared. The last section describes the life science applications of ESI-MS and MALDI-MS of nucleic acids; an account of experiments demonstrating the potential of a method, and of the bona fide solving of problems by ESI and MALDI is given. © 1997 John Wiley & Sons, Inc.

N-Alkylnicotinium halides: A class of cationic matrix additives for enhancing the sensitivity in negative ion Fast-Atom bombardment mass spectrometry of polyanionic analytes

The addition of some surfactants to the fast-atom bombardment (FAB) matrix previously has been demonstrated to enhance analyte signals in fast-atom bombardment mass spectrometry. In particular, cationic surfactants appear to enhance the negative ion FAB detectability of analytes that exist as anionic species in the matrix solution. It has been proposed that the charged surfactant concentrates the oppositely charged analyte near the surface, which results in larger signals for the analyte. Cationic surfactants that contain a fixed positive charge and an additional basic site were prepared with different hydrophobic moieties and were evaluated for their effectiveness as FAB matrix additives. The compound N-octylnico-tinium bromide (ONBr) is shown to improve greatly the analyte-related signals in negative ion fast-atom bombardment mass spectrometry for a variety of polyanionic analytes, relative to other surfactants (e.g., cetylpyridinium salts). This surfactant not only enhances detectability, but also simplifies the pseudomolecular ion region of the resulting spectra by reducing or eliminating metal cation adduct peaks. The simple mechanism of enhancement via surface activity is evaluated, and alternative mechanisms are considered. It is clearly shown that ONBr, as a FAB matrix additive, will allow mass spectrometry to be used for the analysis of anionic compounds that normally exhibit very low responses.

Analysis of sub-microgram quantities of nucleotides by fast atom bombardment mass spectrometry

Nucleotides of the structure P1,Pn-di(adenosine-5')-n-phosphate (n = di- through penta-) in the form of salts, and P1,P4-di(guanosine-5')tetraphosphate sodium salt have been analyzed by fast atom bombardment (FAB) mass spectrometry. A 0.2 molar solution of p-toluenesulfonic acid in glycerol has been evaluated as a matrix. In this matrix, the metal ions of the nucleotide salts are readily exchanged for protons, resulting in a simple spectrum with only one peak in the molecular ion region corresponding to the free phosphoric acid of the nucleotide plus or minus a proton (positive or negative mode), instead of the multiplicity of peaks arising from a series of metal and matrix adduct ions found with glycerol as matrix. The detection limit for analytes using this matrix is improved by a factor of ten compared to glycerol alone. It appears that the high acidity and the surfactant properties of p-toluenesulfonic acid both contribute to this result. Useful spectra are obtained from 250 ng of each of the above mentioned nucleotides, with the detection limit being somewhat lower in the positive mode. However, both positive and negative FAB spectra are useful and the results are complementary.