Stochastic dynamics mass spectrometric structural analysis of nucleotides

Bojidarka Ivanova

Article ID: 3043
Vol 5, Issue 2, 2024
DOI: https://doi.org/10.54517/aas.v5i2.3043
Received: 4 November 2024; Accepted: 10 December 2024; Available online: 25 December 2024;
Issue release: 30 December 2024

VIEWS - 45 (Abstract)

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Abstract

The paper deals with innovative equations tackling exactly stochastic dynamics mass spectrometric experimental variable intensity of peak per span of scan time. They overcome limitations of classical methods for semi-quantifying analytes developed, so far, and exactly grasp observable variables and their fluctuations; thus, succeeding in determining analytes reliably both quantitatively and 3D structurally via soft ionization mass spectrometry. Given the paper’s goal of illustrating their crucial effect on mass spectrometric methodology as an irreplaceable approach to structurally analyse species, this study offers stochastic dynamics-based analysis of nucleotides. The major contribution is providing empirical justification of aspects of structural mass spectrometry analysing uridines and pseudouridines. The virtual identity of fragmentation patterns causes significant analytical challenges. The same is true for methyl-substituted guanosines which are often determined as mixtures. There are used ultra-high resolution electrospray ionization mass spectrometry, high accuracy computational static and molecular dynamics methods, and chemometrics. The study discusses controversial aspects of classical techniques. It illustrates how the innovative equations resolve disputable problems of structural analysis of nucleotides. It supports advanced formulas for achieving superior performances. There are obtained coefficients of linear correlation |r| = 0.9994–0.99923 determining N1-methyl-pseudouridine modified diphosphate compared with 5-methyluridine diphosphate N-acetylglucosamine. There are determined N2,N2-dimethylguanosine, uridine, pseudouridine, 5-methyl-uridine, 1-methyl-pseudouridine, 5,6-dihydrothymidine, galactosyl-queuosine, mannosyl-queuosine, adenosine, 2’-O-methyl-5-hydroxymethylcytidine, uridine triphosphate, thymidine diphosphate N-acetylglucosamine, 5-methyluridine diphosphate N-acetylglucosamine, and 7-methylguanosine-5’-phosphate modified derivative, respectively.

Keywords

stochastic dynamics mass spectrometry; quantum chemistry; nucleotides; 5-methyl-uridine; 1-methyl-pseudouridine; 3D structural analysis


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