Vibrational Investigation of Nucleobases by Means of Divide and Conquer Semiclassical Dynamics [PDF]
Journal of Chemical Physics 150, 224107 (2019), 2019 In this work we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine.
arxiv +1 more source
Mechanisms of base selection by the E.coli mispaired uracil glycosylase [PDF]
, 2008 The repair of the multitude of single-base lesions formed daily in the cells of all living organisms is accomplished primarily by the base-excision repair (BER) pathway that initiates repair through a series of lesion-selective glycosylases.
Darwanto, Agus +6 more
core +2 more sources
Comment on “Ring-breaking electron attachment to uracil: Following bond dissociations via evolving resonances” [J. Chem. Phys. 128, 174302 (2008)] [PDF]
, 2008 We point out that the assignment of pi* resonances to calculated features in a recent paper by Gianturco et al. [J. Chem.
McKoy, Vincent, Winstead, Carl
core +1 more source
Precluding uracil from DNA [PDF]
Structure, 1996 Two enzymes, dUTP pyrophosphatase and uracil-DNA glycosylase, prevent the misincorporation of uracil into the genome in distinct manners. The atomic structures of these proteins complexed with substrate analogs reveal the structural basis for uracil recognition and suggest a novel mechanism of DNA repair.
Dmitry G Vassylyev, Kosuke Morikawa
openaire +3 more sources
Synthesis of 5-substituted 2'-deoxyuridine-5'-phosphonate analogues and evaluation of their antiviral activity [PDF]
, 2012 A small series of 5-(hetero)aryl-modified nucleoside phosphonates was synthesized via an 8-step procedure including a Wittig reaction and Suzuki-Miyaura coupling.
Balzarini, Jan +4 more
core +1 more source
, 2017 The S66 benchmark for noncovalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit.
Karton, Amir +3 more
core +2 more sources
Catalytic mechanism of alpha-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. [PDF]
, 2013 Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism.
Aherne +101 more
core +2 more sources
A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily [PDF]
Nucleic Acids Research, 2015 Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms.
Sang, Pau Biak +4 more
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QM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl$_3$ [PDF]
, 2008 A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H$...$N Hydrogen bond geometry.
arxiv +1 more source
Meteorites and the RNA World: A Thermodynamic Model of Nucleobase Synthesis within Planetesimals [PDF]
2016, Astrobiology, Vol. 16, Issue 11, pp. 853-872, 2016 The possible meteorite parent body origin of Earth's pregenetic nucleobases is substantiated by the guanine (G), adenine (A) and uracil (U) measured in various meteorites. Cytosine (C) and thymine (T) however are absent in meteorites, making the emergence of a RNA and later RNA/DNA/protein world problematic.
arxiv +1 more source