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Rapid, inexpensive, sequence-independent fluorescent labeling of phosphorothioate DNA.
Biophys J
April 2023
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina. Electronic address:
Fluorescently labeled oligonucleotides are powerful tools for characterizing DNA processes; however, their use is limited by the cost and sequence requirements of current labeling technologies. Here, we develop an easy, inexpensive, and sequence-independent method for site-specifically labeling DNA oligonucleotides. We utilize commercially synthesized oligonucleotides containing phosphorothioate diester(s) in which a nonbridging oxygen is replaced with a sulfur (PS-DNA).
View Article and Find Full Text PDFPhosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.
ACS Chem Biol
September 2022
Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Förster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with post-transcriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions.
View Article and Find Full Text PDFRevisiting the Tropospheric OH-Initiated Unimolecular Decomposition of Chlorpyrifos and Chlorpyrifos-Methyl: A Theoretical Perspective.
J Phys Chem A
May 2020
Laboratory of Computational Studies on Molecular Systems, eCsMolab Department of Chemistry, ICEx, Federal University of Minas Gerais Pampulha, Belo Horizonte 31270-901, MG, Brazil.
Based on density functional theory (DFT) electronic structure calculations with dispersion correction, we propose new reaction pathways in which no extra reaction step is necessary to account for the formation of 3,5,6-trichloro-2-pyridynol (TCP) within the process of tropospheric OH-initiated unimolecular decomposition of chlorpyrifos (CLP) and chlorpyrifos-methyl (CLPM). Chlorpyrifos and its analogous compound are among the most used organophosphorus pesticides worldwide, and their unimolecular decomposition in the troposphere is a dominant process of removal in the gas phase. The reaction pathways that we put forward have turned out to be the most exergonic ones among the three possible routes for the attack of the hydroxyl radical to the thiophosphoryl (P═S) bond of both CLP and CLPM.
View Article and Find Full Text PDFSulfur Transfer Versus Phenyl Ring Transfer in the Gas Phase: Sequential Loss of CHOH and CHO-P=O from Protonated Phosphorothioates.
J Am Soc Mass Spectrom
March 2019
Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang, 330013, People's Republic of China.
Collisional activation fragmentation of protonated phosphorothioates leads to skeletal rearrangement and formation of aryl sulfenylium cation (R-PhS) via successive eliminations of CHOH and CHO-P=O. To better understand this unusual fragmentation reaction, isotope-labeling experiments and density functional theory (DFT) calculations were carried out to investigate two mechanistic pathways. In route 1, a direct intramolecular transfer of the R-phenyl group occurs from the oxygen atom to the sulfur atom on thiophosphoryl to form methoxyl S-(3-methyl-4-methylsulfanyl-phenyl) phosphonium thiolate (a4), which subsequently dissociates to form the m/z 169 cation.
View Article and Find Full Text PDFNucleobase modification by an RNA enzyme.
Nucleic Acids Res
February 2017
Dept. of Biochemistry, University of Missouri, Columbia, MO, USA.
Ribozymes can catalyze phosphoryl or nucleotidyl transfer onto ribose hydroxyls of RNA chains. We report a single ribozyme that performs both reactions, with a nucleobase serving as initial acceptor moiety. This unprecedented combined reaction was revealed while investigating potential contributions of ribose hydroxyls to catalysis by kinase ribozyme K28.
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