Gas-phase interactions between Ba and deprotonated cytosine (C ) were studied in [C Ba] and [C BaC] complexes by IRMPD spectroscopy coupled to tandem mass-spectrometry in combination with DFT calculations. For the [C BaC] complex only one [C KAN1O-Ba-C ] isomer was found, although the presence of another structure cannot be excluded. This isomer features a central tetracoordinated Ba that simultaneously interacts with keto-amino [C ] deprotonated on N1 and neutral keto-amino C. Both moieties are in different planes as a consequence of an additional NH…O=C hydrogen bond between C and [C ] . A sequential IRMPD dynamics is observed in this complex. For the [C Ba] complex produced by electrospray ionization two isomers ([C KAN1OBa] and [C KAN3OBa] ) were identified, in which Ba interacts simultaneously with the C=O group and the N1 or N3 atom of the keto-amino [C ] , respectively. A comparison with the related [C Pb] complex (J. Y. Salpin et al., Chem. Phys. Chem. 2014, 15, 2959-2971) is also presented.
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http://dx.doi.org/10.1002/cphc.202000696 | DOI Listing |
Phys Chem Chem Phys
January 2024
Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
June 2023
Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists.
View Article and Find Full Text PDFJ Phys Chem Lett
December 2022
Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.
When strands of DNA encapsulate silver clusters, supramolecular optical chromophores develop. However, how a particular structure endows a specific spectrum remains poorly understood. Here, we used neutron diffraction to map protonation in (AC)-Ag, a green-emitting fluorophore with a "Big Dipper" arrangement of silvers.
View Article and Find Full Text PDFAnal Chim Acta
September 2022
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China; Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China. Electronic address:
Cytosine and protonated cytosine base pairs (C·CH)-supported i-motif conformation has been widely employed in some interdisciplinary fields such as biology, medicine and chemistry. In this work, we report a new electrochemical biosensing method for the detection of glucose oxidase (GOx) and urease based on pH-induced DNA conformational-change. The constructed platform mainly includes TdT-mediated catalytic synthesis, GOx- or urease-catalyzed biological reaction and pH-induced DNA conformational-change.
View Article and Find Full Text PDFPhys Chem Chem Phys
April 2022
Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA.
It has been shown previously in protonated, deprotonated and ionized guanine-cytosine base pairs that intra-base pair proton transfer from the N1-H at the Watson-Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure-kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), , [9MG·9MG]˙, [9MOG·9MG]˙ and [9MOG·9MOG]˙.
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