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Liao CC, Yau S. The Effects of Potential and pH on the Adsorption of Guanine on the Au(111) Electrode. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2495-2501. [PMID: 35167284 DOI: 10.1021/acs.langmuir.1c02943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The adsorption of nucleobase at a gold electrode has been a model system to study the interaction between biomolecule and metal, which is relevant to the development of sensors and molecular electronics. The current study has employed in situ scanning tunneling microscopy (STM) and voltammetry to investigate the adsorption configuration and spatial structure of guanine (G) on a well-defined Au(111) electrode in perchloric acid (HClO4) and neutral phosphate buffer solution (PBS) containing 50 μM G. Potential control had a profound effect on the adsorption of the G molecule on the Au(111) electrode. No adsorption of G was observed at a potential more negative than 0 V in HClO4 and -0.2 V (versus Ag/AgCl) in PBS; shifting potential positively triggered a rapid adsorption of G to yield a well-ordered G array. Different spatial structures of G admolecules were imaged with STM in HClO4 and PBS, suggesting that ions in the electrolyte were important in this adsorption event. Shifting potential positively caused a more compact G adlayer with molecules adopting a tilted orientation. Meanwhile, G molecules continued to deposit on the Au(111) electrode leading to a multilayer G film. These processes were reversible to the potential modulation. G admolecules on the Au(111) electrode could be irreversibly oxidized in 0.1 M PBS, which resulted in a prominent peak at 0.74 V in the voltammogram. This oxidation process could be used to analyze the G molecule in a sample.
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Affiliation(s)
- Chiu-Ching Liao
- Department of Chemistry, National Central University Chungli County, Taoyuan City 32001 Taiwan, ROC
| | - Shuehlin Yau
- Department of Chemistry, National Central University Chungli County, Taoyuan City 32001 Taiwan, ROC
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3
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Mashmoushi N, Juhász DR, Coughlan NJA, Schneider BB, Le Blanc JCY, Guna M, Ziegler BE, Campbell JL, Hopkins WS. UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban. J Phys Chem A 2021; 125:8187-8195. [PMID: 34432451 DOI: 10.1021/acs.jpca.1c05564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two ion populations of protonated Rivaroxaban, [C19H18ClN3O5S + H]+, are separated under pure N2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.
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Affiliation(s)
- Nour Mashmoushi
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Daniel R Juhász
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | | | | | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Blake E Ziegler
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Bedrock Scientific, Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Centre for Eye and Vision Research, New Territories 999077, Hong Kong
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Cheng R, Loire E, Martens J, Fridgen TD. An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase. Phys Chem Chem Phys 2020; 22:2999-3007. [DOI: 10.1039/c9cp06393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO
- Campus Universite d’Orsay
- France
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Nijmegen
- The Netherlands
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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Halder A, Data D, Seelam PP, Bhattacharyya D, Mitra A. Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches. ACS OMEGA 2019; 4:7354-7368. [PMID: 31459834 PMCID: PMC6648064 DOI: 10.1021/acsomega.8b03689] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/12/2019] [Indexed: 06/10/2023]
Abstract
Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (E HB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting E HB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇2ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor-hydrogen distance, and (v) hydrogen-acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and E HB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.
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Affiliation(s)
- Antarip Halder
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhruv Data
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Preethi P. Seelam
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhananjay Bhattacharyya
- Computational
Science Division, Saha Institute of Nuclear
Physics(SINP), 1/AF,
Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
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