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Wang S, Ju P, Liu W, Chi J, Jiang T, Chi Z, Wang S, Qiu R, Sun C. A novel photoelectrochemical self-screening aptamer biosensor based on CAU-17-derived Bi 2WO 6/Bi 2S 3 for rapid detection of quorum sensing signal molecules. Anal Chim Acta 2024; 1304:342558. [PMID: 38637055 DOI: 10.1016/j.aca.2024.342558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
Quorum sensing signal molecule is an important biomarker released by some microorganisms, which can regulate the adhesion and aggregation of marine microorganisms on the surface of engineering facilities. Thus, it is significant to exploit a convenient method that can effectively monitor the formation and development of marine biofouling. In this work, an advanced photoelectrochemical (PEC) aptamer biosensing platform was established and firstly applied for the rapid and ultrasensitive determination of N-(3-Oxodecanoyl)-l-homoserine lactone (3-O-C10-HL) released from marine fouling microorganism Ponticoccus sp. PD-2. The visible-light-driven Bi2WO6/Bi2S3 heterojunction derived from metal-organic frameworks (MOFs) CAU-17 and self-screened aptamer were employed as the photoactive materials and bioidentification elements, respectively. Appropriate amount of MoS2 quantum dots (QDs) conjugated with single-stranded DNA were introduced by hybridization to enhance the photocurrent response of the PEC biosensor. The self-screening aptamer can specifically recognize 3-O-C10-HL, accompanied by increasing the steric hindrance and forcing MoS2 QDs to leave the electrode surface, resulting in an obvious reduction of photocurrent and achieving a dual-inhibition signal amplification effect. Under the optimized conditions, the photocurrent response of PEC aptasensor was linear with 3-O-C10-HL concentration from 1 nM to 10 μM, and the detection limit was as low as 0.26 nM. The detection strategy also showed a high reproducibility, superior specificity and good stability. This work not only provides a simple, rapid and ultrasensitive PEC aptamer biosensing strategy for monitoring quorum sensing signal molecules in marine biofouling, but also broadens the application of MOFs-based heterojunctions in PEC sensors.
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Affiliation(s)
- Shiliang Wang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China; Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China
| | - Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China
| | - Weixing Liu
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, PR China
| | - Jingtian Chi
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, No. 238 Songling Road, Qingdao, 266100, PR China
| | - Tiantong Jiang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, PR China
| | - Shuai Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China.
| | - Ri Qiu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China.
| | - Chengjun Sun
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, PR China.
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2
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Yang YH, He R, Qin Y, Zhang L. Metal-ion-triggered symmetry breaking of completely achiral azobenzene amphiphiles in water. NANOSCALE 2024. [PMID: 38639490 DOI: 10.1039/d3nr06668a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Achieving control over symmetry breaking of completely achiral components in the aqueous phase is a significant challenge in supramolecular chemistry. Herein, we demonstrate that it is possible to construct chiral nanoassemblies by introducing metal ions (Zn2+, Fe3+, Al3+, Cu2+, and Ca2+) into completely achiral azobenzene amphiphiles with key structural factors in the pure aqueous phase. It is found that the coordination interactions, π-π stacking, hydrophilic and hydrophobic interactions, hydrogen bonding, and electrostatic interactions are crucial to the metal-ion-induced symmetry breaking of completely achiral building blocks. This study may provide an intriguing model system for constructing chiral assemblies based on completely achiral molecules.
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Affiliation(s)
- Yun-Han Yang
- PCFM Lab, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Ran He
- PCFM Lab, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Yang Qin
- PCFM Lab, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Ling Zhang
- PCFM Lab, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
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3
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Liu S, Meng S, Wang M, Li W, Dong N, Liu D, Li Y, You T. In-depth interpretation of aptamer-based sensing on electrode: Dual-mode electrochemical-photoelectrochemical sensor for the ratiometric detection of patulin. Food Chem 2023; 410:135450. [PMID: 36640656 DOI: 10.1016/j.foodchem.2023.135450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/12/2022] [Accepted: 01/07/2023] [Indexed: 01/10/2023]
Abstract
Electrochemical aptasensors have been extensively used to quantify food contaminants (e.g., mycotoxin) by using high-affinity aptamer for target recognition. Yet, analytical performance of aptasensors using different aptamers can be varied for the same target. Here, four aptamers with different sequences (i.e., A22, A34, A42, and A45) of patulin (PAT) were selected to estimate sensing behaviors at electrodes with electrochemical (EC) and photoelectrochemical (PEC) assays. Synergistic effect of steric hindrance and electron transfer distance was found to significantly affect EC and PEC response for PAT at aptasensors fabricated with A22, A34, A42, or A45. Eventually, A22 emerged to be the optimal aptamer for aptasensing, despite the highest affinity of A42 to PAT. The A22-based EC-PEC dual-mode ratiometric aptasensor offered a linear range of 50 fg mL-1 - 500 ng mL-1 with a detection limit of 30 fg mL-1 for PAT, and it was applied to apple product (i.e., juice, puree) analysis.
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Affiliation(s)
- Shuda Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shuyun Meng
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Meng Wang
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Wenjia Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Na Dong
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dong Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Yuye Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Tianyan You
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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4
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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5
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Kaminský J, Andrushchenko V, Bouř P. Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment. RSC Adv 2021; 11:8411-8419. [PMID: 35423314 PMCID: PMC8695171 DOI: 10.1039/d1ra00076d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components. The conformation space was explored by molecular dynamics (MD), the electronic spectra were generated using time dependent density functional theory (TDDFT). The sum over state (SOS) method was employed for MCD. The results show that accounting for the dynamics is crucial for reproduction of the experiment. While unpolarized absorption spectroscopy is relatively indifferent, ECD reflects the conformation and geometry dispersion more. MCD spectra provide variable response dependent on the wavelength and structural change. In general, MCD samples the structure more locally than ECD. Simple computational tests suggest that the optical spectroscopies coupled with the computational tools provide useful information about nucleic acid components, including base pairing and stacking.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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6
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Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
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7
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Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory. Int J Mol Sci 2018; 19:ijms19082346. [PMID: 30096923 PMCID: PMC6122091 DOI: 10.3390/ijms19082346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
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8
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Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
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Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
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9
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Šmidlehner T, Piantanida I, Pescitelli G. Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids - tutorial. Beilstein J Org Chem 2018; 14:84-105. [PMID: 29441133 PMCID: PMC5789433 DOI: 10.3762/bjoc.14.5] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 01/19/2023] Open
Abstract
The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute; P. O. Box 180, 10002 Zagreb, Croatia
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, via Moruzzi 13, Pisa, Italy
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10
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Gattuso H, García-Iriepa C, Sampedro D, Monari A, Marazzi M. Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations. J Chem Theory Comput 2017; 13:3290-3296. [DOI: 10.1021/acs.jctc.7b00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hugo Gattuso
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Cristina García-Iriepa
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
- Unidad
Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
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11
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Miyahara T, Nakatsuji H, Sugiyama H. Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study. J Phys Chem A 2016; 120:9008-9018. [PMID: 27809523 DOI: 10.1021/acs.jpca.6b08023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.
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Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
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12
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Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
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13
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14
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Loco D, Jurinovich S, Di Bari L, Mennucci B. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved? Phys Chem Chem Phys 2016; 18:866-77. [PMID: 26646952 DOI: 10.1039/c5cp06341h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.
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Affiliation(s)
- Daniele Loco
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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15
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Nørby MS, Steinmann C, Olsen JMH, Li H, Kongsted J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J Chem Theory Comput 2016; 12:5050-5057. [DOI: 10.1021/acs.jctc.6b00706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Morten Steen Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Hui Li
- Department
of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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16
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Padula D, Di Bari L, Pescitelli G. The “Case of Two Compounds with Similar Configuration but Nearly Mirror Image CD Spectra” Refuted. Reassignment of the Absolute Configuration of N-Formyl-3′,4′-dihydrospiro[indan-1,2′(1′H)-pyridine]. J Org Chem 2016; 81:7725-32. [DOI: 10.1021/acs.joc.6b01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Padula
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K
| | - Lorenzo Di Bari
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
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17
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Gattuso H, Spinello A, Terenzi A, Assfeld X, Barone G, Monari A. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures. J Phys Chem B 2016; 120:3113-21. [DOI: 10.1021/acs.jpcb.6b00634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Gattuso
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Angelo Spinello
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Alessio Terenzi
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
- Institute
of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, Vienna, Austria
| | - Xavier Assfeld
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Giampaolo Barone
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Antonio Monari
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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18
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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19
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Espinosa Leal LA, Karpenko A, Swasey S, Gwinn EG, Rojas-Cervellera V, Rovira C, Lopez-Acevedo O. The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers. J Phys Chem Lett 2015; 6:4061-6. [PMID: 26722777 DOI: 10.1021/acs.jpclett.5b01864] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
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Affiliation(s)
| | - Alexander Karpenko
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
| | - Steven Swasey
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Elisabeth G Gwinn
- Department of Physics, University of California , Santa Barbara, California 93106-9510, United States
| | - Victor Rojas-Cervellera
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Olga Lopez-Acevedo
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
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20
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Gattuso H, Assfeld X, Monari A. Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1640-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Norman P, Parello J, Polavarapu PL, Linares M. Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory. Phys Chem Chem Phys 2015; 17:21866-79. [DOI: 10.1039/c5cp02481a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.
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Affiliation(s)
- Patrick Norman
- Department of Physics
- Chemistry and Biology
- Linköping University
- SE-581 83 Linköping
- Sweden
| | - Joseph Parello
- Department of Chemistry
- Vanderbilt University
- Nashville
- USA
| | | | - Mathieu Linares
- Department of Physics
- Chemistry and Biology
- Linköping University
- SE-581 83 Linköping
- Sweden
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