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Cárdenas G, Lucia‐Tamudo J, Mateo‐delaFuente H, Palmisano VF, Anguita‐Ortiz N, Ruano L, Pérez‐Barcia Á, Díaz‐Tendero S, Mandado M, Nogueira JJ. MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations. J Comput Chem 2023; 44:516-533. [PMID: 36507763 PMCID: PMC10107847 DOI: 10.1002/jcc.27018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.
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Affiliation(s)
- Gustavo Cárdenas
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | | | | | | | - Lorena Ruano
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | - Sergio Díaz‐Tendero
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
- Condensed Matter Physics Center (IFIMAC)Universidad Autónoma de MadridMadridSpain
| | - Marcos Mandado
- Department of Physical ChemistryUniversity of VigoVigoSpain
| | - Juan J. Nogueira
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
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2
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Zhang L, Yue C, Zhang L, Zhang P, Wang L, Lei M, Pu M. A DFT study on the isomerization mechanism of azobenzene derivatives on silicon substrates. NEW J CHEM 2022. [DOI: 10.1039/d2nj04631h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The cis–trans isomerization mechanism of azobenzenesulfonamide derivatives on silicon substrates was investigated using DFT. The most favorable cooperative mode of the N2 inversion of the L followed by the N1 inversion of the R was proposed.
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Affiliation(s)
- Lulu Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Caiwei Yue
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Lin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Peihuan Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Luocong Wang
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Min Pu
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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3
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Barbosa N, Sagresti L, Brancato G. Photoinduced azobenzene-modified DNA dehybridization: insights into local and cooperativity effects from a molecular dynamics study. Phys Chem Chem Phys 2021; 23:25170-25179. [PMID: 34730143 DOI: 10.1039/d1cp04032d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoresponsive azobenzene-modified DNA (RNA) has become a very fruitful material for nanotechnology due to the capability of switching on and off hybridization (i.e., duplex formation) in smart nanostructures. This nanomaterial exploits the well-known azobenzene trans/cis photo-isomerization. In fact, it has been found that DNA tethered with trans-azobenzene shows normal nucleic acid recognition and hybridization, while the cis form destabilizes the duplex configuration, eventually leading to DNA unzipping. However, while the working principle of the light-triggered DNA dehybridization is apparent, specific details of this mechanism still remain elusive to experiments. Previous in silico studies successfully addressed some aspects (e.g., local structural effects, thermal stability, and early events of azobenzene photoisomerization) of this challenging molecular process characterized by timescales spanning several orders of magnitude, from picoseconds (i.e., azobenzene photoisomerization) to micro- and milli-seconds (i.e., complete strand detachment). In this work, inspired by a recent report by Asanuma and coworkers, we focus on the local and cooperativity effects played by multiple azobenzene units on a 10-mer azobenzene-modified DNA duplex. Using molecular dynamics (MD) simulations, we investigated nine systems equipped with a variable number (from 1 to 7) of photoswitch units and different configurations, focusing our analysis on the initial events (from few ps to hundreds of ns) characterizing DNA destabilization upon trans-to-cis isomerization, such as hydrogen bonding breakage and base pair misalignment. Results highlight, on one hand, the local effects of single azobenzene units on DNA duplex structure and, on the other hand, the cooperative role that multiple photoswitches show in enhancing and accelerating DNA dehybridization following trans-to-cis conversion, in agreement with previously reported data and observations.
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Affiliation(s)
- Nuno Barbosa
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Luca Sagresti
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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4
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Palmisano VF, Gómez-Rodellar C, Pollak H, Cárdenas G, Corry B, Faraji S, Nogueira JJ. Binding of azobenzene and p-diaminoazobenzene to the human voltage-gated sodium channel Na v1.4. Phys Chem Chem Phys 2021; 23:3552-3564. [PMID: 33514952 DOI: 10.1039/d0cp06140a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Nav1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel.
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Affiliation(s)
- Vito F Palmisano
- Department of Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.
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O’Neill RT, Boulatov R. The many flavours of mechanochemistry and its plausible conceptual underpinnings. Nat Rev Chem 2021; 5:148-167. [PMID: 37117533 DOI: 10.1038/s41570-020-00249-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2020] [Indexed: 12/12/2022]
Abstract
Mechanochemistry describes diverse phenomena in which mechanical load affects chemical reactivity. The fuzziness of this definition means that it includes processes as seemingly disparate as motor protein function, organic synthesis in a ball mill, reactions at a propagating crack, chemical actuation, and polymer fragmentation in fast solvent flows and in mastication. In chemistry, the rate of a reaction in a flask does not depend on how fast the flask moves in space. In mechanochemistry, the rate at which a material is deformed affects which and how many bonds break. In other words, in some manifestations of mechanochemistry, macroscopic motion powers otherwise endergonic reactions. In others, spontaneous chemical reactions drive mechanical motion. Neither requires thermal or electrostatic gradients. Distinct manifestations of mechanochemistry are conventionally treated as being conceptually independent, which slows the field in its transformation from being a collection of observations to a rigorous discipline. In this Review, we highlight observations suggesting that the unifying feature of mechanochemical phenomena may be the coupling between inertial motion at the microscale to macroscale and changes in chemical bonding enabled by transient build-up and relaxation of strains, from macroscopic to molecular. This dynamic coupling across multiple length scales and timescales also greatly complicates the conceptual understanding of mechanochemistry.
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7
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Hu Y, Xu C, Ye L, Gu FL, Zhu C. Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces. Phys Chem Chem Phys 2021; 23:5236-5243. [PMID: 33629668 DOI: 10.1039/d0cp06104b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation. The present TD(DFT) simulation provides accurate calculation for conical intersections between the first-excited and ground states. Thus, simulated quantum yield and lifetime of 0.23 and 620 fs (0.15 and 600 fs) for E-to-Z (Z-to-E) isomerization are in good (relatively good) agreement with experimental observation of 0.25 and 480 fs (0.24 and 430 fs), respectively. Simulated results reveal that photoisomerization pathways are initially uphill to conical intersection zones on the S1 potential energy surface and then downhill to product zones. Three types of representative conical intersections are found for determining photoisomerization mechanisms: one is the rotation type responsible for reactive isomerization and the other two are close to E and Z configurations, respectively, only for nonreactive isomerization. The present conclusions can be held in general for similar large NAIP systems of photoinduced isomerization based on E and Z configurations.
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Affiliation(s)
- Ying Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Linfeng Ye
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chaoyuan Zhu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan. and Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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8
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Gholamjani Moghaddam K, Giudetti G, Sipma W, Faraji S. Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex. Phys Chem Chem Phys 2020; 22:26944-26954. [PMID: 33206064 DOI: 10.1039/d0cp04392c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.
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9
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Yin YD, Zhang L, Leng XZ, Gu ZY. Harnessing biological nanopore technology to track chemical changes. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Klaja O, Frank JA, Trauner D, Bondar AN. Potential energy function for a photo-switchable lipid molecule. J Comput Chem 2020; 41:2336-2351. [PMID: 32749723 DOI: 10.1002/jcc.26387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/07/2020] [Accepted: 07/04/2020] [Indexed: 11/06/2022]
Abstract
Photo-switchable lipids are synthetic lipid molecules used in photo-pharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photo-switchable lipids interact with membranes or ion channels is poorly understood. To facilitate all-atom simulations that could provide a molecular picture of membranes with photo-switchable lipids, we derived force field parameters for atomistic computations of the azobenzene-based fatty acid FAAzo-4. We implemented a Phyton-based algorithm to make the optimization of atomic partial charges more efficient. Overall, the parameters we derived give good description of the equilibrium structure, torsional properties, and non-bonded interactions for the photo-switchable lipid in its trans and cis intermediate states, and crystal lattice parameters for trans-FAAzo-4. These parameters can be extended to all-atom descriptions of various photo-switchable lipids that have an azobenzene moiety.
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Affiliation(s)
- Oskar Klaja
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Berlin, Germany
| | - James A Frank
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York, USA
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Berlin, Germany
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11
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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12
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Garnier L, Sarraute S, Israëli Y, Bonal C, Malfreyt P. Associations of Water-Soluble Macrocyclic Hosts with 4-Aminoazobenzene: Impact of pH. J Phys Chem B 2018; 122:11953-11961. [PMID: 30466260 DOI: 10.1021/acs.jpcb.8b09127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An investigation of the pH effect on the inclusion complexes of β-cyclodextrins and calixarenesulfonates with 4-aminoazobenzene was conducted both by experiments and molecular simulations. The whole thermodynamic characterizations of the association between hosts and 4-aminoazobenzene ( K, Δr G0, Δr H0, and TΔr S0) were determined by UV-visible spectroscopy. β-Cyclodextrin inclusion complexes are not affected by pH change unlike those obtained with calixarenes. All the studied systems were enthalpically favored. Nevertheless, the entropic behavior is different depending on the host. In order to interpret these experimental results, molecular simulations were used to calculate the number of atoms inserted into the cage-like host compounds and the number of water molecules expelled from the cavity.
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Affiliation(s)
- Ludovic Garnier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand , France
| | - Sabine Sarraute
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand , France
| | - Yael Israëli
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand , France
| | - Christine Bonal
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand , France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand , F-63000 Clermont-Ferrand , France
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13
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Zhang H, Fu H, Shao X, Chipot C, Monari A, Dehez F, Cai W. Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions. Phys Chem Chem Phys 2018; 20:22645-22651. [PMID: 30132482 DOI: 10.1039/c8cp03836h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In biological environments and in aqueous solution, DNA generally adopts the canonical B conformation. Recently, an azobenzene photoswitch containing a polyamine chain with three positive charges was shown to induce a reversible conformational transition between the A and B forms of DNA, the transition being triggered by trans-cis isomerization of the photoswitch upon non-covalent intercalation. It was proposed that, in its trans conformation, azobenzene stabilizes the A form of DNA. The structural details and the mechanism upon which trans-azobenzene induces the B-to-A DNA transition remain, however, unclear. In the present work, two possible intercalating modes of trans-azobenzene, from the minor groove and from the major groove, were investigated with all-atom molecular-dynamics simulations. Intercalation from the major groove was found to be the most probable binding mode due to favorable electrostatic and π-π stacking interactions. The free-energy profile associated with the B-to-A conformational transition reveals that intercalation from the major groove leads to a conformational change of DNA, showing a slight tendency to interconvert from B- to A-DNA, in agreement with the CD spectrum obtained from the experiment. However, the presence of only one interacting azobenzene is not sufficient to lead to a global conformational change to A-DNA. The present results are expected to serve in the design of DNA switches, which can induce reversible DNA conformational changes.
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Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.
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Zhang P, Jiang J, Yuan R, Zhuo Y, Chai Y. Highly Ordered and Field-Free 3D DNA Nanostructure: The Next Generation of DNA Nanomachine for Rapid Single-Step Sensing. J Am Chem Soc 2018; 140:9361-9364. [DOI: 10.1021/jacs.8b04648] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Pu Zhang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Jie Jiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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15
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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16
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Wu D, Wang YT, Fang WH, Cui G, Thiel W. QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role. Chem Asian J 2018; 13:780-784. [PMID: 29446260 DOI: 10.1002/asia.201800006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/07/2018] [Indexed: 01/10/2023]
Abstract
The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S1 state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.
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Affiliation(s)
- Dan Wu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ya-Ting Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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17
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Hu ZL, Li ZY, Ying YL, Zhang J, Cao C, Long YT, Tian H. Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore. Anal Chem 2018. [PMID: 29516718 DOI: 10.1021/acs.analchem.8b00096] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min-1, respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.
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Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Zi-Yuan Li
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
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18
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Makarov DE. Perspective: Mechanochemistry of biological and synthetic molecules. J Chem Phys 2016; 144:030901. [PMID: 26801011 DOI: 10.1063/1.4939791] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.
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Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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19
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Stauch T, Dreuw A. Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis. Chem Rev 2016; 116:14137-14180. [PMID: 27767298 DOI: 10.1021/acs.chemrev.6b00458] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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20
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Zhang J, Yan Y, Samai S, Ginger DS. Dynamic Melting Properties of Photoswitch-Modified DNA: Shearing versus Unzipping. J Phys Chem B 2016; 120:10706-10713. [DOI: 10.1021/acs.jpcb.6b08297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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21
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Chandramouli B, Di Maio D, Mancini G, Brancato G. Introducing an artificial photo-switch into a biological pore: A model study of an engineered α-hemolysin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:689-97. [DOI: 10.1016/j.bbamem.2015.12.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 12/06/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022]
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22
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Yan Y, Samai S, Bischoff KL, Zhang J, Ginger DS. Photocontrolled DNA Hybridization Stringency with Fluorescence Detection in Heterogeneous Assays. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Kristi L. Bischoff
- Mel
and Enid Zuckerman College of Public Heath, University of Arizona, Tucson, Arizona 85724, United States
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23
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24
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Thevarpadam J, Bessi I, Binas O, Gonçalves DPN, Slavov C, Jonker HRA, Richter C, Wachtveitl J, Schwalbe H, Heckel A. Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif. Angew Chem Int Ed Engl 2016; 55:2738-42. [PMID: 26805928 DOI: 10.1002/anie.201510269] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/11/2015] [Indexed: 01/04/2023]
Abstract
The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+) ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.
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Affiliation(s)
- Julie Thevarpadam
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Irene Bessi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Diana P N Gonçalves
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Chavdar Slavov
- Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Hendrik R A Jonker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
| | - Alexander Heckel
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
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25
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Thevarpadam J, Bessi I, Binas O, Gonçalves DPN, Slavov C, Jonker HRA, Richter C, Wachtveitl J, Schwalbe H, Heckel A. Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510269] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Julie Thevarpadam
- Goethe University Frankfurt; Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences; Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Irene Bessi
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Diana P. N. Gonçalves
- Goethe University Frankfurt; Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences; Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Chavdar Slavov
- Institute for Physical and Theoretical Chemistry; Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry; Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Alexander Heckel
- Goethe University Frankfurt; Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences; Max-von-Laue-Strasse 9 60438 Frankfurt Germany
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26
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Stauch T, Dreuw A. Stiff-stilbene photoswitch ruptures bonds not by pulling but by local heating. Phys Chem Chem Phys 2016; 18:15848-53. [PMID: 27228965 DOI: 10.1039/c6cp02395a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The forces generated by stiff-stilbene during photoswitching are too low to cause bond rupture, which is instead initiated by heating.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing
- 69120 Heidelberg
- Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing
- 69120 Heidelberg
- Germany
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27
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Hu D, Huang J, Xie Y, Yue L, Zhuang X, Lan Z. Nonadiabatic dynamics and photoisomerization of biomimetic photoswitches. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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28
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Liu K, Wen Y, Shi T, Li Y, Li F, Zhao YL, Huang C, Yi T. DNA gated photochromism and fluorescent switch in a thiazole orange modified diarylethene. Chem Commun (Camb) 2015; 50:9141-4. [PMID: 24989898 DOI: 10.1039/c4cc02783c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Thiazole orange-modified diarylethene (1) shows weak fluorescence but no photochromism in aqueous solution. When binding with DNA, the fluorescence of 1 is enhanced drastically and the photochromic reactivity is unlocked. This kind of DNA-responsive photoswitchable system can be used for imaging nucleic acids within cells.
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Affiliation(s)
- Keyin Liu
- Department of Chemistry, and Concerted Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China.
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29
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30
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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31
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Konda SSM, Avdoshenko SM, Makarov DE. Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules. J Chem Phys 2014; 140:104114. [PMID: 24628159 DOI: 10.1063/1.4867500] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a method for computing the activation barrier for chemical reactions involving molecules subjected to mechanical stress. The method avoids reactant and transition-state saddle optimizations at every force by, instead, solving the differential equations governing the force dependence of the critical points (i.e., minima and saddles) on the system's potential energy surface (PES). As a result, only zero-force geometry optimization (or, more generally, optimization performed at a single force value) is required by the method. In many cases, minima and transition-state saddles only exist within a range of forces and disappear beyond a certain critical point. Our method identifies such force-induced instabilities as points at which one of the Hessian eigenvalues vanishes. We elucidate the nature of those instabilities as fold and cusp catastrophes, where two or three critical points on the force-modified PES coalesce, and provide a classification of various physically distinct instability scenarios, each illustrated with a concrete chemical example.
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Affiliation(s)
| | - Stanislav M Avdoshenko
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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32
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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33
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Parker SM, Smeu M, Franco I, Ratner MA, Seideman T. Molecular junctions: can pulling influence optical controllability? NANO LETTERS 2014; 14:4587-4591. [PMID: 25072807 DOI: 10.1021/nl501629c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We suggest the combination of single molecule pulling and optical control as a way to enhance control over the electron transport characteristics of a molecular junction. We demonstrate using a model junction consisting of biphenyl-dithiol coupled to gold contacts. The junction is pulled while optically manipulating the dihedral angle between the two rings. Quantum dynamics simulations show that molecular pulling enhances the degree of control over the dihedral angle and hence over the transport properties.
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Affiliation(s)
- Shane M Parker
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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34
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Rivero D, Fernández-González MÁ, Frutos LM. Tuning molecular excitation energy with external forces. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
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Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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36
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Zapata F, Fernández-González MÁ, Rivero D, Álvarez Á, Marazzi M, Frutos LM. Toward an Optomechanical Control of Photoswitches by Tuning Their Spectroscopical Properties: Structural and Dynamical Insights into Azobenzene. J Chem Theory Comput 2014; 10:312-23. [DOI: 10.1021/ct4007629] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Felipe Zapata
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Miguel Ángel Fernández-González
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Daniel Rivero
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Ángel Álvarez
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Marco Marazzi
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Luis Manuel Frutos
- Departamento de Química
Analítica, Química Física e Ingeniería
Química, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
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37
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Yan Y, Wang X, Chen JIL, Ginger DS. Photoisomerization Quantum Yield of Azobenzene-Modified DNA Depends on Local Sequence. J Am Chem Soc 2013; 135:8382-7. [DOI: 10.1021/ja403249u] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | - Xin Wang
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | | | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
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38
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Zhang J, Zou Q, Tian H. Photochromic materials: more than meets the eye. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:378-99. [PMID: 22911949 DOI: 10.1002/adma.201201521] [Citation(s) in RCA: 500] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Indexed: 05/12/2023]
Abstract
Photochromic materials are a family of compounds which can undergo reversible photo-switches between two different states or isomers with remarkably different properties. Inspired by their smart photo-switchable characteristics, a variety of light-driven functional materials have been exploited, such as ultrahigh-density optical data storage, molecular switches, logic gates, molecular wires, optic/electronic devices, sensors, bio-imaging and so on. This review commences with a brief description of exciting progress in this field, from systems in solution to modified functional surfaces. Further development of these photo-switchable systems into practical applications as well as existing challenges are also discussed and put in prospect.
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Affiliation(s)
- Junji Zhang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China
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39
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Ulrich S, Dumy P, Boturyn D, Renaudet O. Engineering of biomolecules for sensing and imaging applications. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50001-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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Naserian-Nik AM, Tahani M, Karttunen M. Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details. RSC Adv 2013. [DOI: 10.1039/c3ra23213a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Yan Y, Chen JIL, Ginger DS. Photoswitchable oligonucleotide-modified gold nanoparticles: controlling hybridization stringency with photon dose. NANO LETTERS 2012; 12:2530-2536. [PMID: 22493996 DOI: 10.1021/nl300739n] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a new class of stimulus-responsive DNA-functionalized gold nanoparticles that incorporate azobenzene-modified oligonucleotides. Beyond the classic directed assembly and sensing behaviors associated with oligonucleotide-modified nanoparticles, these particles also exhibit reversible photoswitching of their assembly behavior. Exposure to UV light induces a trans-cis isomerization of the azobenzene which destabilizes the DNA duplex, resulting in dissociation of the nanoparticle assemblies. The isomerization is reversible upon exposure to blue light, resulting in rehybridization and reassembly of the DNA-linked nanoparticle clusters. We show that perfectly complementary and partially mismatched strands exhibit clearly distinguishable photoinduced melting properties, and we demonstrate that photon dose can thus be used in place of temperature or ionic strength to control hybridization stringency with the ability to discriminate single-base mismatches.
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Affiliation(s)
- Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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Teng MJ, Jia XR, Yang S, Chen XF, Wei Y. Reversible tuning luminescent color and emission intensity: a dipeptide-based light-emitting material. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:1255-61. [PMID: 22298129 DOI: 10.1002/adma.201104592] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 12/27/2011] [Indexed: 05/05/2023]
Abstract
A smart luminescent material whose emission color and emission intensity can be separately modulated by external force is demonstrated. The rational manipulation of rich noncovalent interactions and fluorophore packing style promotes an in-depth understanding between supramolecular structure and photophysical property and offers an effective strategy to modulate the light-emitting property in a predicative way.
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Affiliation(s)
- Ming-Jun Teng
- Beijing National Laboratory for Molecular Sciences and Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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Menghetti S, Alderighi M, Galli G, Tantussi F, Morandini M, Fuso F, Allegrini M. All-optical pulsed writing in azobenzene copolymer films in the sub-millisecond regime. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm30596h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Konda SSM, Brantley JN, Bielawski CW, Makarov DE. Chemical reactions modulated by mechanical stress: Extended Bell theory. J Chem Phys 2011; 135:164103. [DOI: 10.1063/1.3656367] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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