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Han M, Zhang W, Lu L, Ma S, Feng S. Enhanced Ultrasensitive Photoelectrochemical Probe for Phosphate Detection in Water Based on a Zirconium-Porphyrin Framework. ACS APPLIED MATERIALS & INTERFACES 2022; 14:28280-28288. [PMID: 35686366 DOI: 10.1021/acsami.2c04645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Excessive phosphate poses a serious ecological and human health risk, and thereby, monitoring its trace concentration is of great significance to environmental protection and human health. In this work, a zirconium-porphyrin framework (PCN-222) with excellent stability and unique luminescence properties was designed to modify the surface of the indium tin oxide electrode, which was first used as a photoelectrochemical (PEC) probe for phosphate detection. The PCN-222-modified PEC probe demonstrated an excellent selectivity and stability and indicated a linear response to phosphate in the range of 0-106 nM with a limit of detection (LOD) as low as 1.964 nM. To the best of our knowledge, this is the phosphate probe with the lowest LOD, and this is also the first signal-on PEC probe toward phosphate based on PCN-222. More importantly, the PEC probe can be validated for the good applicability of trace phosphate detection in real water samples, indicating a good application prospect. Finally, a series of electrochemical and spectroscopic studies have proved that phosphate can bind to the indium tin oxide (ITO)/PCN-222 electrode, which shortens the distance of the space charge region while reducing the bandwidth and thus facilitates the transfer of photogenerated electrons across the energy band barrier to reduce O2 in the electrolyte, producing an enhanced cathodic photocurrent signal. The proposed strategy of the highly sensitive PEC probe provides a promising platform for more effective label-free phosphate monitoring in the environment and organisms.
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Affiliation(s)
- Meirong Han
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
| | - Weijie Zhang
- Department of Chemistry, University of North Texas CHEM 305D, 1508 W Mulberry St, Denton, Texas 76201, United States
| | - Liping Lu
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
- Key Laboratory of Materials for Energy Conversion and Storage of Shanxi Province, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
| | - Shengqian Ma
- Department of Chemistry, University of North Texas CHEM 305D, 1508 W Mulberry St, Denton, Texas 76201, United States
| | - Sisi Feng
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of the Education Ministry, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
- Key Laboratory of Materials for Energy Conversion and Storage of Shanxi Province, Shanxi University, Taiyuan, Shanxi 030006, P. R. China
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2
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Moumen E, Bazzi L, El Hankari S. Metal-organic frameworks and their composites for the adsorption and sensing of phosphate. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214376] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Fingerhut BP, Schauss J, Kundu A, Elsaesser T. Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation. Biophys J 2021; 120:5322-5332. [PMID: 34715079 PMCID: PMC8715182 DOI: 10.1016/j.bpj.2021.10.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg2+) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg2+ pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg2+ ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg2+-excess concentrations and comparison with fluorescence titration measurements shows that on average 20-30% of the Mg2+ ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.
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4
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Ma CY, Pezzotti S, Schwaab G, Gebala M, Herschlag D, Havenith M. Cation enrichment in the ion atmosphere is promoted by local hydration of DNA. Phys Chem Chem Phys 2021; 23:23203-23213. [PMID: 34622888 PMCID: PMC8797164 DOI: 10.1039/d1cp01963e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrostatic interactions are central to the structure and function of nucleic acids, including their folding, condensation, and interaction with proteins and other charged molecules. These interactions are profoundly affected by ions surrounding nucleic acids, the constituents of the so-called ion atmosphere. Here, we report precise Fourier Transform-Terahertz/Far-Infrared (FT-THz/FIR) measurements in the frequency range 30-500 cm-1 for a 24-bp DNA solvated in a series of alkali halide (NaCl, NaF, KCl, CsCl, and CsF) electrolyte solutions which are sensitive to changes in the ion atmosphere. Cation excess in the ion atmosphere is detected experimentally by observation of cation modes of Na+, K+, and Cs+ in the frequency range between 70-90 cm-1. Based on MD simulations, we propose that the magnitude of cation excess (which is salt specific) depends on the ability of the electrolyte to perturb the water network at the DNA interface: In the NaF atmosphere, the ions reduce the strength of interactions between water and the DNA more than in case of a NaCl electrolyte. Here, we explicitly take into account the solvent contribution to the chemical potential in the ion atmosphere: A decrease in the number of bound water molecules in the hydration layer of DNA is correlated with enhanced density fluctuations, which decrease the free energy cost of ion-hydration, thus promoting further ion accumulation within the DNA atmosphere. We propose that taking into account the local solvation is crucial for understanding the ion atmosphere.
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Affiliation(s)
- Chun Yu Ma
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany.
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany.
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany.
| | - Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany.
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5
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Elsaesser T, Schauss J, Kundu A, Fingerhut BP. Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions. J Phys Chem B 2021; 125:3899-3908. [PMID: 33834783 PMCID: PMC8154594 DOI: 10.1021/acs.jpcb.1c01502] [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] [Indexed: 11/29/2022]
Abstract
![]()
Electric interactions
have a strong impact on the structure and
dynamics of biomolecules in their native water environment. Given
the variety of water arrangements in hydration shells and the femto-
to subnanosecond time range of structural fluctuations, there is a
strong quest for sensitive noninvasive probes of local electric fields.
The stretching vibrations of phosphate groups, in particular the asymmetric
(PO2)− stretching vibration νAS(PO2)−, allow for a quantitative
mapping of dynamic electric fields in aqueous environments via a field-induced
redshift of their transition frequencies and concomitant changes of
vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular
systems of increasing complexity, including dimethyl phosphate (DMP),
short DNA and RNA duplex structures, and transfer RNA (tRNA) in water.
A combination of linear infrared absorption, two-dimensional infrared
(2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives
quantitative insight in electric-field tuning rates of vibrational
frequencies, electric field and fluctuation amplitudes, and molecular
interaction geometries. Beyond neat water environments, the formation
of contact ion pairs of phosphate groups with Mg2+ ions
is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct
vibrational band. The frequency positions of contact geometries are
determined by an interplay of attractive electric and repulsive exchange
interactions.
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Affiliation(s)
- Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin 12489, Germany
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Benassi JC, Barbosa FAR, Grinevicius VMAS, Ourique F, Coelho D, Felipe KB, Braga AL, Filho DW, Pedrosa RC. Novel Dihydropyrimidinone-Derived Selenoesters as Potential Cytotoxic Agents to Human Hepatocellular Carcinoma: Molecular Docking and DNA Fragmentation. Anticancer Agents Med Chem 2021; 21:703-715. [PMID: 32723262 DOI: 10.2174/1871520620666200728124640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/18/2020] [Accepted: 05/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVE Evidence point out promising anticancer activities of Dihydropyrimidinones (DHPM) and organoselenium compounds. This study aimed to evaluate the cytotoxic and antiproliferative potential of DHPM-derived selenoesters (Se-DHPM), as well as their molecular mechanisms of action. METHODS Se-DHPM cytotoxicity was evaluated against cancer lines (HeLa, HepG2, and MCF-7) and normal cells (McCoy). HepG2 clonogenic assay allowed verifying antiproliferative effects. The propidium iodide/ orange acridine fluorescence readings showed the type of cell death induced after treatments (72h). Molecular simulations with B-DNA and 49H showed docked positions (AutoDock Vina) and trajectories/energies (GROMACS). In vitro molecular interactions used CT-DNA and 49H applying UV-Vis absorbance and fluorescence. Comet assay evaluated DNA fragmentation of HepG2 cells. Flow cytometry analysis verified HepG2 cell cycle effects. Levels of proteins (β-actin, p53, BAX, HIF-1α, γH2AX, PARP-1, cyclin A, CDK-2, and pRB) were quantified by immunoblotting. RESULTS Among Se-DHPM, 49H was selectively cytotoxic to HepG2 cells, reduced cell proliferation, and increased BAX (80%), and p53 (66%) causing apoptosis. Molecular assays revealed 49H inserted in the CT-DNA molecule causing the hypochromic effect. Docking simulations showed H-bonds and hydrophobic interactions, which kept the ligand partially inserted into the DNA minor groove. 49H increased the DNA damage (1.5 fold) and γH2AX level (153%). Besides, treatments reduced PARP-1 (60%) and reduced pRB phosphorylation (21%) as well as decreased cyclin A (46%) arresting cell cycle at the G1 phase. CONCLUSION Together all data obtained confirmed the hypothesis of disruptive interactions between Se-DHPM and DNA, thereby highlighting its potential as a new anticancer drug.
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Affiliation(s)
- Jean C Benassi
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Flavio A R Barbosa
- Department of Chemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Fabiana Ourique
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Daniela Coelho
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Karina B Felipe
- Departament of Clinical Analysis, Federal University of Parana, Curitiba, Brazil
| | - Antônio L Braga
- Department of Chemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Danilo W Filho
- Departament of Ecology and Zoology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rozangela C Pedrosa
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
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7
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Aqueous Contact Ion Pairs of Phosphate Groups with Na+, Ca2+ and Mg2+ – Structural Discrimination by Femtosecond Infrared Spectroscopy and Molecular Dynamics Simulations. Z PHYS CHEM 2020. [DOI: 10.1515/zpch-2020-1614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
The extent of contact and solvent shared ion pairs of phosphate groups with Na+, Ca2+ and Mg2+ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spectra, the nonlinear spectra reveal contact ion pairs with increased sensitivity because the spectra accentuate differences in peak frequency, transition dipole moment strength, and excited state lifetime. The experimental results are corroborated by long time scale MD simulations, benchmarked by density functional simulations on phosphate-ion-water clusters. The microscopic interpretation reveals subtle structural differences of ion pairs formed by the phosphate group and the ions Na+, Ca2+ and Mg2+. Intricate properties of the solvation shell around the phosphate group and the ion are essential to explain the experimental observations. The present work addresses a challenging to probe topic with the help of a model system and establishes new experimental data of contact ion pair formation, thereby underlining the potential of nonlinear 2D-IR spectroscopy as an analytical probe of phosphate-ion interactions in complex biological systems.
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Chalyavi F, Adeyiga O, Weiner JM, Monzy JN, Schmitz AJ, Nguyen JK, Fenlon EE, Brewer SH, Odoh SO, Tucker MJ. 2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks. J Chem Phys 2020; 152:074201. [PMID: 32087671 PMCID: PMC7028433 DOI: 10.1063/1.5138654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Olajumoke Adeyiga
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Julia M. Weiner
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Judith N. Monzy
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Andrew J. Schmitz
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Justin K. Nguyen
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Edward E. Fenlon
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, Lancaster, Pennsylvania 17604-3003, USA
| | - Samuel O. Odoh
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89557, USA
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9
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Fritzsch R, Greetham GM, Clark IP, Minnes L, Towrie M, Parker AW, Hunt NT. Monitoring Base-Specific Dynamics during Melting of DNA-Ligand Complexes Using Temperature-Jump Time-Resolved Infrared Spectroscopy. J Phys Chem B 2019; 123:6188-6199. [PMID: 31268327 DOI: 10.1021/acs.jpcb.9b04354] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ultrafast time-resolved infrared spectroscopy employing nanosecond temperature-jump initiation has been used to study the melting of double-stranded (ds)DNA oligomers in the presence and absence of minor groove-binding ligand Hoechst 33258. Ligand binding to ds(5'-GCAAATTTCC-3'), which binds Hoechst 33258 in the central A-tract region with nanomolar affinity, causes a dramatic increase in the timescales for strand melting from 30 to ∼250 μs. Ligand binding also suppresses premelting disruption of the dsDNA structure, which takes place on 100 ns timescales and includes end-fraying. In contrast, ligand binding to the ds(5'-GCATATATCC-3') sequence, which exhibits an order of magnitude lower affinity for Hoechst 33258 than the A-tract motif, leads to an increase by only a factor of 5 in melting timescales and reduced suppression of premelting sequence perturbation and end-fraying. These results demonstrate a dynamic impact of the minor groove ligand on the dsDNA structure that correlates with binding strength and thermodynamic stabilization of the duplex. Moreover, the ability of the ligand to influence base pairs distant from the binding site has potential implications for allosteric communication mechanisms in dsDNA.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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10
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Schauss J, Dahms F, Fingerhut BP, Elsaesser T. Phosphate-Magnesium Ion Interactions in Water Probed by Ultrafast Two-Dimensional Infrared Spectroscopy. J Phys Chem Lett 2019; 10:238-243. [PMID: 30599134 DOI: 10.1021/acs.jpclett.8b03568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electric interactions between ions and ionic molecular groups in aqueous solution play a fundamental role in chemistry and biology. While Mg2+ ions are known to strongly affect the structure and folding dynamics of biomolecules, the relevance of different solvation geometries and the underlying interactions are mainly unresolved. We study dynamics and couplings between the hydrated Mg2+ and the dimethylphosphate anion, an established model system for the DNA and RNA backbone. The asymmetric (PO2-) stretching vibration serves as a sensitive noninvasive probe of phosphate-ion interactions. Femtosecond two-dimensional infrared (2D-IR) spectroscopy directly maps Mg2+ ions in contact with the phosphate groups via a distinct blue-shifted signature in the 2D spectrum. Data for different Mg2+ concentrations are analyzed by microscopic density functional theory modeling of cluster geometries and associated spectroscopic features, providing spatial assignments of the observed 2D-IR signatures. Phosphate-ion interactions arising from electrostatic Coulomb forces and exchange repulsion are the predominant origin of the observed frequency shifts.
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Affiliation(s)
- Jakob Schauss
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Fabian Dahms
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Berlin 12489 , Germany
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11
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Szymborska-Małek K, Komorowska M, Gąsior-Głogowska M. Effects of Near Infrared Radiation on DNA. DLS and ATR-FTIR Study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:258-267. [PMID: 28723592 DOI: 10.1016/j.saa.2017.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/13/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100nm) for 5, 10, and 20min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation. For the NIR-treated samples (at room temperature) the B form was better conserved than in the control sample independently of the irradiation period. Above 50°C a considerable increase in the A form was only observed for 10min NIR exposed samples. The hydrodynamic radius, (Rh), studied by the dynamic light scattering, showed drastic decrease with the increasing irradiation time. Principal components analysis (PCA) allowed to detect the spectral features correlated with the NIR effect and thermal stability of the DNA films. Obtained results strongly support the idea that the photoionization of water by NIR radiation in presence of DNA molecules is the main factor influencing on its physicochemical properties.
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Affiliation(s)
- Katarzyna Szymborska-Małek
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Box 1410, 50-950 Wroclaw 2, Poland
| | - Małgorzata Komorowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland.
| | - Marlena Gąsior-Głogowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland
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12
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Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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13
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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14
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Liu Y, Guchhait B, Siebert T, Fingerhut BP, Elsaesser T. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044015. [PMID: 28405593 PMCID: PMC5384856 DOI: 10.1063/1.4980075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/31/2017] [Indexed: 05/15/2023]
Abstract
Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.
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Affiliation(s)
- Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
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15
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Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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16
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Siebert T, Guchhait B, Liu Y, Fingerhut BP, Elsaesser T. Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface. J Phys Chem Lett 2016; 7:3131-6. [PMID: 27468144 DOI: 10.1021/acs.jpclett.6b01369] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Range and magnitude of electric fields at biomolecular interfaces and their fluctuations in a time window down to the subpicosecond regime have remained controversial, calling for electric-field mapping in space and time. Here, we trace fluctuating electric fields at the surface of native salmon DNA via their interactions with backbone vibrations in a wide range of hydration levels by building the water shell layer by layer. Femtosecond two-dimensional infrared spectroscopy and ab initio based theory establish water molecules in the first two layers as the predominant source of interfacial electric fields, which fluctuate on a 300 fs time scale with an amplitude of 25 MV/cm due to thermally excited water motions. The observed subnanometer range of these electric interactions is decisive for biochemical structure and function.
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Affiliation(s)
- Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
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17
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Guchhait B, Liu Y, Siebert T, Elsaesser T. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:043202. [PMID: 26798841 PMCID: PMC4720115 DOI: 10.1063/1.4936567] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/12/2015] [Indexed: 05/28/2023]
Abstract
DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.
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Affiliation(s)
- Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin, Germany
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18
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Hithell G, Shaw DJ, Donaldson PM, Greetham GM, Towrie M, Burley GA, Parker AW, Hunt NT. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA. J Phys Chem B 2016; 120:4009-18. [PMID: 27079484 DOI: 10.1021/acs.jpcb.6b02112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.
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Affiliation(s)
- Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Daniel J Shaw
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M Donaldson
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Gregory M Greetham
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Michael Towrie
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Anthony W Parker
- Research Complex at Harwell, Harwell Science and Innovation Campus, STFC Central Laser Facility , Didcot OX11 0QX, U.K
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, U.K
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19
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Siebert T, Guchhait B, Liu Y, Costard R, Elsaesser T. Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA–Water Interface. J Phys Chem B 2015; 119:9670-7. [DOI: 10.1021/acs.jpcb.5b04499] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Torsten Siebert
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2a, D-12489 Berlin, Germany
| | - Biswajit Guchhait
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2a, D-12489 Berlin, Germany
| | - Yingliang Liu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2a, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2a, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2a, D-12489 Berlin, Germany
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20
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Costard R, Tyborski T, Fingerhut BP, Elsaesser T. Ultrafast phosphate hydration dynamics in bulk H2O. J Chem Phys 2015; 142:212406. [DOI: 10.1063/1.4914152] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Tobias Tyborski
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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21
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Costard R, Tyborski T, Fingerhut BP. Anharmonicities and coherent vibrational dynamics of phosphate ions in bulk H2O. Phys Chem Chem Phys 2015; 17:29906-17. [DOI: 10.1039/c5cp04502a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2D IR spectroscopy reveals Fermi resonances and long lived quantum beats for phosphate ions in water.
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Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin
- Germany
| | - Tobias Tyborski
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin
- Germany
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie
- D-12489 Berlin
- Germany
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22
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Ashihara S. ELECTROCHEMISTRY 2014; 82:762-765. [DOI: 10.5796/electrochemistry.82.762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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23
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Greve C, Elsaesser T. Ultrafast two-dimensional infrared spectroscopy of guanine-cytosine base pairs in DNA oligomers. J Phys Chem B 2013; 117:14009-17. [PMID: 24127664 DOI: 10.1021/jp408229k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
NH and OH stretching excitations of hydrated double-stranded DNA oligomers containing guanine-cytosine (GC) base pairs in a Watson-Crick geometry are studied by two-dimensional (2D) infrared spectroscopy. The 2D spectra measured at a low hydration level (∼4 water molecules/base pair) are dominated by NH stretch contributions from the NH2 groups of G and C and the NH group of G. Partially hydrated NH2 groups display red-shifted NH stretch frequencies and a mixing of the wave functions of the two local NH oscillators via the mechanical vibrational coupling. The NH stretch lifetimes are of the order of 200-300 fs. Weak couplings exist between NH stretch oscillators within a base pair, while interactions between neighboring GC pairs in the double helix are negligible. The absence of spectral diffusion on a 1 ps time scale suggests a relatively rigid structure of the hydrogen bonds between DNA and residual water molecules. 2D spectra recorded with fully hydrated DNA oligomers exhibit NH and OH stretch contributions with a weak influence of water fluctuations on the NH stretch lineshapes. The femtosecond spectral diffusion of OH stretch excitations is slower than that in bulk H2O and originates from structural fluctuations of the water shell and the formation of a vibrationally hot ground state by vibrational relaxation. We compare our findings with measurements on hydrated adenine-thymine DNA oligomers and anhydrous GC base pairs in solution.
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Affiliation(s)
- Christian Greve
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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24
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Dwyer JR, Szyc Ł, Nibbering ETJ, Elsaesser T. Note: an environmental cell for transient spectroscopy on solid samples in controlled atmospheres. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:036101. [PMID: 23556853 DOI: 10.1063/1.4794092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A sample cell for performing time-resolved spectroscopy on solid samples within an atmosphere of controlled vapor composition was designed and constructed. Control over vapor composition was accomplished using a combination of passive sealing and chemical agents. Performance characteristics especially well-suited to studies using femtosecond mid-infrared spectroscopy were achieved by the use of ultrathin silicon nitride windows and a rapid and reproducible sample cell exchange mechanism.
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Affiliation(s)
- Jason R Dwyer
- Department of Chemistry, 51 Lower College Rd., University of Rhode Island, Kingston, Rhode Island 02881, USA.
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25
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Elsaesser T, Szyc Ł, Yang M. Ultrafast structural and vibrational dynamics of the hydration shell around DNA. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134106004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Costard R, Greve C, Heisler IA, Elsaesser T. Ultrafast Energy Redistribution in Local Hydration Shells of Phospholipids: A Two-Dimensional Infrared Study. J Phys Chem Lett 2012; 3:3646-3651. [PMID: 26291000 DOI: 10.1021/jz3018978] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structural and functional properties of phospholipids are strongly influenced by dynamics of their hydration shells. Here, we show that local water pools as small as three water molecules around the polar headgroups in phospholipid reverse micelles (dioleoylphosphatidylcholine, DOPC) serve as efficient sinks of excess energy released during vibrational relaxation. Transient two-dimensional (2D) infrared spectra of OH stretching excitations of H2O shells demonstrate a subpicosecond buildup of a hot water ground state, in which excess energy is randomized in low-frequency modes. An analysis of center line slopes of the 2D spectra reveals kinetics of energy dissipation that are significantly faster than structural fluctuations of the water pool and remain unchanged at intermediate hydration levels between three and eight water molecules per polar headgroup. Our results suggest that confined small water pools in biomolecular systems are sufficient to dissipate excess energy originating from the decay of electronic or vibrational excitations.
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Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
| | - Christian Greve
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
| | - Ismael A Heisler
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
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27
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Costard R, Levinger NE, Nibbering ETJ, Elsaesser T. Ultrafast Vibrational Dynamics of Water Confined in Phospholipid Reverse Micelles. J Phys Chem B 2012; 116:5752-9. [DOI: 10.1021/jp3039016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 A, D-12489 Berlin, Germany
| | - Nancy E. Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
| | - Erik T. J. Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 A, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Str. 2 A, D-12489 Berlin, Germany
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28
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Yang M, Szyc Ł, Elsaesser T. Vibrational dynamics of the water shell of DNA studied by femtosecond two-dimensional infrared spectroscopy. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Yang M, Szyc Ł, Elsaesser T. Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy. J Phys Chem B 2011; 115:13093-100. [PMID: 21972952 DOI: 10.1021/jp208166w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.
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Affiliation(s)
- Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany
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30
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Levinger NE, Costard R, Nibbering ETJ, Elsaesser T. Ultrafast energy migration pathways in self-assembled phospholipids interacting with confined water. J Phys Chem A 2011; 115:11952-9. [PMID: 21928826 DOI: 10.1021/jp206099a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phospholipids self-assembled into reverse micelles in benzene are introduced as a new model system to study elementary processes relevant for energy transport in hydrated biological membranes. Femtosecond vibrational spectroscopy gives insight into the dynamics of the antisymmetric phosphate stretching vibration ν(AS)(PO(2))(-), a sensitive probe of local phosphate-water interactions and energy transport. The decay of the ν(AS)(PO(2))(-) mode with a 300-fs lifetime transfers excess energy to a subgroup of phospholipid low-frequency modes, followed by redistribution among phospholipid vibrations within a few picoseconds. The latter relaxation is accelerated by adding a confined water pool, an efficient heat sink in which the excess energy induces weakening or breaking of water-water and water-phospholipid hydrogen bonds. In parallel to vibrational relaxation, resonant energy transfer between ν(AS)(PO(2))(-) oscillators delocalizes the initial excitation.
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Affiliation(s)
- Nancy E Levinger
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany.
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31
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Yang M, Szyc Ł, Elsaesser T. Femtosecond Two-Dimensional Infrared Spectroscopy of Adenine-Thymine Base Pairs in DNA Oligomers. J Phys Chem B 2011; 115:1262-7. [DOI: 10.1021/jp1090697] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
| | - Łukasz Szyc
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
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