1
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Meng W, Peng HC, Liu Y, Stelling A, Wang L. Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels. J Phys Chem B 2023; 127:2351-2361. [PMID: 36898003 DOI: 10.1021/acs.jpcb.2c08915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The carbonyl stretching modes have been widely used in linear and two-dimensional infrared (IR) spectroscopy to probe the conformation, interaction, and biological functions of nucleic acids. However, due to their universal appearance in nucleobases, the IR absorption bands of nucleic acids are often highly congested in the 1600-1800 cm-1 region. Following the fruitful applications in proteins, 13C isotope labels have been introduced to the IR measurements of oligonucleotides to reveal their site-specific structural fluctuations and hydrogen bonding conditions. In this work, we combine recently developed frequency and coupling maps to develop a theoretical strategy that models the IR spectra of oligonucleotides with 13C labels directly from molecular dynamics simulations. We apply the theoretical method to nucleoside 5'-monophosphates and DNA double helices and demonstrate how elements of the vibrational Hamiltonian determine the spectral features and their changes upon isotope labeling. Using the double helices as examples, we show that the calculated IR spectra are in good agreement with experiments and the 13C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.
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Affiliation(s)
- Wenting Meng
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Allison Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
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2
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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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3
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Zolotoukhina T, Yamada M, Iwakura S. Vibrational Spectra of Nucleotides in the Presence of the Au Cluster Enhancer in MD Simulation of a SERS Sensor. BIOSENSORS 2021; 11:37. [PMID: 33572778 PMCID: PMC7911439 DOI: 10.3390/bios11020037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/29/2022]
Abstract
Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm-1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20-nucleotide interaction have been evaluated.
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Affiliation(s)
- Tatiana Zolotoukhina
- Department of Mechanical Engineering, University of Toyama, Toyama 930-8555, Japan
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4
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Price DA, Kartje ZJ, Hughes JA, Hill TD, Loth TM, Watts JK, Gagnon KT, Moran SD. Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G-Quadruplexes. Chembiochem 2020; 21:2792-2804. [PMID: 32372560 DOI: 10.1002/cbic.202000136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Infrared spectroscopy detects the formation of G-quadruplexes in guanine-rich nucleic acid sequences through shifts in the guanine C=O stretch mode. Here, we use ultrafast 2D infrared (IR) spectroscopy and isotope substitution to show that these shifts arise from vibrational delocalization among stacked G-quartets. This provides a direct measure of the sizes of locally ordered motifs in heterogeneous samples with substantial disordered regions. We find that parallel-stranded, potassium-bound DNA G-quadruplexes are limited to five consecutive G-quartets and 3-4 consecutive layers are preferred for longer polyguanine tracts. The resulting potassium-dependent G-quadruplex assembly landscape reflects the polyguanine tract lengths found in genomes, the ionic conditions prevalent in healthy mammalian cells, and the onset of structural disorder in disease states. Our study describes spectral markers that can be used to probe other G-quadruplex structures and provides insight into the fundamental limits of their formation in biological and artificial systems.
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Affiliation(s)
- David A Price
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Joanna A Hughes
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Tayler D Hill
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Taylor M Loth
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
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5
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Green JA, Improta R. Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study. Phys Chem Chem Phys 2020; 22:5509-5522. [PMID: 32104818 DOI: 10.1039/c9cp06373k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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6
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Van Hoozen BL, Petersen PB. Vibrational tug-of-war: The pKAdependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids. J Chem Phys 2018; 148:134309. [PMID: 29626887 DOI: 10.1063/1.5026675] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brian L. Van Hoozen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Poul B. Petersen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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7
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Fritzsch R, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Hunt NT. Rapid Screening of DNA–Ligand Complexes via 2D-IR Spectroscopy and ANOVA–PCA. Anal Chem 2018; 90:2732-2740. [DOI: 10.1021/acs.analchem.7b04727] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robby Fritzsch
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
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8
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Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017; 117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.
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Affiliation(s)
| | - Joshua S. Ostrander
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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9
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Ramakers LAI, Hithell G, May JJ, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Hunt NT. 2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model. J Phys Chem B 2017; 121:1295-1303. [PMID: 28102674 DOI: 10.1021/acs.jpcb.7b00345] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
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Affiliation(s)
- Lennart A I Ramakers
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - John J May
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
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10
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Hithell G, González-Jiménez M, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Wynne K, Hunt NT. Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA. Phys Chem Chem Phys 2017; 19:10333-10342. [DOI: 10.1039/c7cp00054e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Changes in the structural and solvation dynamics of DNA upon duplex melting are observed by 2D-IR and optical Kerr-effect spectroscopies.
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Affiliation(s)
- Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
| | | | - Gregory M. Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Paul M. Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Anthony W. Parker
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street
- Glasgow
- UK
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow
- Glasgow
- UK
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
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11
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Ho JJ, Skoff DR, Ghosh A, Zanni MT. Structural Characterization of Single-Stranded DNA Monolayers Using Two-Dimensional Sum Frequency Generation Spectroscopy. J Phys Chem B 2015. [PMID: 26222775 DOI: 10.1021/acs.jpcb.5b07078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA-covered materials are important in technological applications such as biosensors and microarrays, but obtaining structural information on surface-bound biomolecules is experimentally challenging. In this paper, we structurally characterize single-stranded DNA monolayers of poly(thymine) from 10 to 25 bases in length with an emerging surface technique called two-dimensional sum frequency generation (2D SFG) spectroscopy. These experiments are carried out by adding a mid-IR pulse shaper to a femtosecond broad-band SFG spectrometer. Cross peaks and 2D line shapes in the 2D SFG spectra provide information about structure and dynamics. Because the 2D SFG spectra are heterodyne detected, the monolayer spectra can be directly compared to 2D infrared (2D IR) spectra of poly(thymine) in solution, which aids interpretation. We simulate the 2D SFG spectra using DFT calculations and an excitonic Hamiltonian that relates the molecular geometry to the vibrational coupling. Intrabase cross peaks help define the orientation of the bases and interbase cross peaks, created by coupling between bases, and resolves features not observed in 1D SFG spectra that constrain the relative geometries of stacked bases. We present a structure for the poly(T) oligomer that is consistent with the 2D SFG data. These experiments provide insight into the DNA monolayer structure and set precedent for studying complex biomolecules on surfaces with 2D SFG spectroscopy.
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Affiliation(s)
- Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - David R Skoff
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ayanjeet Ghosh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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12
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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13
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Abstract
A proton transfer process is usually dominant in several biological phenomena such as the energy relaxation of photo-excited DNA base pairs and a charge relay process in Ser-His-Glu.
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Affiliation(s)
- Hiroto Tachikawa
- Division of Materials Chemistry
- Graduate School of Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Tomoya Takada
- Department of Material Chemistry
- Asahikawa National College of Technology
- Asahikawa 071-8142
- Japan
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14
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Galindo-Murillo R, Roe DR, Cheatham TE. On the absence of intrahelical DNA dynamics on the μs to ms timescale. Nat Commun 2014; 5:5152. [PMID: 25351257 PMCID: PMC4215645 DOI: 10.1038/ncomms6152] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023] Open
Abstract
DNA helices display a rich tapestry of motion on both short (<100 ns) and long (>1 ms) timescales. However, with the exception of mismatched or damaged DNA, experimental measures indicate that motions in the 1 μs to 1 ms range are effectively absent, which is often attributed to difficulties in measuring motions in this time range. We hypothesized that these motions have not been measured because there is effectively no motion on this timescale, as this provides a means to distinguish faithful Watson-Crick base-paired DNA from damaged DNA. The absence of motion on this timescale would present a 'static' DNA sequence-specific structure that matches the encounter timescales of proteins, thereby facilitating recognition. Here we report long-timescale (~10-44 μs) molecular dynamics simulations of a B-DNA duplex structure that addresses this hypothesis using both an 'Anton' machine and large ensembles of AMBER GPU simulations.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
| | - Daniel R Roe
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
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