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Jones NC, Nielsen SB, Hoffmann SV. On the delocalization length in RNA single strands of cytosine: how many bases see the light? Phys Chem Chem Phys 2020; 22:2188-2192. [DOI: 10.1039/c9cp05292e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.
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Affiliation(s)
- Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
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2
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Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
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Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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3
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Miyahara T, Nakatsuji H, Sugiyama H. Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study. J Phys Chem A 2016; 120:9008-9018. [PMID: 27809523 DOI: 10.1021/acs.jpca.6b08023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.
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Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute , Kyodai Katsura Venture Plaza, North building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan
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Espinosa Leal LA, Karpenko A, Swasey S, Gwinn EG, Rojas-Cervellera V, Rovira C, Lopez-Acevedo O. The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers. J Phys Chem Lett 2015; 6:4061-6. [PMID: 26722777 DOI: 10.1021/acs.jpclett.5b01864] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
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Affiliation(s)
| | - Alexander Karpenko
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
| | - Steven Swasey
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Elisabeth G Gwinn
- Department of Physics, University of California , Santa Barbara, California 93106-9510, United States
| | - Victor Rojas-Cervellera
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Olga Lopez-Acevedo
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
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Wakabayashi M, Yokojima S, Fukaminato T, Ohtani H, Nakamura S. Anisotropic elliptical dichroism and influence of imperfection of circular polarization upon anisotropic circular dichroism. J Chem Phys 2015; 142:154102. [PMID: 25903861 DOI: 10.1063/1.4917174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In spite of the importance of anisotropic circular dichroism, in practice, it is difficult to get rid of the artifacts that arise from the imperfection of the circular polarization. Undesirable linear dichroism, interference of two orthogonal polarization states, and linear birefringence prevent us from making accurate measurements. We propose a theoretical method for evaluating the contributions of the first two, which are thought to be the main artifacts when specimens are not thick enough. Using the time-dependent perturbation theory and taking into account the direction of light propagation toward an orientationally fixed molecule, we formulated the transition probability of systems perturbed by arbitrarily polarized light and the absorption difference associated with two kinds of polarized light. We also formulated, as an extension of the dissymmetry factor of circular dichroism, a newly defined dissymmetry factor associated with two arbitrary polarization states. Furthermore, we considered a mixed-state of photon ensemble in which polarization states distribute at a certain width around a certain average. Although the purity of polarization and ellipticity does not correspond immediately, by considering the mixed state it is possible to treat them consistently. We used quantum statistical mechanics to describe the absorption difference for two kinds of photon ensembles and applied the consequent formula to examine the reported experimental results of single-molecule chiroptical responses under discussion in the recent past. The artifacts are theoretically suggested to be sensitive to the incident direction of elliptically polarized light and to the oriented systems, the ellipticity, and the orientation of ellipse. The mixed state has little, if any, effect when the polarization state distribution is narrow.
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Affiliation(s)
- Masamitsu Wakabayashi
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Satoshi Yokojima
- Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachiouji-shi, Tokyo 192-0392, Japan
| | - Tuyoshi Fukaminato
- Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hiroyuki Ohtani
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Shinichiro Nakamura
- RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Wu P, Yu Y, McGhee CE, Tan LH, Lu Y. Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7849-72. [PMID: 25205057 PMCID: PMC4275547 DOI: 10.1002/adma.201304891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/02/2014] [Indexed: 05/22/2023]
Abstract
In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.
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Affiliation(s)
- Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang Yu
- Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Claire E. McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Li Huey Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Wakabayashi M, Yokojima S, Fukaminato T, Shiino KI, Irie M, Nakamura S. Anisotropic dissymmetry factor, g: theoretical investigation on single molecule chiroptical spectroscopy. J Phys Chem A 2014; 118:5046-57. [PMID: 24919679 DOI: 10.1021/jp409559t] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A formula for an anisotropic dissymmetry factor g evaluating the chiroptical response of orientationally fixed molecules is derived. Incorporating zeroth- and first-order multipole expansion terms, it is applied to bridged triarylamine helicene molecules to examine the experimental results of single-molecule chiroptical spectroscopy. The ground- and excited-state wave functions and a series of transition moments required for the evaluation of the anisotropic g value are calculated using time-dependent density functional theory (TDDFT). The probability histograms obtained for simulated g values, uniformly sampled in regard to the direction of light propagation toward the fixed molecule, show that even for a given diastereomer, the dissymmetry factors have positive and negative values and can deviate from their averages to a considerable extent when the angle between the electric dipole transition moment and the propagation vector of the incident light is near 0 or 180°.
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Affiliation(s)
- Masamitsu Wakabayashi
- Department of Biomolecular Engineering, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Miyahara T, Nakatsuji H, Sugiyama H. Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study. J Phys Chem A 2012; 117:42-55. [DOI: 10.1021/jp3085556] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute,
JST, CREST, Kyodai Katsura Venture Plaza,
North Building 107, 1-36 Goryo-Oohara, Nishikyo-ku, Kyoto 615-8245,
Japan
| | - Hiroshi Sugiyama
- Department of Chemistry,
Graduate
School of Science, Kyoto University, Kitashirakawa-Oiwakecho,
Sakyo-Ku, Kyoto 606-8502, Japan
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Matsuo K, Namatame H, Taniguchi M, Gekko K. Vacuum-ultraviolet electronic circular dichroism study of methyl α-D-glucopyranoside in aqueous solution by time-dependent density functional theory. J Phys Chem A 2012; 116:9996-10003. [PMID: 22950837 DOI: 10.1021/jp306914s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vacuum-ultraviolet (VUV) electronic circular dichroism (ECD) spectrum of methyl α-D-glucopyranoside (methyl α-D-Glc) was measured down to 163 nm in aqueous solution using a synchrotron-radiation VUV-ECD spectrophotometer. The spectrum exhibited two characteristic ECD peaks around 170 nm, which depend on the trans (T) and gauche (G) configurations of the hydroxymethyl group at C-5. To elucidate the influences of the T and G configurations on the spectrum, the ECD spectra of three rotamers (α-GT, α-GG, and α-TG) of methyl α-D-Glc were calculated using time-dependent density functional theory (TDDFT) combined with molecular dynamics simulation. A linear combination of the ECD spectra of these three rotamers, which differ markedly from each other, produced a methyl α-D-Glc spectrum similar to that observed experimentally. The spectrum was assignable to the n-σ* transitions of the ring oxygen and methoxy oxygen with minor contributions from the hydroxyl oxygen. The differences in α-GT, α-GG, and α-TG spectra were attributed to fluctuations of the configurations of the hydroxymethyl group at C-5 and the hydroxyl group at C-4, which strongly affected the orientations of intramolecular hydrogen bonds around the ring oxygen. These findings demonstrate that combining VUV-ECD and TDDFT is useful for structural characterization of saccharides in aqueous solution.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan.
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Ghane T, Brancolini G, Varsano D, Di Felice R. Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory. J Phys Chem B 2012; 116:10693-702. [DOI: 10.1021/jp304818s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tahereh Ghane
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
- Department of Physics, University of Modena and Reggio Emilia, Via Campi 213/A,
41125 Modena, Italy
| | - Giorgia Brancolini
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
| | - Daniele Varsano
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
- Department
of Physics, University of Rome “La Sapienza”, Piazzale
Aldo Moro 5, 00185 Rome, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena,
Italy
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Nielsen LM, Hoffmann SV, Brøndsted Nielsen S. Vacuum-ultraviolet circular dichroism reveals DNA duplex formation between short strands of adenine and thymine. Phys Chem Chem Phys 2012; 14:15054-9. [DOI: 10.1039/c2cp42226c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Fukuyama T, Matsuo K, Gekko K. Experimental and theoretical studies of vacuum-ultraviolet electronic circular dichroism of hydroxy acids in aqueous solution. Chirality 2011; 23 Suppl 1:E52-8. [PMID: 21538575 DOI: 10.1002/chir.20962] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 02/24/2011] [Indexed: 11/10/2022]
Abstract
The electronic circular dichroism (ECD) spectra of three L-hydroxy acids (L-lactic acid, (+)-(S)-2-hydroxy-3-methylbutyric acid, and (-)-(S)-2-hydroxyisocaproic acid) were measured down to 160 nm in aqueous solution using a vacuum-ultraviolet ECD spectrophotometer. To assign the two positive peaks around 210 and 175 nm and the one negative peak around 190 nm in the observed spectra, the ECD spectrum of L-lactic acid was calculated using time-dependent density functional theory (DFT) for the optimized structures by DFT and a continuum model. The observed ECD spectrum was successfully reproduced as the average spectrum for four optimized structures with seven water molecules that localized around the COO(-) and OH groups of L-lactic acid. The positive peak around 210 nm and the negative peak around 185 nm in the calculated spectrum were attributable to the nπ* transition of the carboxyl group, with the latter peak also being influenced by the ππ* transition of the carboxyl group; however, the positive peak around 165 nm involved unassignable higher energy transitions. The comparison of the calculated ECD spectra for L-lactic acid and L-alanine revealed that the network with loose hydrogen bonding around the COO(-) and OH groups is responsible for the flexible conformation of hydroxy acids and complicated side-chain dependence of ECD spectra relative to amino acids.
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Affiliation(s)
- Takayuki Fukuyama
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
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Holm AIS, Nielsen LM, Hoffmann SV, Nielsen SB. Vacuum-ultraviolet circular dichroism spectroscopy of DNA: a valuable tool to elucidate topology and electronic coupling in DNA. Phys Chem Chem Phys 2010; 12:9581-96. [PMID: 20607185 DOI: 10.1039/c003446k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular dichroism (CD) is a powerful technique to obtain information on electronic transitions and has been used extensively for studies on DNA. Most experiments are done in the UV region but new information is often revealed from extending the wavelength region down into the vacuum ultraviolet (VUV) region. Such experiments are most easily carried out with synchrotron radiation (SR) light sources that provide large photon fluxes. Here we provide a summary of the SRCD data taken on different DNA strands with emphasis on results from our own laboratory within the last five years.(1-3) Signal intensities in the VUV are often significantly larger than those in the UV, and the electronic coupling between bases may increase with excitation energy. CD spectroscopy is particularly useful for investigating the extent of electronic coupling within a strand, i.e., the degree of delocalisation of the excited-state electronic wavefunction. The spatial extent of the wavefunction may be limited to just one base or it extends over two or more bases in a stack or between bases on different strands.(4,5) The actual character of the electronically excited state is linked to base composition and sequence as well as DNA folding motif (A-, B-, Z-DNA, triplexes, quadruplexes, etc.). The latter depends on experimental conditions such as solution acidity, temperature, ionic strength, and solvent.
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Affiliation(s)
- Anne Ivalu Sander Holm
- Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm, Sweden.
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