1
|
Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
Collapse
Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| |
Collapse
|
2
|
Ameixa J, Bald I. Unraveling the Complexity of DNA Radiation Damage Using DNA Nanotechnology. Acc Chem Res 2024; 57:1608-1619. [PMID: 38780304 PMCID: PMC11154965 DOI: 10.1021/acs.accounts.4c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Radiation cancer therapies use different ionizing radiation qualities that damage DNA molecules in tumor cells by a yet not completely understood plethora of mechanisms and processes. While the direct action of the radiation is significant, the byproducts of the water radiolysis, mainly secondary low-energy electrons (LEEs, <20 eV) and reactive oxygen species (ROS), can also efficiently cause DNA damage, in terms of DNA strand breakage or DNA interstrand cross-linking. As a result, these types of DNA damage evolve into mutations hindering DNA replication, leading to cancer cell death. Concomitant chemo-radiotherapy explores the addition of radiosensitizing therapeutics commonly targeting DNA, such as platinum derivatives and halogenated nucleosides, to enhance the harmful effects of ionizing radiation on the DNA molecule. Further complicating the landscape of DNA damage are secondary structures such as G-quadruplexes occurring in telomeric DNA. These structures protect DNA from radiation damage, rendering them as promising targets for new and more selective cancer radiation treatments, rather than targeting linear DNA. However, despite extensive research, there is no single paradigm approach to understanding the mysterious way in which ionizing radiation causes DNA damage. This is due to the multidisciplinary nature of the field of research, which deals with multiple levels of biological organization, from the molecular building blocks of life toward cells and organisms, as well as with complex multiscale radiation-induced effects. Also, intrinsic DNA features, such as DNA topology and specific oligonucleotide sequences, strongly influence its response to damage from ionizing radiation. In this Account, we present our studies focused on the absolute quantification of photon- and low-energy electron-induced DNA damage in strategically selected target DNA sequences. Our methodology involves using DNA origami nanostructures, specifically the Rothemund triangle, as a platform to expose DNA sequences to either low-energy electrons or vacuum-ultraviolet (VUV, <15 eV) photons and subsequent atomic force microscopy (AFM) analysis. Through this approach, the effects of the DNA sequence, incorporation of halogenated radiosensitizers, DNA topology, and the radiation quality on radiation-induced DNA strand breakage have been systematically assessed and correlated with fundamental photon- and electron-driven mechanisms underlying DNA radiation damage. At lower energies, these mechanisms include dissociative electron attachment (DEA), where electrons attach to DNA molecules causing strand breaks, and dissociative photoexcitation of DNA. Additionally, further dissociative processes such as photoionization and electron impact contribute to the complex cascade of DNA damage events induced by ionizing radiation. We expect that emerging DNA origami-based approaches will lead to a paradigm shift in research fields associated with DNA damage and suggest future directions, which can foster the development of technological applications in nanomedicine, e.g., optimized cancer treatments or the molecular design of optimized radiosensitizing therapeutics.
Collapse
Affiliation(s)
- João Ameixa
- Institute
of Chemistry, Hybrid Nanostructures, University
of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Centre
of Physics and Technological Research (CEFITEC), Department of Physics,
NOVA School of Science and Technology, University
NOVA of Lisbon, Campus de Caparica 2829-516, Portugal
| | - Ilko Bald
- Institute
of Chemistry, Hybrid Nanostructures, University
of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| |
Collapse
|
3
|
Kogikoski S, Ameixa J, Mostafa A, Bald I. Lab-on-a-DNA origami: nanoengineered single-molecule platforms. Chem Commun (Camb) 2023; 59:4726-4741. [PMID: 37000514 PMCID: PMC10111202 DOI: 10.1039/d3cc00718a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.
Collapse
Affiliation(s)
- Sergio Kogikoski
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - João Ameixa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Amr Mostafa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Ilko Bald
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| |
Collapse
|
4
|
Chomicz-Mańka L, Czaja A, Falkiewicz K, Zdrowowicz M, Biernacki K, Demkowicz S, Izadi F, Arthur-Baidoo E, Denifl S, Zhu Z, Tufekci BA, Harris R, Bowen KH, Rak J. Intramolecular Proton Transfer in the Radical Anion of Cytidine Monophosphate Sheds Light on the Sensitivities of Dry vs Wet DNA to Electron Attachment-Induced Damage. J Am Chem Soc 2023; 145:9059-9071. [PMID: 37040588 PMCID: PMC10141262 DOI: 10.1021/jacs.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Single-strand breaks (SSBs) induced via electron attachment were previously observed in dry DNA under ultrahigh vacuum (UHV), while hydrated electrons were found not able to induce this DNA damage in an aqueous solution. To explain these findings, crossed electron-molecular beam (CEMB) and anion photoelectron spectroscopy (aPES) experiments coupled to density functional theory (DFT) modeling were used to demonstrate the fundamental importance of proton transfer (PT) in radical anions formed via electron attachment. Three molecular systems were investigated: 5'-monophosphate of 2'-deoxycytidine (dCMPH), where PT in the electron adduct is feasible, and two ethylated derivatives, 5'-diethylphosphate and 3',5'-tetraethyldiphosphate of 2'-deoxycytidine, where PT is blocked due to substitution of labile protons with the ethyl residues. CEMB and aPES experiments confirmed the cleavage of the C3'/C5'-O bond as the main dissociation channel related to electron attachment in the ethylated derivatives. In the case of dCMPH, however, electron attachment (in the aPES experiments) yielded its parent (intact) radical anion, dCMPH-, suggesting that its dissociation was inhibited. The aPES-measured vertical detachment energy of the dCMPH- was found to be 3.27 eV, which agreed with its B3LYP/6-31++G(d,p)-calculated value and implied that electron-induced proton transfer (EIPT) had occurred during electron attachment to the dCMPH model nucleotide. In other words, EIPT, subduing dissociation, appeared to be somewhat protective against SSB. While EIPT is facilitated in solution compared to the dry environment, the above findings are consistent with the stability of DNA against hydrated electron-induced SSB in solution versus free electron-induced SSB formation in dry DNA.
Collapse
Affiliation(s)
- Lidia Chomicz-Mańka
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Anna Czaja
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Karina Falkiewicz
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena Zdrowowicz
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Karol Biernacki
- Department of Organic Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Sebastian Demkowicz
- Department of Organic Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Farhad Izadi
- Institut für Ionenphysik und Angewandte Physik and Center for Biomolecular Sciences Innsbruck, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Eugene Arthur-Baidoo
- Institut für Ionenphysik und Angewandte Physik and Center for Biomolecular Sciences Innsbruck, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Biomolecular Sciences Innsbruck, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Zhaoguo Zhu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Burak Ahmet Tufekci
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rachel Harris
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kit H Bowen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Janusz Rak
- Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
5
|
Narayanan S J J, Bachhar A, Tripathi D, Dutta AK. Electron Attachment to Wobble Base Pairs. J Phys Chem A 2023; 127:457-467. [PMID: 36622294 DOI: 10.1021/acs.jpca.2c07469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.
Collapse
Affiliation(s)
- Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Arnab Bachhar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| |
Collapse
|
6
|
Sala L, Lyshchuk H, Šáchová J, Chvátil D, Kočišek J. Different Mechanisms of DNA Radiosensitization by 8-Bromoadenosine and 2'-Deoxy-2'-fluorocytidine Observed on DNA Origami Nanoframe Supports. J Phys Chem Lett 2022; 13:3922-3928. [PMID: 35472278 PMCID: PMC9083549 DOI: 10.1021/acs.jpclett.2c00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
DNA origami nanoframes with two parallel DNA sequences are used to evaluate the effect of nucleoside substituents on radiation-induced DNA damage. Double strand breaks (DSB) of DNA are counted using atomic force microscopy (AFM), and total number of lesions is evaluated using real-time polymerase chain reaction (RT-PCR). Enhanced AT or GC content does not increase the number of DNA strand breaks. Incorporation of 8-bromoadenosine results in the highest enhancement in total number of lesions; however, the highest enhancement in DSB is observed for 2'-deoxy-2'-fluorocytidine, indicating different mechanisms of radiosensitization by nucleoside analogues with the halogen substituent on base or sugar moieties, respectively. "Bystander" effects are observed, when the number of DSB in a sequence is enhanced by a substituent in the parallel DNA sequence. The present approach eliminates limitations of previously developed methods and motivates detailed studies of poorly understood conformation or bystander effects in radiation induced damage to DNA.
Collapse
Affiliation(s)
- Leo Sala
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
| | - Hlib Lyshchuk
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
| | - Jana Šáchová
- Laboratory
of Genomics and Bioinformatics, Institute
of Molecular Genetics of the CAS, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - David Chvátil
- Nuclear
Physics Institute of the CAS, Řež 130, 250 68 Řež, Czech
Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
| |
Collapse
|
7
|
Cornetta LM, Martinez TJ, Varella MTDN. Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces. Phys Chem Chem Phys 2022; 24:6845-6855. [PMID: 35253036 DOI: 10.1039/d1cp05663h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromo-uracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the resonance state and describes the formation of Br- anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.
Collapse
Affiliation(s)
- Lucas M Cornetta
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Rua Sérgio Buarque de Holanda, 777 - Cidade Universitária, Campinas, São Paulo, Brazil.
| | - Todd J Martinez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, USA.,SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090, São Paulo, São Paulo, Brazil
| |
Collapse
|
8
|
Chakraborty D, Giri A, Nandi D. Dissociation dynamics in low energy electron attachment to ammonia using velocity slice imaging. Phys Chem Chem Phys 2019; 21:21908-21917. [PMID: 31553032 DOI: 10.1039/c9cp03973b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complete dissociation dynamics of low energy electron attachment to the ammonia molecule has been studied using velocity slice imaging (VSI) spectrometry. One low energy resonant peak around 5.5 eV and a broad resonance around 10.5 eV incident electron energies have been observed. The resonant states mainly dissociate via H- and NH2- fragments, though for the upper resonant state, the signature of NH- fragments is also predicted due to a three-body dissociation process. Kinetic energy and angular distributions of the NH2- fragment anions are measured simultaneously around the two resonances. Based on our experimental observations, we conclude that a temporary negative ion (TNI) state with A1 symmetry is responsible for the lower resonance. Whereas, we find strong evidence for the existence of a TNI state having A1 symmetry at the 10.5 eV resonance for the first time.
Collapse
Affiliation(s)
- Dipayan Chakraborty
- Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India.
| | | | | |
Collapse
|
9
|
Vogel S, Ebel K, Heck C, Schürmann RM, Milosavljević AR, Giuliani A, Bald I. Vacuum-UV induced DNA strand breaks - influence of the radiosensitizers 5-bromouracil and 8-bromoadenine. Phys Chem Chem Phys 2019; 21:1972-1979. [PMID: 30633275 DOI: 10.1039/c8cp06813e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Radiation therapy is a basic part of cancer treatment. To increase the DNA damage in carcinogenic cells and preserve healthy tissue at the same time, radiosensitizing molecules such as halogenated nucleobase analogs can be incorporated into the DNA during the cell reproduction cycle. In the present study 8.44 eV photon irradiation induced single strand breaks (SSB) in DNA sequences modified with the radiosensitizer 5-bromouracil (5BrU) and 8-bromoadenine (8BrA) are investigated. 5BrU was incorporated in the 13mer oligonucleotide flanked by different nucleobases. It was demonstrated that the highest SSB cross sections were reached, when cytosine and thymine were adjacent to 5BrU, whereas guanine as a neighboring nucleobase decreases the activity of 5BrU indicating that competing reaction mechanisms are active. This was further investigated with respect to the distance of guanine to 5BrU separated by an increasing number of adenine nucleotides. It was observed that the SSB cross sections were decreasing with an increasing number of adenine spacers between guanine and 5BrU until the SSB cross sections almost reached the level of a non-modified DNA sequence, which demonstrates the high sequence dependence of the sensitizing effect of 5BrU. 8BrA was incorporated in a 13mer oligonucleotide as well and the strand breaks were quantified upon 8.44 eV photon irradiation in direct comparison to a non-modified DNA sequence of the same composition. No clear enhancement of the SSB yield of the modified in comparison to the non-modified DNA sequence could be observed. Additionally, secondary electrons with a maximum energy of 3.6 eV were generated when using Si as a substrate giving rise to further DNA damage. A clear enhancement in the SSB yield can be ascertained, but to the same degree for both the non-modified DNA sequence and the DNA sequence modified with 8BrA.
Collapse
Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | | | | | | | | | | | | |
Collapse
|
10
|
Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
Collapse
Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
| | | |
Collapse
|
11
|
McKee AD, Schaible MJ, Rosenberg RA, Kundu S, Orlando TM. Low energy secondary electron induced damage of condensed nucleotides. J Chem Phys 2019; 150:204709. [PMID: 31153208 DOI: 10.1063/1.5090491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10-18 cm2) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.
Collapse
Affiliation(s)
- A D McKee
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R A Rosenberg
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - S Kundu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| |
Collapse
|
12
|
Zhou L, Liu W, Brodeur N, Cloutier P, Zheng Y, Sanche L. Absolute cross sections for chemoradiation therapy: Damages to cisplatin-DNA complexes induced by 10 eV electrons. J Chem Phys 2019; 150:195101. [PMID: 31117770 DOI: 10.1063/1.5090259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In chemoradiation therapy, the synergy between the radiation and the chemotherapeutic agent (CA) can result in a super-additive treatment. A priori, this increased effectiveness could be estimated from model calculations, if absolute cross sections (ACSs) involved in cellular damage are substantially higher, when the CA binds to DNA. We measure ACSs for damages induced by 10 eV electrons, when DNA binds to the CA cisplatin as in chemotherapy. At this energy, DNA is damaged essentially by the decay of core-excited transient anions into bond-breaking channels. Films of cisplatin-DNA complexes of ratio 5:1 with thicknesses 10, 15, and 20 nm were irradiated in vacuum during 5-30 s. Conformation changes were quantified by electrophoresis and yields extrapolated from exposure-response curves. Base damages (BDs) were revealed and quantified by enzymatic treatment. The ACSs were generated from these yields by two mathematical models. For 3197 base-pair plasmid DNA, ACS for single strand breaks, double strand breaks (DSBs), crosslinks, non-DSB cluster damages, and total BDs is 71 ± 2, 9.3 ± 0.4, 10.1 ± 0.3, 8.2 ± 0.3, and 115 ± 2 ×10-15 cm2, respectively. These ACSs are higher than those of nonmodified DNA by factors of 1.6 ± 0.1, 2.2 ± 0.1, 1.3 ± 0.1, 1.3 ± 0.3, and 2.1 ± 0.4, respectively. Since LEEs are produced in large quantities by radiolysis and strongly interact with biomolecules, we expect such enhancements to produce substantial additional damages in the DNA of the nucleus of cancer cells during concomitant chemoradiation therapy. The increase damage appears sufficiently large to justify more elaborate simulations, which could provide a quantitative evaluation of molecular sensitization by Pt-CAs.
Collapse
Affiliation(s)
- Limei Zhou
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Wenhui Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Nicolas Brodeur
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry, Fuzhou University, Fuzhou 350116, People's Republic of China
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté of Médecine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| |
Collapse
|
13
|
Vogel S, Ebel K, Schürmann RM, Heck C, Meiling T, Milosavljevic AR, Giuliani A, Bald I. Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks - Influence of the DNA Sequence and Substrate. Chemphyschem 2019; 20:823-830. [PMID: 30719805 DOI: 10.1002/cphc.201801152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/01/2019] [Indexed: 12/28/2022]
Abstract
DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3×10-16 cm2 . The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.
Collapse
Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Kenny Ebel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Robin M Schürmann
- Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Christian Heck
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Till Meiling
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron SOLEIL, 91192, Gif-sur-Yvette, France.,UAR 1008 CEPIA, INRA, 44316, Nantes, France
| | - Ilko Bald
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| |
Collapse
|
14
|
Ramakrishnan S, Ijäs H, Linko V, Keller A. Structural stability of DNA origami nanostructures under application-specific conditions. Comput Struct Biotechnol J 2018; 16:342-349. [PMID: 30305885 PMCID: PMC6169152 DOI: 10.1016/j.csbj.2018.09.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022] Open
Abstract
With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis. Since many of those applications rely on structurally intact, well-definedDNA origami shapes, the issue of DNA origami stability under numerous application-relevant environmental conditions has received increasing interest in the past few years. In this mini-review we discuss the structural stability, denaturation, and degradation of DNA origami nanostructures under different conditions relevant to the fields of biophysics and biochemistry, biomedicine, and materials science, and the methods to improve their stability for desired applications.
Collapse
Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
- University of Jyväskylä, Department of Biological and Environmental Science, P. O. Box 35, FI-40014 Jyväskylä, Finland
| | - Veikko Linko
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| |
Collapse
|
15
|
Schürmann R, Vogel S, Ebel K, Bald I. The Physico-Chemical Basis of DNA Radiosensitization: Implications for Cancer Radiation Therapy. Chemistry 2018. [PMID: 29522244 DOI: 10.1002/chem.201800804] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
High-energy radiation is used in combination with radiosensitizing therapeutics to treat cancer. The most common radiosensitizers are halogenated nucleosides and cisplatin derivatives, and recently also metal nanoparticles have been suggested as potential radiosensitizing agents. The radiosensitizing action of these compounds can at least partly be ascribed to an enhanced reactivity towards secondary low-energy electrons generated along the radiation track of the high-energy primary radiation, or to an additional emission of secondary reactive electrons close to the tumor tissue. This is referred to as physico-chemical radiosensitization. In this Concept article we present current experimental methods used to study fundamental processes of physico-chemical radiosensitization and discuss the most relevant classes of radiosensitizers. Open questions in the current discussions are identified and future directions outlined, which can lead to optimized treatment protocols or even novel therapeutic concepts.
Collapse
Affiliation(s)
- Robin Schürmann
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Stefanie Vogel
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| |
Collapse
|
16
|
Rackwitz J, Bald I. Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology. Chemistry 2018; 24:4680-4688. [PMID: 29359819 DOI: 10.1002/chem.201705889] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 12/19/2022]
Abstract
During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG)2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A)2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT)2 to 5'-(GGG ATT)4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K+ ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy.
Collapse
Affiliation(s)
- Jenny Rackwitz
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| |
Collapse
|
17
|
Schürmann R, Bald I. Effect of adsorption kinetics on dissociation of DNA-nucleobases on gold nanoparticles under pulsed laser illumination. Phys Chem Chem Phys 2018; 19:10796-10803. [PMID: 28244511 DOI: 10.1039/c6cp08433h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photothermal therapy is a novel approach to destroy cancer cells by an increase of temperature due to laser illumination of gold nanoparticles (GNPs) that are incorporated into the cells. Here, we study the decomposition of DNA nucleobases via irradiation of gold nanoparticles with ns-laser pulses. The kinetics of the adsorption and decomposition process is described by a theoretical model based on the Langmuir assumptions and correlated with experimentally determined reaction rates revealing a strong influence of the nucleobase specific adsorption. Beside the four nucleobases, their brominated analogs, which are potential radiosensitizers in cancer therapy, are also investigated and show a significant modification of the decomposition rates. The fastest decomposition rates are observed for adenine, 8-bromoadenine, 8-bromoguanine and 5-bromocytosine. These results are in good agreement with the relative adsorption rates that are determined from the aggregation kinetics of the GNPs taking the effect of an inhomogeneous surface into account. For adenine and its brominated analog, the decomposition products are further analyzed by surface enhanced Raman scattering (SERS) indicating a strong fragmentation of the molecules into their smallest subunits.
Collapse
Affiliation(s)
- Robin Schürmann
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Potsdam, Germany.
| | | |
Collapse
|
18
|
Chen W, Chen S, Dong Y, Cloutier P, Zheng Y, Sanche L. Absolute cross-sections for DNA strand breaks and crosslinks induced by low energy electrons. Phys Chem Chem Phys 2018; 18:32762-32771. [PMID: 27878170 DOI: 10.1039/c6cp05201k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute cross sections (CSs) for the interaction of low energy electrons with condensed macromolecules are essential parameters to accurately model ionizing radiation induced reactions. To determine CSs for various conformational DNA damage induced by 2-20 eV electrons, we investigated the influence of the attenuation length (AL) and penetration factor (f) using a mathematical model. Solid films of supercoiled plasmid DNA with thicknesses of 10, 15 and 20 nm were irradiated with 4.6, 5.6, 9.6 and 14.6 eV electrons. DNA conformational changes were quantified by gel electrophoresis, and the respective yields were extrapolated from exposure-response curves. The absolute CS, AL and f values were generated by applying the model developed by Rezaee et al. The values of AL were found to lie between 11 and 16 nm with the maximum at 14.6 eV. The absolute CSs for the loss of the supercoiled (LS) configuration and production of crosslinks (CL), single strand breaks (SSB) and double strand breaks (DSB) induced by 4.6, 5.6, 9.6 and 14.6 eV electrons are obtained. The CSs for SSB are smaller, but similar to those for LS, indicating that SSB are the main conformational damage. The CSs for DSB and CL are about one order of magnitude smaller than those of LS and SSB. The value of f is found to be independent of electron energy, which allows extending the absolute CSs for these types of damage within the range 2-20 eV, from previous measurements of effective CSs. When comparison is possible, the absolute CSs are found to be in good agreement with those obtained from previous similar studies with double-stranded DNA. The high values of the absolute CSs of 4.6 and 9.6 eV provide quantitative evidence for the high efficiency of low energy electrons to induce DNA damage via the formation of transient anions.
Collapse
Affiliation(s)
- Wenzhuang Chen
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China.
| | - Shiliang Chen
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China.
| | - Yanfang Dong
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China.
| | - Pierre Cloutier
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Yi Zheng
- Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, P. R. China.
| | - Léon Sanche
- Group in the Radiation Sciences, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| |
Collapse
|
19
|
Ramakrishnan S, Krainer G, Grundmeier G, Schlierf M, Keller A. Cation-Induced Stabilization and Denaturation of DNA Origami Nanostructures in Urea and Guanidinium Chloride. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702100. [PMID: 29024433 DOI: 10.1002/smll.201702100] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/18/2017] [Indexed: 06/07/2023]
Abstract
The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na+ and Mg2+ concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl. These inverse behaviors are rationalized by a salting-out of Gdm+ to the hydrophobic DNA base stack. The effect of cation-induced DNA origami denaturation by GdmCl deserves consideration in the design of single-molecule studies and may potentially be exploited in future applications such as selective denaturation for purification purposes.
Collapse
Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307, Dresden, Germany
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307, Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| |
Collapse
|
20
|
Schürmann R, Tsering T, Tanzer K, Denifl S, Kumar SVK, Bald I. Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low-Energy Electrons (0.5-9 eV). Angew Chem Int Ed Engl 2017; 56:10952-10955. [PMID: 28670830 DOI: 10.1002/anie.201705504] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/20/2022]
Abstract
Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross-section for oligonucleotides modified with 8-bromoadenine (8Br A). These results were evaluated against DEA measurements with isolated 8Br A in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.
Collapse
Affiliation(s)
- Robin Schürmann
- Department of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Strasse 11, 12489, Berlin, Germany
| | - Thupten Tsering
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba Mumbai, 400 005, India
| | - Katrin Tanzer
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Stephan Denifl
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - S V K Kumar
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba Mumbai, 400 005, India
| | - Ilko Bald
- Department of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Strasse 11, 12489, Berlin, Germany
| |
Collapse
|
21
|
Schürmann R, Tsering T, Tanzer K, Denifl S, Kumar SVK, Bald I. Resonante Bildung von Strangbrüchen in sensibilisierten Oligonukleotiden induziert durch niederenergetische Elektronen (0.5-9.0 eV). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Robin Schürmann
- Institut für Chemie - Physikalische Chemie; Universität Potsdam; Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Deutschland
- Abteilung 1 - Analytische Chemie und Referenzmaterialien; Bundesanstalt für Materialforschung und -prüfung; Richard-Willstätter Str. 11 12489 Berlin Deutschland
| | - Thupten Tsering
- Tata Institute of Fundamental Research; Homi Bhabha Road Colaba Mumbai 400 005 Indien
| | - Katrin Tanzer
- Institut für Ionenphysik und Angewandte Physik; Universität Innsbruck; Technikerstraße 25 A-6020 Innsbruck Österreich
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik; Universität Innsbruck; Technikerstraße 25 A-6020 Innsbruck Österreich
| | - S. V. K. Kumar
- Tata Institute of Fundamental Research; Homi Bhabha Road Colaba Mumbai 400 005 Indien
| | - Ilko Bald
- Institut für Chemie - Physikalische Chemie; Universität Potsdam; Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Deutschland
- Abteilung 1 - Analytische Chemie und Referenzmaterialien; Bundesanstalt für Materialforschung und -prüfung; Richard-Willstätter Str. 11 12489 Berlin Deutschland
| |
Collapse
|
22
|
Sieradzka A, Gorfinkiel JD. Theoretical study of resonance formation in microhydrated molecules. II. Thymine-(H2O)n, n = 1,2,3,5. J Chem Phys 2017; 147:034303. [DOI: 10.1063/1.4993946] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Agnieszka Sieradzka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jimena D. Gorfinkiel
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| |
Collapse
|
23
|
Schürmann R, Tanzer K, Dąbkowska I, Denifl S, Bald I. Stability of the Parent Anion of the Potential Radiosensitizer 8-Bromoadenine Formed by Low-Energy (<3 eV) Electron Attachment. J Phys Chem B 2017; 121:5730-5734. [PMID: 28525718 DOI: 10.1021/acs.jpcb.7b02130] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
8-Bromoadenine (8BrA) is a potential DNA radiosensitizer for cancer radiation therapy due to its efficient interaction with low-energy electrons (LEEs). LEEs are a short-living species generated during the radiation damage of DNA by high-energy radiation as it is applied in cancer radiation therapy. Electron attachment to 8BrA in the gas phase results in a stable parent anion below 3 eV electron energy in addition to fragmentation products formed by resonant exocyclic bond cleavages. Density functional theory (DFT) calculations of the 8BrA- anion reveal an exotic bond between the bromine and the C8 atom with a bond length of 2.6 Å, where the majority of the charge is located on bromine and the spin is mainly located on the C8 atom. The detailed understanding of such long-lived anionic states of nucleobase analogues supports the rational development of new therapeutic agents, in which the enhancement of dissociative electron transfer to the DNA backbone is critical to induce DNA strand breaks in cancerous tissue.
Collapse
Affiliation(s)
- Robin Schürmann
- Institute of Chemistry - Physical Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany
| | - Katrin Tanzer
- Institute of Ion Physics and Applied Physics and Center for Molecular Biosciences, University of Innsbruck , Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Iwona Dąbkowska
- Department of Chemistry, University of Gdansk , Sobieskiego 18, Gdansk, 80-952, Poland
| | - Stephan Denifl
- Institute of Ion Physics and Applied Physics and Center for Molecular Biosciences, University of Innsbruck , Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Ilko Bald
- Institute of Chemistry - Physical Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany
| |
Collapse
|
24
|
Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
25
|
Schürmann R, Bald I. Real-time monitoring of plasmon induced dissociative electron transfer to the potential DNA radiosensitizer 8-bromoadenine. NANOSCALE 2017; 9:1951-1955. [PMID: 28098304 DOI: 10.1039/c6nr08695k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The excitation of localized surface plasmons in noble metal nanoparticles (NPs) results in different nanoscale effects such as electric field enhancement, the generation of hot electrons and a temperature increase close to the NP surface. These effects are typically exploited in diverse fields such as surface-enhanced Raman scattering (SERS), NP catalysis and photothermal therapy (PTT). Halogenated nucleobases are applied as radiosensitizers in conventional radiation cancer therapy due to their high reactivity towards secondary electrons. Here, we use SERS to study the transformation of 8-bromoadenine (8BrA) into adenine on the surface of Au and AgNPs upon irradiation with a low-power continuous wave laser at 532, 633 and 785 nm, respectively. The dissociation of 8BrA is ascribed to a hot-electron transfer reaction and the underlying kinetics are carefully explored. The reaction proceeds within seconds or even milliseconds. Similar dissociation reactions might also occur with other electrophilic molecules, which must be considered in the interpretation of respective SERS spectra. Furthermore, we suggest that hot-electron transfer induced dissociation of radiosensitizers such as 8BrA can be applied in the future in PTT to enhance the damage of tumor tissue upon irradiation.
Collapse
Affiliation(s)
- R Schürmann
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14776 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - I Bald
- Institute of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14776 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| |
Collapse
|
26
|
Olejko L, Bald I. FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems. RSC Adv 2017. [DOI: 10.1039/c7ra02114c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Artificial light harvesting complexes find applications in photosynthesis, photovoltaics and chemical sensors. Here, we present the characterization and optimization of a multi-color artificial light harvesting system on DNA origami structures.
Collapse
Affiliation(s)
- L. Olejko
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
| | - I. Bald
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
| |
Collapse
|
27
|
Rackwitz J, Kopyra J, Dąbkowska I, Ebel K, Ranković ML, Milosavljević AR, Bald I. Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603464] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jenny Rackwitz
- Institute of Chemistry-Physical Chemistry; University of Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
| | - Janina Kopyra
- Faculty of Sciences; Siedlce University; 3 Maja 54 08-110 Siedlce Poland
| | - Iwona Dąbkowska
- Department of Chemistry; University of Gdańsk; 80-952 Gdańsk Poland
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry; University of Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
| | - MiloŠ Lj. Ranković
- Institute of Physics Belgrade; University of Belgrade; Pregrevica 118 11080 Belgrade Serbia
| | - Aleksandar R. Milosavljević
- Institute of Physics Belgrade; University of Belgrade; Pregrevica 118 11080 Belgrade Serbia
- SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192; Gif sur Yvette Cedex France
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry; University of Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
- Department 1-Analytical Chemistry and Reference Materials; BAM Federal Institute for Materials Research and Testing; Richard-Willstätter Str. 11 12489 Berlin Germany
| |
Collapse
|
28
|
Rackwitz J, Kopyra J, Dąbkowska I, Ebel K, Ranković ML, Milosavljević AR, Bald I. Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine. Angew Chem Int Ed Engl 2016; 55:10248-52. [PMID: 27481662 DOI: 10.1002/anie.201603464] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/16/2016] [Indexed: 11/09/2022]
Abstract
2-Fluoroadenine ((2F) A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F) A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F) A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F) A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F) A at 5.5, 10, and 15 eV are very similar. Thus, (2F) A can be considered an effective radiosensitizer operative at a wide range of electron energies.
Collapse
Affiliation(s)
- Jenny Rackwitz
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Janina Kopyra
- Faculty of Sciences, Siedlce University, 3 Maja 54, 08-110, Siedlce, Poland
| | - Iwona Dąbkowska
- Department of Chemistry, University of Gdańsk, 80-952, Gdańsk, Poland
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - MiloŠ Lj Ranković
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080, Belgrade, Serbia
| | - Aleksandar R Milosavljević
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080, Belgrade, Serbia.,SOLEIL, l'Orme des Merisiers, St. Aubin, BP48, 91192, Gif sur Yvette Cedex, France
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany. .,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.
| |
Collapse
|
29
|
Ramakrishnan S, Krainer G, Grundmeier G, Schlierf M, Keller A. Structural stability of DNA origami nanostructures in the presence of chaotropic agents. NANOSCALE 2016; 8:10398-10405. [PMID: 27142120 DOI: 10.1039/c6nr00835f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.
Collapse
Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, 33098 Paderborn, Germany.
| | | | | | | | | |
Collapse
|
30
|
Olejko L, Cywiński PJ, Bald I. An ion-controlled four-color fluorescent telomeric switch on DNA origami structures. NANOSCALE 2016; 8:10339-10347. [PMID: 27138897 DOI: 10.1039/c6nr00119j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K(+) ions even in the presence of high Na(+) concentrations. Here, we demonstrate that the K(+)-selective G-quadruplex formation is reversible when using a cryptand to remove K(+) from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.
Collapse
Affiliation(s)
- L Olejko
- Department of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | | | | |
Collapse
|
31
|
Prinz J, Heck C, Ellerik L, Merk V, Bald I. DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity. NANOSCALE 2016; 8:5612-20. [PMID: 26892770 PMCID: PMC4778414 DOI: 10.1039/c5nr08674d] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/11/2016] [Indexed: 05/17/2023]
Abstract
DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 10(10), which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.
Collapse
Affiliation(s)
- J Prinz
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany.
| | - C Heck
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany and Department of Chemistry + SALSA, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - L Ellerik
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany.
| | - V Merk
- Department of Chemistry + SALSA, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - I Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany
| |
Collapse
|
32
|
Kumar SVK, Tare ST, Upalekar YV, Tsering T. Dose controlled low energy electron irradiator for biomolecular films. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:034302. [PMID: 27036792 DOI: 10.1063/1.4944812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at -20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.
Collapse
Affiliation(s)
- S V K Kumar
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Satej T Tare
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Yogesh V Upalekar
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Thupten Tsering
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| |
Collapse
|
33
|
Vogel S, Rackwitz J, Schürman R, Prinz J, Milosavljević AR, Réfrégiers M, Giuliani A, Bald I. Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage. J Phys Chem Lett 2015; 6:4589-93. [PMID: 26536162 DOI: 10.1021/acs.jpclett.5b02238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.
Collapse
Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | - Jenny Rackwitz
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | - Robin Schürman
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing , Richard-Willstätter Str. 11, 12489 Berlin, Germany
| | - Julia Prinz
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | | | | | - Alexandre Giuliani
- Synchrotron SOLEIL , 91192 Gif-sur-Yvette, France
- UAR 1008 CEPIA, INRA, 44316 Nantes, France
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing , Richard-Willstätter Str. 11, 12489 Berlin, Germany
| |
Collapse
|
34
|
Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy. Molecules 2014; 19:13803-23. [PMID: 25191873 PMCID: PMC6271098 DOI: 10.3390/molecules190913803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/21/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022] Open
Abstract
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
Collapse
|