Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Cervantes-Salguero, Keitel; Biaggne, Austin; Youngsman, John M.; Ward, Brett M.; Kim, Young C.; Li, Lan; Hall, John A.; Knowlton, William B.; Graugnard, Elton; Kuang, Wan

doi:10.3390/ijms23147690

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Journal Article · Tue Jul 12 00:00:00 EDT 2022 · International Journal of Molecular Sciences (Online)

DOI:https://doi.org/10.3390/ijms23147690· OSTI ID:1876010

^[1]; ^[2]; ^[2]; Ward, Brett M. ^[2]; Kim, Young C. ^[3]; ^[4]; ^[2]; ^[2]; ^[4]; Kuang, Wan ^[2]

Boise State Univ., ID (United States); Boise State University
Boise State Univ., ID (United States)
U.S. Naval Research Lab., Washington, DC (United States)
Boise State Univ., ID (United States); Center for Advanced Energy Studies, Idaho Falls, ID (United States)

Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (Φ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5's orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, Φ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.

View Accepted Manuscript (DOE)

Research Organization:: Boise State Univ., ID (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; Department of Navy, Office of Naval Science

Grant/Contract Number:: SC0020089

OSTI ID:: 1876010

Journal Information:: International Journal of Molecular Sciences (Online), Journal Name: International Journal of Molecular Sciences (Online) Journal Issue: 14 Vol. 23; ISSN 1422-0067

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

References (95)

LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds Wang, Xiao; Deshmukh, Rahul; Sha, Ruojie Angewandte Chemie International Edition, Vol. 61, Issue 5 https://doi.org/10.1002/ANIE.202115155	journal	December 2021
50 years of DNA ‘Breathing’: Reflections on old and new approaches [For special issue of biopolymers on 50 years of nucleic acids research] von Hippel, Peter H.; Johnson, Neil P.; Marcus, Andrew H. Biopolymers https://doi.org/10.1002/BIP.22347	journal	July 2013
Nanoarchitectonics for Hybrid and Related Materials for Bio-Oriented Applications Ariga, Katsuhiko; Leong, David Tai; Mori, Taizo Advanced Functional Materials, Vol. 28, Issue 27 https://doi.org/10.1002/adfm.201702905	journal	September 2017
Materialistic Interfaces with Nucleic Acids: Principles and Their Impact Li, Bang Lin; Zhang, Hang; Li, Nian Bing Advanced Functional Materials https://doi.org/10.1002/adfm.202201172	journal	March 2022
Double‐ to Single‐Strand Transition Induces Forces and Motion in DNA Origami Nanostructures Gür, Fatih N.; Kempter, Susanne; Schueder, Florian Advanced Materials, Vol. 33, Issue 37 https://doi.org/10.1002/adma.202101986	journal	August 2021
Graphene Energy Transfer for Single‐Molecule Biophysics, Biosensing, and Super‐Resolution Microscopy Kamińska, Izabela; Bohlen, Johann; Yaadav, Renukka Advanced Materials, Vol. 33, Issue 42 https://doi.org/10.1002/adma.202105719	journal	October 2021
The Many Facets of Molecular Orientation in Organic Optoelectronics Hofmann, Alexander; Schmid, Markus; Brütting, Wolfgang Advanced Optical Materials, Vol. 9, Issue 21 https://doi.org/10.1002/adom.202101004	journal	August 2021
Enhanced Light–Matter Interaction and Polariton Relaxation by the Control of Molecular Orientation Ishii, Tomohiro; Bencheikh, Fatima; Forget, Sébastien Advanced Optical Materials, Vol. 9, Issue 22 https://doi.org/10.1002/adom.202101048	journal	September 2021
Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer Chen, Bin; Huang, Qiuling; Qu, Zhibei Angewandte Chemie International Edition, Vol. 60, Issue 12 https://doi.org/10.1002/anie.202014466	journal	February 2021
Interaction of cyanine dyes with nucleic acids. XXI. Arguments for half-intercalation model of interaction Yarmoluk, S. M.; Lukashov, S. S.; Ogul'Chansky, T. Yu. Biopolymers, Vol. 62, Issue 4 https://doi.org/10.1002/bip.1016	journal	January 2001
The Role of Molecular Dipole Orientation in Single-Molecule Fluorescence Microscopy and Implications for Super-Resolution Imaging Backlund, Mikael P.; Lew, Matthew D.; Backer, Adam S. ChemPhysChem, Vol. 15, Issue 4 https://doi.org/10.1002/cphc.201300880	journal	December 2013
Development and testing of a general amber force field Wang, Junmei; Wolf, Romain M.; Caldwell, James W. Journal of Computational Chemistry, Vol. 25, Issue 9 https://doi.org/10.1002/jcc.20035	journal	January 2004
GROMACS: Fast, flexible, and free Van Der Spoel, David; Lindahl, Erik; Hess, Berk Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20291	journal	January 2005
A glow discharge unit to render electron microscope grids and other surfaces hydrophilic Aebi, Ueli; Pollard, Thomas D. Journal of Electron Microscopy Technique, Vol. 7, Issue 1 https://doi.org/10.1002/jemt.1060070104	journal	September 1987
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
DNA base stacking involving adenine and 2-aminopurine van Mourik, Tanja; Hogan, Simon W. L. Structural Chemistry, Vol. 27, Issue 1 https://doi.org/10.1007/s11224-015-0708-3	journal	December 2015
An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer Toupkanloo, Hossein Azizi; Rahmani, Zoha Applied Biological Chemistry, Vol. 61, Issue 2 https://doi.org/10.1007/s13765-018-0348-6	journal	February 2018
Methods for spherical data analysis and visualization Leong, Philip; Carlile, Simon Journal of Neuroscience Methods, Vol. 80, Issue 2 https://doi.org/10.1016/S0165-0270(97)00201-X	journal	April 1998
Engineering couplings for exciton transport using synthetic DNA scaffolds Hart, Stephanie M.; Chen, Wei Jia; Banal, James L. Chem, Vol. 7, Issue 3 https://doi.org/10.1016/j.chempr.2020.12.020	journal	March 2021
Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments Levitus, Marcia; Ranjit, Suman Quarterly Reviews of Biophysics, Vol. 44, Issue 1 https://doi.org/10.1017/S0033583510000247	journal	November 2010
Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms Mirkovic, Tihana; Ostroumov, Evgeny E.; Anna, Jessica M. Chemical Reviews, Vol. 117, Issue 2 https://doi.org/10.1021/acs.chemrev.6b00002	journal	March 2016
Assessing the Current State of Amber Force Field Modifications for DNA Galindo-Murillo, Rodrigo; Robertson, James C.; Zgarbová, Marie Journal of Chemical Theory and Computation, Vol. 12, Issue 8 https://doi.org/10.1021/acs.jctc.6b00186	journal	July 2016
Cryogenic Far-Field Fluorescence Nanoscopy: Evaluation with DNA Origami Furubayashi, Taku; Ishida, Keita; Nakata, Eiji The Journal of Physical Chemistry B, Vol. 124, Issue 35 https://doi.org/10.1021/acs.jpcb.0c04721	journal	August 2020
Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds Mass, Olga A.; Wilson, Christopher K.; Roy, Simon K. The Journal of Physical Chemistry B, Vol. 124, Issue 43 https://doi.org/10.1021/acs.jpcb.0c06480	journal	October 2020
Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation Zacharias, Martin The Journal of Physical Chemistry B, Vol. 124, Issue 46 https://doi.org/10.1021/acs.jpcb.0c07670	journal	November 2020
Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates Roy, Simon K.; Mass, Olga A.; Kellis, Donald L. The Journal of Physical Chemistry B, Vol. 125, Issue 50 https://doi.org/10.1021/acs.jpcb.1c07602	journal	December 2021
Can a DNA Origami Structure Constrain the Position and Orientation of an Attached Dye Molecule? Mathur, Divita; Kim, Young C.; Díaz, Sebastián A. The Journal of Physical Chemistry C, Vol. 125, Issue 2 https://doi.org/10.1021/acs.jpcc.0c09258	journal	December 2020
DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity Ochmann, Sarah E.; Joshi, Himanshu; Büber, Ece Nano Letters, Vol. 21, Issue 20 https://doi.org/10.1021/acs.nanolett.1c02584	journal	October 2021
Electrostatic Effect of Functional Surfaces on the Activity of Adsorbed Enzymes: Simulations and Experiments Zheng, He; Yang, Sheng-Jiang; Zheng, Yong-Chao ACS Applied Materials & Interfaces, Vol. 12, Issue 31 https://doi.org/10.1021/acsami.0c08080	journal	July 2020
Doping Evolution and Junction Formation in Stacked Cyanine Dye Light-Emitting Electrochemical Cells Jenatsch, Sandra; Wang, Lei; Bulloni, Matia ACS Applied Materials & Interfaces, Vol. 8, Issue 10 https://doi.org/10.1021/acsami.5b12055	journal	March 2016
Efficient One-Step PEG-Silane Passivation of Glass Surfaces for Single-Molecule Fluorescence Studies Gidi, Yasser; Bayram, Serene; Ablenas, Christopher J. ACS Applied Materials & Interfaces, Vol. 10, Issue 46 https://doi.org/10.1021/acsami.8b15796	journal	October 2018
Defining the Basis of Cyanine Phototruncation Enables a New Approach to Single-Molecule Localization Microscopy Matikonda, Siddharth S.; Helmerich, Dominic A.; Meub, Mara ACS Central Science, Vol. 7, Issue 7 https://doi.org/10.1021/acscentsci.1c00483	journal	June 2021
DNA Nanostructures: Current Challenges and Opportunities for Cellular Delivery Lacroix, Aurélie; Sleiman, Hanadi F. ACS Nano, Vol. 15, Issue 3 https://doi.org/10.1021/acsnano.0c06136	journal	February 2021
Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures Hübner, Kristina; Joshi, Himanshu; Aksimentiev, Aleksei ACS Nano, Vol. 15, Issue 3 https://doi.org/10.1021/acsnano.0c10259	journal	March 2021
A Single Molecule Polyphenylene-Vinylene Photonic Wire Madsen, Mikael; Bakke, Mette R.; Gudnason, Daniel A. ACS Nano, Vol. 15, Issue 6 https://doi.org/10.1021/acsnano.0c10922	journal	May 2021
Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects Green, Christopher M.; Hughes, William L.; Graugnard, Elton ACS Nano, Vol. 15, Issue 7 https://doi.org/10.1021/acsnano.1c01976	journal	June 2021
Exciton Delocalization in a DNA-Templated Organic Semiconductor Dimer Assembly Wang, Xiao; Sha, Ruojie; Knowlton, William B. ACS Nano, Vol. 16, Issue 1 https://doi.org/10.1021/acsnano.1c09143	journal	January 2022
An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases Kellis, Donald L.; Sarter, Christopher; Cannon, Brittany L. ACS Nano, Vol. 13, Issue 3 https://doi.org/10.1021/acsnano.8b07504	journal	February 2019
Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds Engelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H. ACS Nano, Vol. 13, Issue 5 https://doi.org/10.1021/acsnano.9b01025	journal	April 2019
DNA Origami Route for Nanophotonics Kuzyk, Anton; Jungmann, Ralf; Acuna, Guillermo P. ACS Photonics, Vol. 5, Issue 4 https://doi.org/10.1021/acsphotonics.7b01580	journal	February 2018
Developing DNA Nanotechnology Using Single-Molecule Fluorescence Tsukanov, Roman; Tomov, Toma E.; Liber, Miran Accounts of Chemical Research, Vol. 47, Issue 6 https://doi.org/10.1021/ar500027d	journal	May 2014
The Structure of Cyanine 5 Terminally Attached to Double-Stranded DNA: Implications for FRET Studies Iqbal, Asif; Wang, Lihua; Thompson, Katherine C. Biochemistry, Vol. 47, Issue 30 https://doi.org/10.1021/bi800773f	journal	July 2008
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model Bayly, Christopher I.; Cieplak, Piotr; Cornell, Wendy The Journal of Physical Chemistry, Vol. 97, Issue 40 https://doi.org/10.1021/j100142a004	journal	October 1993
Toward True DNA Base-Stacking Energies: MP2, CCSD(T), and Complete Basis Set Calculations Hobza, Pavel; Šponer, Jiří Journal of the American Chemical Society, Vol. 124, Issue 39 https://doi.org/10.1021/ja026759n	journal	October 2002
Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity Sindbert, Simon; Kalinin, Stanislav; Nguyen, Hien Journal of the American Chemical Society, Vol. 133, Issue 8 https://doi.org/10.1021/ja105725e	journal	March 2011
Development of a Robust Model System of FRET using Base Surrogates Tethering Fluorophores for Strict Control of Their Position and Orientation within DNA Duplex Kato, Tomohiro; Kashida, Hiromu; Kishida, Hideo Journal of the American Chemical Society, Vol. 135, Issue 2 https://doi.org/10.1021/ja309279w	journal	January 2013
Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides Gorman, Jeffrey; Orsborne, Sarah R. E.; Sridhar, Akshay Journal of the American Chemical Society, Vol. 144, Issue 1 https://doi.org/10.1021/jacs.1c10241	journal	December 2021
Photophysical and Dynamical Properties of Doubly Linked Cy3–DNA Constructs Stennett, Elana M. S.; Ma, Ning; van der Vaart, Arjan The Journal of Physical Chemistry B, Vol. 118, Issue 1 https://doi.org/10.1021/jp410976p	journal	December 2013
Improved Parametrization of Li ⁺ , Na ⁺ , K ⁺ , and Mg ²⁺ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems Yoo, Jejoong; Aksimentiev, Aleksei The Journal of Physical Chemistry Letters, Vol. 3, Issue 1 https://doi.org/10.1021/jz201501a	journal	December 2011
DNA Nanoarchitectonics: Assembled DNA at Interfaces Howorka, Stefan Langmuir, Vol. 29, Issue 24 https://doi.org/10.1021/la3045785	journal	February 2013
DNA nanotechnology Seeman, Nadrian C.; Sleiman, Hanadi F. Nature Reviews Materials, Vol. 3, Issue 1 https://doi.org/10.1038/natrevmats.2017.68	journal	November 2017
Folding DNA to create nanoscale shapes and patterns Rothemund, Paul W. K. Nature, Vol. 440, Issue 7082, p. 297-302 https://doi.org/10.1038/nature04586	journal	March 2006
Self-assembly of DNA into nanoscale three-dimensional shapes Douglas, Shawn M.; Dietz, Hendrik; Liedl, Tim Nature, Vol. 459, Issue 7245 https://doi.org/10.1038/nature08016	journal	May 2009
Optimized measurements of separations and angles between intra-molecular fluorescent markers Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9621	journal	October 2015
Programmed coherent coupling in a synthetic DNA-based excitonic circuit Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi Nature Materials, Vol. 17, Issue 2 https://doi.org/10.1038/nmat5033	journal	November 2017
Placing molecules with Bohr radius resolution using DNA origami Funke, Jonas J.; Dietz, Hendrik Nature Nanotechnology, Vol. 11, Issue 1 https://doi.org/10.1038/nnano.2015.240	journal	October 2015
The biological applications of DNA nanomaterials: current challenges and future directions Ma, Wenjuan; Zhan, Yuxi; Zhang, Yuxin Signal Transduction and Targeted Therapy, Vol. 6, Issue 1 https://doi.org/10.1038/s41392-021-00727-9	journal	October 2021
All-optical field-free three-dimensional orientation of asymmetric-top molecules Lin, Kang; Tutunnikov, Ilia; Qiang, Junjie Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07567-2	journal	December 2018
Anti-quenching NIR-II molecular fluorophores for in vivo high-contrast imaging and pH sensing Wang, Shangfeng; Fan, Yong; Li, Dandan Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09043-x	journal	March 2019
How to control single-molecule rotation Simpson, Grant J.; García-López, Víctor; Daniel Boese, A. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12605-8	journal	October 2019
Designed folding pathway of modular coiled-coil-based proteins Aupič, Jana; Strmšek, Žiga; Lapenta, Fabio Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21185-5	journal	February 2021
An alternative approach to nucleic acid memory Dickinson, George D.; Mortuza, Golam Md; Clay, William Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22277-y	journal	April 2021
RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds Geary, Cody; Grossi, Guido; McRae, Ewan K. S. Nature Chemistry, Vol. 13, Issue 6 https://doi.org/10.1038/s41557-021-00679-1	journal	May 2021
Constructing covalent organic nanoarchitectures molecule by molecule via scanning probe manipulation Zhong, Qigang; Ihle, Alexander; Ahles, Sebastian Nature Chemistry, Vol. 13, Issue 11 https://doi.org/10.1038/s41557-021-00773-4	journal	September 2021
Exploiting chemistry and molecular systems for quantum information science Wasielewski, Michael R.; Forbes, Malcolm D. E.; Frank, Natia L. Nature Reviews Chemistry, Vol. 4, Issue 9 https://doi.org/10.1038/s41570-020-0200-5	journal	July 2020
An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions Schueder, Florian; Stein, Johannes; Stehr, Florian Nature Methods, Vol. 16, Issue 11 https://doi.org/10.1038/s41592-019-0584-7	journal	October 2019
Rotaxane rings promote oblique packing and extended lifetimes in DNA-templated molecular dye aggregates Barclay, Matthew S.; Roy, Simon K.; Huff, Jonathan S. Communications Chemistry, Vol. 4, Issue 1 https://doi.org/10.1038/s42004-021-00456-8	journal	February 2021
DNA origami Dey, Swarup; Fan, Chunhai; Gothelf, Kurt V. Nature Reviews Methods Primers, Vol. 1, Issue 1 https://doi.org/10.1038/s43586-020-00009-8	journal	January 2021
Plasmon resonance tuning using DNA origami actuation Piantanida, Luca; Naumenko, Denys; Torelli, Emanuela Chemical Communications, Vol. 51, Issue 23 https://doi.org/10.1039/C5CC00778J	journal	January 2015
Measuring local conformations and conformational disorder of (Cy3) ₂ dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy Heussman, Dylan; Kittell, Justin; Kringle, Loni Faraday Discussions, Vol. 216 https://doi.org/10.1039/C8FD00245B	journal	January 2019
Single-molecule DNA origami aptasensors for real-time biomarker detection Cervantes-Salguero, Keitel; Freeley, Mark; Chávez, Jorge L. Journal of Materials Chemistry B, Vol. 8, Issue 30 https://doi.org/10.1039/D0TB01291B	journal	January 2020
Progress and perspective on chiral plasmonic nanostructures enabled by DNA programming methodology Yang, Hao; Li, Huacheng; Tang, Pan Materials Advances, Vol. 2, Issue 22 https://doi.org/10.1039/D1MA00781E	journal	January 2021
How fluorescent labels affect the kinetics of the toehold-mediated DNA strand displacement reaction Li, Chengxu; Li, Zhigang; Han, Wenjie Chemical Communications, Vol. 58, Issue 39 https://doi.org/10.1039/D2CC01072K	journal	January 2022
Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections Chai, Jeng-Da; Head-Gordon, Martin Physical Chemistry Chemical Physics, Vol. 10, Issue 44 https://doi.org/10.1039/b810189b	journal	January 2008
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
How does basis set superposition error change the potential surfaces for hydrogen‐bonded dimers? Simon, Sílvia; Duran, Miquel; Dannenberg, J. J. The Journal of Chemical Physics, Vol. 105, Issue 24 https://doi.org/10.1063/1.472902	journal	December 1996
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids Iqbal, A.; Arslan, S.; Okumus, B. Proceedings of the National Academy of Sciences, Vol. 105, Issue 32 https://doi.org/10.1073/pnas.0801707105	journal	August 2008
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Olson, W. K.; Gorin, A. A.; Lu, X. -J. Proceedings of the National Academy of Sciences, Vol. 95, Issue 19 https://doi.org/10.1073/pnas.95.19.11163	journal	September 1998
Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations Deniz, A. A.; Dahan, M.; Grunwell, J. R. Proceedings of the National Academy of Sciences, Vol. 96, Issue 7 https://doi.org/10.1073/pnas.96.7.3670	journal	March 1999
The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors Boys, S.F.; Bernardi, F. Molecular Physics, Vol. 19, Issue 4, p. 553-566 https://doi.org/10.1080/00268977000101561	journal	October 1970
Fluorescent J-aggregates of cyanine dyes: basic research and applications review Bricks, Julia L.; Slominskii, Yuri L.; Panas, Ihor D. Methods and Applications in Fluorescence, Vol. 6, Issue 1 https://doi.org/10.1088/2050-6120/AA8D0D	journal	December 2017
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging Ovesný, Martin; Křížek, Pavel; Borkovec, Josef Bioinformatics, Vol. 30, Issue 16 https://doi.org/10.1093/bioinformatics/btu202	journal	May 2014
Dinucleotides as simple models of the base stacking-unstacking component of DNA ‘breathing’ mechanisms Beyerle, Eric R.; Dinpajooh, Mohammadhasan; Ji, Huiying Nucleic Acids Research, Vol. 49, Issue 4 https://doi.org/10.1093/nar/gkab015	journal	January 2021
Choice of fluorophore affects dynamic DNA nanostructures Jahnke, Kevin; Grubmüller, Helmut; Igaev, Maxim Nucleic Acids Research, Vol. 49, Issue 7 https://doi.org/10.1093/nar/gkab201	journal	March 2021
Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases Mignon, P. Nucleic Acids Research, Vol. 33, Issue 6 https://doi.org/10.1093/nar/gki317	journal	March 2005
Passive linear nanoscale optical and molecular electronics device synthesis from nanoparticles Yurke, Bernard; Kuang, Wan Physical Review A, Vol. 81, Issue 3 https://doi.org/10.1103/PhysRevA.81.033814	journal	March 2010
The Fisher-Bingham Distribution on the Sphere Kent, John T. Journal of the Royal Statistical Society: Series B (Methodological), Vol. 44, Issue 1 https://doi.org/10.1111/j.2517-6161.1982.tb01189.x	journal	September 1982
A self-assembled nanoscale robotic arm controlled by electric fields Kopperger, Enzo; List, Jonathan; Madhira, Sushi Science, Vol. 359, Issue 6373 https://doi.org/10.1126/science.aao4284	journal	January 2018
Absolute and arbitrary orientation of single-molecule shapes Gopinath, Ashwin; Thachuk, Chris; Mitskovets, Anya Science, Vol. 371, Issue 6531 https://doi.org/10.1126/science.abd6179	journal	February 2021
Imaging Dynamic Processes in Multiple Dimensions and Length Scales Filbrun, Seth L.; Zhao, Fei; Chen, Kuangcai Annual Review of Physical Chemistry, Vol. 73, Issue 1 https://doi.org/10.1146/annurev-physchem-090519-034100	journal	April 2022
Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters Aguet, Francois; Geissbühler, Stefan; Märki, Iwan Optics Express, Vol. 17, Issue 8 https://doi.org/10.1364/OE.17.006829	journal	January 2009
Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks Cervantes-Salguero, Keitel; Hamada, Shogo; Nomura, Shin-ichiro Nanomaterials, Vol. 5, Issue 1 https://doi.org/10.3390/nano5010208	journal	February 2015
FRET nanoscopy enables seamless imaging of molecular assemblies with sub-nanometer resolution Budde, Jan-Hendrik; van der Voort, Nicolaas; Felekyan, Suren arXiv https://doi.org/10.48550/arXiv.2108.00024	preprint	January 2021

Similar Records

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

Journal Article · Tue Jan 17 23:00:00 EST 2023 · Journal of Chemical Physics · OSTI ID:1909709

Related Subjects

77 NANOSCIENCE AND NANOTECHNOLOGY
DNA origami
DNA-PAINT
cyanine Cy5 dyes
density function theory
dipolar imaging
dye intercalation
mechanical stretching
molecular dynamics simulations
nanoarchitectural control
super-resolution microscopy

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

Citation Formats

References (95)

Similar Records

Related Subjects