Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Mass, Olga A.; Wilson, Christopher Kimo; Roy, Simon K.; Barclay, Matthew S.; Patten, Lance K.; Terpetschnig, Ewald A.; Lee, Jeunghoon; Pensack, Ryan D.; Yurke, Bernard; Knowlton, William B.

doi:10.1021/acs.jpcb.0c06480

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Journal Article · Wed Oct 14 00:00:00 EDT 2020 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

DOI:https://doi.org/10.1021/acs.jpcb.0c06480· OSTI ID:1670511

^[1]; ^[2]; ^[2]; ^[2]; ^[2]; ^[3]; ^[2]; ^[2]; ^[2]; ^[2]

Boise State Univ., ID (United States); Boise State University, Division of Research and Economic Development
Boise State Univ., ID (United States)
SETA BioMedicals, LLC, Urbana, IL (United States)

Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. DNA is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations—transverse dimer, adjacent dimer, and tetramer—were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes were obtained by simultaneous fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of dye mutual orientation in the aggregates enabled close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. Furthermore, these results encourage the application of squaraine-based aggregates in next generation systems driven by molecular excitons.

View Accepted Manuscript (DOE)

Research Organization:: Boise State University, ID (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); MJ Murdock Charitable Trust; Idaho State Board of Education

Grant/Contract Number:: SC0020089

OSTI ID:: 1670511

Journal Information:: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Journal Name: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry Journal Issue: 43 Vol. 124; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (120)

Exciton Transport in Molecular Aggregates - From Natural Antennas to Synthetic Chromophore Systems Brixner, Tobias; Hildner, Richard; Köhler, Jürgen Advanced Energy Materials, Vol. 7, Issue 16 https://doi.org/10.1002/aenm.201700236	journal	July 2017
Über die Veränderlichkeit der Absorptionsspektren in Lösungen und die Nebenvalenzen als ihre Ursache Scheibe, G. Angewandte Chemie, Vol. 50, Issue 11 https://doi.org/10.1002/ange.19370501103	journal	March 1937
Cyclotrimethine Dyes Derived from Squaric Acid Treibs, A.; Jacob, K. Angewandte Chemie International Edition in English, Vol. 4, Issue 8 https://doi.org/10.1002/anie.196506941	journal	August 1965
Alternating Hetero H Aggregation of Different Dyes by Interstrand Stacking from Two DNA-Dye Conjugates Kashida, Hiromu; Asanuma, Hiroyuki; Komiyama, Makoto Angewandte Chemie International Edition, Vol. 43, Issue 47 https://doi.org/10.1002/anie.200460870	journal	December 2004
Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular Beacon Hara, Yuichi; Fujii, Taiga; Kashida, Hiromu Angewandte Chemie International Edition, Vol. 49, Issue 32 https://doi.org/10.1002/anie.201001459	journal	July 2010
J-Aggregates: From Serendipitous Discovery to Supramolecular Engineering of Functional Dye Materials Würthner, Frank; Kaiser, Theo E.; Saha-Möller, Chantu R. Angewandte Chemie International Edition, Vol. 50, Issue 15 https://doi.org/10.1002/anie.201002307	journal	March 2011
A DNA-Based Light-Harvesting Antenna Garo, Florian; Häner, Robert Angewandte Chemie International Edition, Vol. 51, Issue 4 https://doi.org/10.1002/anie.201103295	journal	December 2011
Hybridization-Sensitive On–Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching Ikeda, Shuji; Okamoto, Akimitsu Chemistry – An Asian Journal, Vol. 3, Issue 6 https://doi.org/10.1002/asia.200800014	journal	June 2008
Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering Kashida, Hiromu; Tanaka, Masayuki; Baba, Seiki Chemistry - A European Journal, Vol. 12, Issue 3 https://doi.org/10.1002/chem.200500111	journal	January 2006
DNA-Assisted Self-Assembly of Pyrene Foldamers Häner, Robert; Samain, Florent; Malinovskii, Vladimir L. Chemistry - A European Journal, Vol. 15, Issue 23 https://doi.org/10.1002/chem.200900369	journal	June 2009
Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton Theory Fujii, Taiga; Kashida, Hiromu; Asanuma, Hiroyuki Chemistry - A European Journal, Vol. 15, Issue 39 https://doi.org/10.1002/chem.200900962	journal	October 2009
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Theory of excitation transfer in coupled nanostructures – from quantum dots to light harvesting complexes Richter, Marten; Ahn, Kwang Jun; Knorr, Andreas physica status solidi (b), Vol. 243, Issue 10 https://doi.org/10.1002/pssb.200668053	journal	August 2006
Red Chlorophylls in the Exciton Model of Photosystem I Vaitekonis, Sarunas; Trinkunas, Gediminas; Valkunas, Leonas Photosynthesis Research, Vol. 86, Issue 1-2 https://doi.org/10.1007/s11120-005-2747-x	journal	November 2005
Synthesis, spectral properties and photostabilities of symmetrical and unsymmetrical squarines; a new class of flourophores with long-wavelength exiciation and emmision Terpetsching, Ewald; Szmacinski, Henryk; Lakowicz, Joseph R. Analytica Chimica Acta, Vol. 282, Issue 3 https://doi.org/10.1016/0003-2670(93)80128-8	journal	October 1993
Studies of polaron motion Holstein, T. Annals of Physics, Vol. 8, Issue 3 https://doi.org/10.1016/0003-4916(59)90002-8	journal	November 1959
Extended dipole model for aggregates of dye molecules Czikklely, V.; Forsterling, H. D.; Kuhn, H. Chemical Physics Letters, Vol. 6, Issue 3 https://doi.org/10.1016/0009-2614(70)80220-2	journal	August 1970
Nucleic acid junctions and lattices Seeman, Nadrian C. Journal of Theoretical Biology, Vol. 99, Issue 2 https://doi.org/10.1016/0022-5193(82)90002-9	journal	November 1982
Synthesis and characterization of unsymmetrical squaraines: a new class of cyanine dyes Terpetschnig, E. Dyes and Pigments, Vol. 21, Issue 3 https://doi.org/10.1016/0143-7208(93)85016-S	journal	January 1993
A unified theory of radiative and radiationless molecular energy transfer Andrews, D. L. Chemical Physics, Vol. 135, Issue 2 https://doi.org/10.1016/0301-0104(89)87019-3	journal	August 1989
Theory of exciton-vibrational dynamics in molecular dimers Kühn, Oliver; Renger, Thomas; May, Volkhard Chemical Physics, Vol. 204, Issue 1 https://doi.org/10.1016/0301-0104(95)00448-3	journal	March 1996
The Molecular Exciton Model McRae, E. G.; Kasha, M. Physical Processes in Radiation Biology https://doi.org/10.1016/B978-1-4831-9824-8.50007-4	book	January 1964
The J-band of organic dyes: lineshape and coherence length Eisfeld, Alexander; Briggs, John S. Chemical Physics, Vol. 281, Issue 1 https://doi.org/10.1016/S0301-0104(02)00594-3	journal	July 2002
Ultrafast excitation energy transfer dynamics in photosynthetic pigment–protein complexes Renger, Thomas; May, Volkhard; Kühn, Oliver Physics Reports, Vol. 343, Issue 3 https://doi.org/10.1016/S0370-1573(00)00078-8	journal	March 2001
The crystal structure of the light-harvesting complex II (B800–850) from Rhodospirillum molischianum Koepke, Juergen; Hu, Xiche; Muenke, Cornelia Structure, Vol. 4, Issue 5 https://doi.org/10.1016/S0969-2126(96)00063-9	journal	May 1996
Functionalized DNA nanostructures for light harvesting and charge separation Albinsson, Bo; Hannestad, Jonas K.; Börjesson, Karl Coordination Chemistry Reviews, Vol. 256, Issue 21-22 https://doi.org/10.1016/j.ccr.2012.02.024	journal	November 2012
A structural model for cyanine dyes templated into the minor groove of DNA Tomlinson, Aimée; Frezza, Brian; Kofke, Matthew Chemical Physics, Vol. 325, Issue 1 https://doi.org/10.1016/j.chemphys.2005.10.007	journal	June 2006
Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectra Abramavicius, Darius; Palmieri, Benoit; Mukamel, Shaul Chemical Physics, Vol. 357, Issue 1-3 https://doi.org/10.1016/j.chemphys.2008.10.010	journal	February 2009
Determining the spatial coherence of excitons from the photoluminescence spectrum in charge-transfer J-aggregates Hestand, Nicholas J.; Spano, Frank C. Chemical Physics, Vol. 481 https://doi.org/10.1016/j.chemphys.2016.06.005	journal	December 2016
Comparison of a series of hydrophilic squaraine and cyanine dyes for use as biological labels Markova, Larysa I.; Terpetschnig, Ewald A.; Patsenker, Leonid D. Dyes and Pigments, Vol. 99, Issue 3 https://doi.org/10.1016/j.dyepig.2013.06.022	journal	December 2013
Synthesis, photophysical properties and applications of NIR absorbing unsymmetrical squaraines: A review Khopkar, Sushil; Shankarling, Ganapati Dyes and Pigments, Vol. 170 https://doi.org/10.1016/j.dyepig.2019.107645	journal	November 2019
Coherent interactions of dyes assembled on DNA Asanuma, Hiroyuki; Fujii, Taiga; Kato, Tomohiro Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 13, Issue 2 https://doi.org/10.1016/j.jphotochemrev.2012.04.002	journal	June 2012
Squaraine dyes: The hierarchical synthesis and its application in optical detection Xia, Guomin; Wang, Hongming Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 31 https://doi.org/10.1016/j.jphotochemrev.2017.03.001	journal	June 2017
Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic Materials Hestand, Nicholas J.; Spano, Frank C. Accounts of Chemical Research, Vol. 50, Issue 2 https://doi.org/10.1021/acs.accounts.6b00576	journal	January 2017
Squaraine Dyes: Molecular Design for Different Applications and Remaining Challenges Ilina, Kristina; MacCuaig, William M.; Laramie, Matthew Bioconjugate Chemistry, Vol. 31, Issue 2 https://doi.org/10.1021/acs.bioconjchem.9b00482	journal	July 2019
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
Organic Optoelectronic Materials: Mechanisms and Applications Ostroverkhova, Oksana Chemical Reviews, Vol. 116, Issue 22 https://doi.org/10.1021/acs.chemrev.6b00127	journal	October 2016
Expanded Theory of H- and J-Molecular Aggregates: The Effects of Vibronic Coupling and Intermolecular Charge Transfer Hestand, Nicholas J.; Spano, Frank C. Chemical Reviews, Vol. 118, Issue 15 https://doi.org/10.1021/acs.chemrev.7b00581	journal	April 2018
Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes Nicoli, Francesca; Roos, Matthias K.; Hemmig, Elisa A. The Journal of Physical Chemistry A, Vol. 120, Issue 50 https://doi.org/10.1021/acs.jpca.6b10939	journal	December 2016
Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System Cannon, Brittany L.; Kellis, Donald L.; Patten, Lance K. The Journal of Physical Chemistry A, Vol. 121, Issue 37 https://doi.org/10.1021/acs.jpca.7b04344	journal	September 2017
Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates Cannon, Brittany L.; Patten, Lance K.; Kellis, Donald L. The Journal of Physical Chemistry A, Vol. 122, Issue 8 https://doi.org/10.1021/acs.jpca.7b12668	journal	February 2018
Explicit Correlated Exciton-Vibrational Dynamics of the FMO Complex Schulze, J.; Kühn, O. The Journal of Physical Chemistry B, Vol. 119, Issue 20 https://doi.org/10.1021/acs.jpcb.5b03928	journal	May 2015
Spectroscopic Studies of Cryptophyte Light Harvesting Proteins: Vibrations and Coherent Oscillations Arpin, Paul C.; Turner, Daniel B.; McClure, Scott D. The Journal of Physical Chemistry B, Vol. 119, Issue 31 https://doi.org/10.1021/acs.jpcb.5b04704	journal	July 2015
Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds Cunningham, Paul D.; Kim, Young C.; Díaz, Sebastián A. The Journal of Physical Chemistry B, Vol. 122, Issue 19 https://doi.org/10.1021/acs.jpcb.8b02134	journal	April 2018
Exciton Dynamics from Strong to Weak Coupling Limit Illustrated on a Series of Squaraine Dimers Röhr, Merle I. S.; Marciniak, Henning; Hoche, Joscha The Journal of Physical Chemistry C, Vol. 122, Issue 15 https://doi.org/10.1021/acs.jpcc.8b00847	journal	March 2018
Davydov Splitting in Squaraine Dimers Zhong, Chuwei; Bialas, David; Collison, Christopher J. The Journal of Physical Chemistry C, Vol. 123, Issue 30 https://doi.org/10.1021/acs.jpcc.9b05297	journal	July 2019
Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency Mazuski, Richard J.; Díaz, Sebastián A.; Wood, Ryan E. The Journal of Physical Chemistry Letters, Vol. 11, Issue 10 https://doi.org/10.1021/acs.jpclett.0c01020	journal	May 2020
Photophysics of J-Aggregate-Mediated Energy Transfer on DNA Banal, James L.; Kondo, Toru; Veneziano, Rémi The Journal of Physical Chemistry Letters, Vol. 8, Issue 23 https://doi.org/10.1021/acs.jpclett.7b01898	journal	November 2017
DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes Huff, Jonathan S.; Davis, Paul H.; Christy, Allison The Journal of Physical Chemistry Letters, Vol. 10, Issue 10 https://doi.org/10.1021/acs.jpclett.9b00404	journal	April 2019
Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling Sawaya, Nicolas P. D.; Rappoport, Dmitrij; Tabor, Daniel P. ACS Nano, Vol. 12, Issue 7 https://doi.org/10.1021/acsnano.8b00584	journal	June 2018
DNA-Templated Assembly of Helical Cyanine Dye Aggregates: A Supramolecular Chain Polymerization Hannah, Kristen C.; Armitage, Bruce A. Accounts of Chemical Research, Vol. 37, Issue 11 https://doi.org/10.1021/ar030257c	journal	November 2004
The Spectral Signatures of Frenkel Polarons in H- and J-Aggregates Spano, Frank C. Accounts of Chemical Research, Vol. 43, Issue 3 https://doi.org/10.1021/ar900233v	journal	March 2010
Density Matrix Analysis and Simulation of Electronic Excitations in Conjugated and Aggregated Molecules Tretiak, Sergei; Mukamel, Shaul Chemical Reviews, Vol. 102, Issue 9 https://doi.org/10.1021/cr0101252	journal	September 2002
Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives Abramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V. Chemical Reviews, Vol. 109, Issue 6 https://doi.org/10.1021/cr800268n	journal	June 2009
DNA-Templated Formation of a Helical Cyanine Dye J-Aggregate Wang, Miaomiao; Silva, Gloria L.; Armitage, Bruce A. Journal of the American Chemical Society, Vol. 122, Issue 41 https://doi.org/10.1021/ja002184n	journal	October 2000
DNA−Dye Conjugates for Controllable H* Aggregation ¹ Asanuma, Hiroyuki; Shirasuka, Kenji; Takarada, Tohru Journal of the American Chemical Society, Vol. 125, Issue 8 https://doi.org/10.1021/ja021153k	journal	February 2003
Analysis of the UV/Vis and CD Spectral Line Shapes of Carotenoid Assemblies: Spectral Signatures of Chiral H -Aggregates Spano, Frank C. Journal of the American Chemical Society, Vol. 131, Issue 12 https://doi.org/10.1021/ja806853v	journal	April 2009
Exciton Interactions in Nonconjugated Squaraine Dimers. Mechanisms for Coupling and Consequences for Photophysics and Photochemistry Liang, Kangning; Farahat, Mohammad S.; Perlstein, Jerry Journal of the American Chemical Society, Vol. 119, Issue 4 https://doi.org/10.1021/ja962091z	journal	January 1997
Molecular Recognition of PNA-Containing Hybrids: Spontaneous Assembly of Helical Cyanine Dye Aggregates on PNA Templates Smith, Jeffrey O.; Olson, Darren A.; Armitage, Bruce A. Journal of the American Chemical Society, Vol. 121, Issue 12 https://doi.org/10.1021/ja9837553	journal	March 1999
Spontaneous Assembly of Helical Cyanine Dye Aggregates on DNA Nanotemplates Seifert, Jennifer L.; Connor, Rebecca E.; Kushon, Stuart A. Journal of the American Chemical Society, Vol. 121, Issue 13 https://doi.org/10.1021/ja984279j	journal	April 1999
Characterization of Chiral H and J Aggregates of Cyanine Dyes Formed by DNA Templating Using Stark and Fluorescence Spectroscopies Chowdhury, Arindam; Wachsmann-Hogiu, Sebastian; Bangal, Prakriti R. The Journal of Physical Chemistry B, Vol. 105, Issue 48 https://doi.org/10.1021/jp012825g	journal	December 2001
Stark Spectroscopy of Size-Selected Helical H-Aggregates of a Cyanine Dye Templated by Duplex DNA. Effect of Exciton Coupling on Electronic Polarizabilities ^† Chowdhury, Arindam; Yu, Liping; Raheem, Izzat The Journal of Physical Chemistry A, Vol. 107, Issue 18 https://doi.org/10.1021/jp021866p	journal	May 2003
Formation of Stable BOBO-3 H-Aggregate Complexes Hinders DNA Hybridization Ruedas-Rama, Maria J.; Alvarez-Pez, Jose M.; Orte, Angel The Journal of Physical Chemistry B, Vol. 114, Issue 27 https://doi.org/10.1021/jp103131r	journal	June 2010
Interaction of YOYO-3 with Different DNA Templates to Form H-Aggregates Ruedas-Rama, Maria J.; Orte, Angel; Martin-Domingo, Maria C. The Journal of Physical Chemistry B, Vol. 118, Issue 23 https://doi.org/10.1021/jp5022888	journal	May 2014
Exciton Delocalization and Transport in Photosystem I of Cyanobacteria Synechococcus elongates : Simulation Study of Coherent Two-Dimensional Optical Signals Abramavicius, Darius; Mukamel, Shaul The Journal of Physical Chemistry B, Vol. 113, Issue 17 https://doi.org/10.1021/jp811339p	journal	April 2009
Pump−Probe Polarization Anisotropy Study of Femtosecond Energy Transfer within the Photosynthetic Reaction Center of Rhodobacter sphaeroides R26 Jonas, David M.; Lang, Matthew J.; Nagasawa, Yutaka The Journal of Physical Chemistry, Vol. 100, Issue 30 https://doi.org/10.1021/jp960708t	journal	January 1996
Excitons in Photosynthetic Purple Bacteria: Wavelike Motion or Incoherent Hopping? Chachisvilis, Mirianas; Kühn, Oliver; Pullerits, Tõnu The Journal of Physical Chemistry B, Vol. 101, Issue 37 https://doi.org/10.1021/jp963360a	journal	September 1997
Helical Aggregation of Cyanine Dyes on DNA Templates: Effect of Dye Structure on Formation of Homo- and Heteroaggregates Garoff, Rachel A.; Litzinger, Elizabeth A.; Connor, Rebecca E. Langmuir, Vol. 18, Issue 16 https://doi.org/10.1021/la025742f	journal	August 2002
Substituent Effects on the Assembly of Helical Cyanine Dye Aggregates in the Minor Groove of a DNA Template ^† Stadler, Andrea L.; Renikuntla, Babu Rao; Yaron, David Langmuir, Vol. 27, Issue 4 https://doi.org/10.1021/la104329c	journal	February 2011
DNA-Controlled Excitonic Switches Graugnard, Elton; Kellis, Donald L.; Bui, Hieu Nano Letters, Vol. 12, Issue 4 https://doi.org/10.1021/nl3004336	journal	January 2012
Excitonic AND Logic Gates on DNA Brick Nanobreadboards Cannon, Brittany L.; Kellis, Donald L.; Davis, Paul H. ACS Photonics, Vol. 2, Issue 3 https://doi.org/10.1021/ph500444d	journal	February 2015
Spectral Absorption and Fluorescence of Dyes in the Molecular State Jelley, Edwin E. Nature, Vol. 138, Issue 3502 https://doi.org/10.1038/1381009a0	journal	December 1936
Molecular, Nematic and Crystal States of I: I-Diethyl--Cyanine Chloride Jelley, Edwin E. Nature, Vol. 139, Issue 3519 https://doi.org/10.1038/139631b0	journal	April 1937
Aggregation of Dyes in Aqueous Solution Vickerstaff, T.; Lemin, D. R. Nature, Vol. 157, Issue 3986 https://doi.org/10.1038/157373a0	journal	March 1946
An immobile nucleic acid junction constructed from oligonucleotides Kallenbach, Neville R.; Ma, Rong-Ine; Seeman, Nadrian C. Nature, Vol. 305, Issue 5937 https://doi.org/10.1038/305829a0	journal	October 1983
Physics of life: The dawn of quantum biology Ball, Philip Nature, Vol. 474, Issue 7351 https://doi.org/10.1038/474272a	journal	June 2011
DNA in a material world Seeman, Nadrian C. Nature, Vol. 421, Issue 6921 https://doi.org/10.1038/nature01406	journal	January 2003
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
Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Engel, Gregory S.; Calhoun, Tessa R.; Read, Elizabeth L. Nature, Vol. 446, Issue 7137 https://doi.org/10.1038/nature05678	journal	April 2007
Complex shapes self-assembled from single-stranded DNA tiles Wei, Bryan; Dai, Mingjie; Yin, Peng Nature, Vol. 485, Issue 7400 https://doi.org/10.1038/nature11075	journal	May 2012
The coming of age of de novo protein design Huang, Po-Ssu; Boyken, Scott E.; Baker, David Nature, Vol. 537, Issue 7620 https://doi.org/10.1038/nature19946	journal	September 2016
Lessons from nature about solar light harvesting Scholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra Nature Chemistry, Vol. 3, Issue 10 https://doi.org/10.1038/nchem.1145	journal	September 2011
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
Quantum entanglement in photosynthetic light-harvesting complexes Sarovar, Mohan; Ishizaki, Akihito; Fleming, Graham R. Nature Physics, Vol. 6, Issue 6 https://doi.org/10.1038/nphys1652	journal	April 2010
Coherence in photosynthesis Scholes, Gregory D. Nature Physics, Vol. 7, Issue 6 https://doi.org/10.1038/nphys2013	journal	June 2011
Squaraine dyes: a mine of molecular materials Sreejith, Sivaramapanicker; Carol, Priya; Chithra, Parayalil J. Mater. Chem., Vol. 18, Issue 3 https://doi.org/10.1039/B707734C	journal	January 2008
Nucleic acid-guided assembly of aromatic chromophores Malinovskii, Vladimir L.; Wenger, Daniel; Häner, Robert Chem. Soc. Rev., Vol. 39, Issue 2 https://doi.org/10.1039/B910030J	journal	January 2010
The DNA three-way junction as a mould for tripartite chromophore assembly Probst, Markus; Wenger, Daniel; Biner, Sarah M. Org. Biomol. Chem., Vol. 10, Issue 4 https://doi.org/10.1039/C1OB06400B	journal	January 2012
A modular LHC built on the DNA three-way junction Probst, Markus; Langenegger, Simon M.; Häner, Robert Chem. Commun., Vol. 50, Issue 2 https://doi.org/10.1039/C3CC47490A	journal	January 2014
Photophysical processes in single molecule organic fluorescent probes Stennett, Elana M. S.; Ciuba, Monika A.; Levitus, Marcia Chem. Soc. Rev., Vol. 43, Issue 4 https://doi.org/10.1039/C3CS60211G	journal	January 2014
Squaraines as light-capturing materials in photovoltaic cells Jiang, Jian-Qiao; Sun, Chun-Lin; Shi, Zi-Fa RSC Adv., Vol. 4, Issue 62 https://doi.org/10.1039/C4RA03972F	journal	January 2014
Self-assembly of organic dyes in supramolecular aggregates Heyne, Belinda Photochemical & Photobiological Sciences, Vol. 15, Issue 9 https://doi.org/10.1039/C6PP00221H	journal	January 2016
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
Coherently and fluorescence-detected two-dimensional electronic spectroscopy: direct comparison on squaraine dimers Malý, Pavel; Lüttig, Julian; Mueller, Stefan Physical Chemistry Chemical Physics, Vol. 22, Issue 37 https://doi.org/10.1039/D0CP03218B	journal	January 2020
Photon harvesting by excimer-forming multichromophores Adeyemi, Oliver O.; Malinovskii, Vladimir L.; Biner, Sarah M. Chemical Communications, Vol. 48, Issue 77 https://doi.org/10.1039/c2cc34183b	journal	January 2012
Preparation of supramolecular chromophoric assemblies using a DNA duplex Kashida, Hiromu; Asanuma, Hiroyuki Physical Chemistry Chemical Physics, Vol. 14, Issue 20 https://doi.org/10.1039/c2cp40520b	journal	January 2012
Synthesis and properties of squaraine-modified DNA Markova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D. Organic & Biomolecular Chemistry, Vol. 10, Issue 45 https://doi.org/10.1039/c2ob26787j	journal	January 2012
Cooperative self-assembly of squaraine dyes Mayerhöffer, Ulrich; Würthner, Frank Chemical Science, Vol. 3, Issue 4 https://doi.org/10.1039/c2sc00996j	journal	January 2012
J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter Markova, Larysa I.; Malinovskii, Vladimir L.; Patsenker, Leonid D. Chemical Communications, Vol. 49, Issue 46 https://doi.org/10.1039/c3cc42103a	journal	January 2013
Control of aggregation-induced emission by DNA hybridization Li, Shaoguang; Langenegger, Simon M.; Häner, Robert Chemical Communications, Vol. 49, Issue 52 https://doi.org/10.1039/c3cc42706d	journal	January 2013
The aggregation of cyanine dyes in aqueous solution Dickinson, H. O. Transactions of the Faraday Society, Vol. 43 https://doi.org/10.1039/tf9474300486	journal	January 1947
Exchange narrowing of the J band of molecular dye aggregates Walczak, P. B.; Eisfeld, A.; Briggs, J. S. The Journal of Chemical Physics, Vol. 128, Issue 4 https://doi.org/10.1063/1.2823730	journal	January 2008
Anomalous strong exchange narrowing in excitonic systems Roden, Jan; Eisfeld, Alexander The Journal of Chemical Physics, Vol. 134, Issue 3 https://doi.org/10.1063/1.3528718	journal	January 2011
Exciton dynamics in chromophore aggregates with correlated environment fluctuations Abramavicius, Darius; Mukamel, Shaul The Journal of Chemical Physics, Vol. 134, Issue 17 https://doi.org/10.1063/1.3579455	journal	May 2011
Optical properties of disordered molecular aggregates: A numerical study Fidder, Henk; Knoester, Jasper; Wiersma, Douwe A. The Journal of Chemical Physics, Vol. 95, Issue 11 https://doi.org/10.1063/1.461317	journal	December 1991
Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA Kringle, Loni; Sawaya, Nicolas P. D.; Widom, Julia The Journal of Chemical Physics, Vol. 148, Issue 8 https://doi.org/10.1063/1.5020084	journal	February 2018
Architecture and mechanism of the light-harvesting apparatus of purple bacteria Hu, X.; Damjanovic, A.; Ritz, T. Proceedings of the National Academy of Sciences, Vol. 95, Issue 11 https://doi.org/10.1073/pnas.95.11.5935	journal	May 1998
DNA-mediated excitonic upconversion FRET switching Kellis, Donald L.; Rehn, Sarah M.; Cannon, Brittany L. New Journal of Physics, Vol. 17, Issue 11 https://doi.org/10.1088/1367-2630/17/11/115007	journal	November 2015
Quantum coherence in biological systems Lloyd, Seth Journal of Physics: Conference Series, Vol. 302 https://doi.org/10.1088/1742-6596/302/1/012037	journal	July 2011
Entanglement dynamics of J-aggregate systems Thilagam, A. Journal of Physics A: Mathematical and Theoretical, Vol. 44, Issue 13 https://doi.org/10.1088/1751-8113/44/13/135306	journal	March 2011
Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection Demchenko, Alexander P. Methods and Applications in Fluorescence, Vol. 8, Issue 2 https://doi.org/10.1088/2050-6120/ab7365	journal	February 2020
Photosynthetic light harvesting: excitons and coherence Fassioli, Francesca; Dinshaw, Rayomond; Arpin, Paul C. Journal of The Royal Society Interface, Vol. 11, Issue 92 https://doi.org/10.1098/rsif.2013.0901	journal	March 2014
Nanoscale Resonance Energy Transfer-Based Devices for Probabilistic Computing Wang, Siyang; Lebeck, Alvin R.; Dwyer, Chris IEEE Micro, Vol. 35, Issue 5 https://doi.org/10.1109/MM.2015.124	journal	September 2015
Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence Lee, H.; Cheng, Y. -C.; Fleming, G. R. Science, Vol. 316, Issue 5830 https://doi.org/10.1126/science.1142188	journal	June 2007
The Protein-Folding Problem, 50 Years On Dill, K. A.; MacCallum, J. L. Science, Vol. 338, Issue 6110 https://doi.org/10.1126/science.1219021	journal	November 2012
Three-Dimensional Structures Self-Assembled from DNA Bricks Ke, Y.; Ong, L. L.; Shih, W. M. Science, Vol. 338, Issue 6111 https://doi.org/10.1126/science.1227268	journal	November 2012
Accurate design of megadalton-scale two-component icosahedral protein complexes Bale, J. B.; Gonen, S.; Liu, Y. Science, Vol. 353, Issue 6297 https://doi.org/10.1126/science.aaf8818	journal	July 2016
Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials Yeates, Todd O. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-070816-033928	journal	May 2017
The Structure and Dynamics of Molecular Excitons Bardeen, Christopher J. Annual Review of Physical Chemistry, Vol. 65, Issue 1 https://doi.org/10.1146/annurev-physchem-040513-103654	journal	April 2014
Energy Transfer Mechanisms and the Molecular Exciton Model for Molecular Aggregates Kasha, Michael Radiation Research, Vol. 20, Issue 1 https://doi.org/10.2307/3571331	journal	September 1963

Similar Records

Effect of Hydrophilicity-Imparting Substituents on Exciton Delocalization in Squaraine Dye Aggregates Covalently Templated to DNA Holliday Junctions

Journal Article · Tue Dec 12 23:00:00 EST 2023 · Nanoscale · OSTI ID:2234233

Related Subjects

36 MATERIALS SCIENCE
71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
77 NANOSCIENCE AND NANOTECHNOLOGY
DNA Holliday junctions
Davydov splitting
Exciton delocalization
H-type packing Scaffolds
Indolenine Squaraine dye-DNA aggregates

Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds

Citation Formats

References (120)

Similar Records

Related Subjects