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Article ; Online: Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions.

Barcenas, German / Biaggne, Austin / Mass, Olga A / Knowlton, William B / Yurke, Bernard / Li, Lan

International journal of molecular sciences

2023 Volume 24, Issue 4

Abstract: Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how ... ...

Abstract	Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye-DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye-DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye-DNA interactions on aggregate orientation and excitonic coupling.
MeSH term(s)	DNA, Cruciform ; Molecular Dynamics Simulation ; Fluorescent Dyes/chemistry ; DNA/chemistry
Chemical Substances	DNA, Cruciform ; squaraine ; Fluorescent Dyes ; DNA (9007-49-2)
Language	English
Publishing date	2023-02-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24044059
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction.

Basu, Shibani / Cervantes-Salguero, Keitel / Yurke, Bernard / Knowlton, William B / Lee, Jeunghoon / Mass, Olga A

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 13

Abstract: A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via ...

Abstract	A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye-dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.
MeSH term(s)	Coloring Agents/chemistry ; Cross-Linking Reagents ; DNA, Cruciform ; Electrophoresis, Gel, Two-Dimensional ; Photochemistry ; Thymine/chemistry
Chemical Substances	Coloring Agents ; Cross-Linking Reagents ; DNA, Cruciform ; Thymine (QR26YLT7LT)
Language	English
Publishing date	2022-06-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27134006
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Article ; Online: Effect of Substituent Location on the Relationship between the Transition Dipole Moments, Difference Static Dipole, and Hydrophobicity in Squaraine Dyes for Quantum Information Devices.

Ketteridge, Maia / Biaggne, Austin / Rau, Ryan / Barcenas, German / Mass, Olga A / Knowlton, William B / Yurke, Bernard / Li, Lan

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 5

Abstract: Aggregates of organic dyes that exhibit excitonic coupling have a wide array of applications, including medical imaging, organic photovoltaics, and quantum information devices. The optical properties of a dye monomer, as a basis of dye aggregate, can be ... ...

Abstract	Aggregates of organic dyes that exhibit excitonic coupling have a wide array of applications, including medical imaging, organic photovoltaics, and quantum information devices. The optical properties of a dye monomer, as a basis of dye aggregate, can be modified to strengthen excitonic coupling. Squaraine (SQ) dyes are attractive for those applications due to their strong absorbance peak in the visible range. While the effects of substituent types on the optical properties of SQ dyes have been previously examined, the effects of various substituent locations have not yet been investigated. In this study, density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to investigate the relationships between SQ substituent location and several key properties of the performance of dye aggregate systems, namely, difference static dipole (Δd), transition dipole moment (μ), hydrophobicity, and the angle (θ) between Δd and μ. We found that attaching substituents along the long axis of the dye could increase μ while placement off the long axis was shown to increase Δd and reduce θ. The reduction in θ is largely due to a change in the direction of Δd as the direction of μ is not significantly affected by substituent position. Hydrophobicity decreases when electron-donating substituents are located close to the nitrogen of the indolenine ring. These results provide insight into the structure-property relationships of SQ dyes and guide the design of dye monomers for aggregate systems with desired properties and performance.
Language	English
Publishing date	2023-02-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28052163
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Article ; Online: Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer.

Mass, Olga A / Watt, Devan R / Patten, Lance K / Pensack, Ryan D / Lee, Jeunghoon / Turner, Daniel B / Yurke, Bernard / Knowlton, William B

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 41, Page(s) 28437–28451

Abstract: ... A ... ...

Abstract	A bacteriochlorophyll
MeSH term(s)	Light-Harvesting Protein Complexes/chemistry ; Computing Methodologies ; Quantum Theory ; Photosynthetic Reaction Center Complex Proteins/chemistry ; DNA
Chemical Substances	Light-Harvesting Protein Complexes ; bacteriochlorin ; Photosynthetic Reaction Center Complex Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2023-10-25
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp01634j
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions.

Pascual, Gissela / Roy, Simon K / Barcenas, German / Wilson, Christopher K / Cervantes-Salguero, Keitel / Obukhova, Olena M / Krivoshey, Alexander I / Terpetschnig, Ewald A / Tatarets, Anatoliy L / Li, Lan / Yurke, Bernard / Knowlton, William B / Mass, Olga A / Pensack, Ryan D / Lee, Jeunghoon

Nanoscale

2024 Volume 16, Issue 3, Page(s) 1206–1222

Abstract: Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light ...

Abstract	Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light harvesting. In a previous study, we found unexpectedly large excitonic interactions (quantified by the excitonic hopping parameter
MeSH term(s)	DNA, Cruciform ; Fluorescent Dyes/chemistry ; Computing Methodologies ; Quantum Theory ; DNA/chemistry ; Hydrophobic and Hydrophilic Interactions ; Cyclobutanes ; Phenols
Chemical Substances	DNA, Cruciform ; squaraine ; Fluorescent Dyes ; DNA (9007-49-2) ; Cyclobutanes ; Phenols
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d3nr04499h
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates.

Roy, Simon K / Mass, Olga A / Kellis, Donald L / Wilson, Christopher K / Hall, John A / Yurke, Bernard / Knowlton, William B

The journal of physical chemistry. B

2021 Volume 125, Issue 50, Page(s) 13670–13684

Abstract: Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been ... ...

Abstract	Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
MeSH term(s)	Coloring Agents ; DNA ; Nucleotides ; Quinolines
Chemical Substances	Coloring Agents ; Nucleotides ; Quinolines ; DNA (9007-49-2)
Language	English
Publishing date	2021-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.1c07602
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates

Roy, Simon K. / Mass, Olga A. / Kellis, Donald L. / Wilson, Christopher K. / Hall, John A. / Yurke, Bernard / Knowlton, William B.

Journal of physical chemistry. 2021 Dec. 13, v. 125, no. 50

2021

Abstract	Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
Keywords	DNA ; absorption ; chemical bonding ; circular dichroism spectroscopy ; nucleotides
Language	English
Dates of publication	2021-1213
Size	p. 13670-13684.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.1c07602
Database	NAL-Catalogue (AGRICOLA)

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Article: Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates

Mass, Olga A. / Wilson, Christopher K. / Barcenas, German / Terpetschnig, Ewald. A. / Obukhova, Olena M. / Kolosova, Olga S. / Tatarets, Anatoliy L. / Li, Lan / Yurke, Bernard / Knowlton, William B. / Pensack, Ryan. D. / Lee, Jeunghoon

Journal of physical chemistry. 2022 Feb. 10, v. 126, no. 7

2022

Abstract: Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the ... ...

Abstract	Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn–Renger–May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm–¹). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
Keywords	DNA ; absorption ; aggregation behavior ; chemical bonding ; circular dichroism spectroscopy ; dyes ; fluorescence ; hydrophilicity ; hydrophobicity ; models
Language	English
Dates of publication	2022-0210
Size	p. 3475-3488.
Publishing place	American Chemical Society
Document type	Article
ISSN	1932-7455
DOI	10.1021/acs.jpcc.1c08981
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis.

Meares, Adam / Susumu, Kimihiro / Mathur, Divita / Lee, Sang Ho / Mass, Olga A / Lee, Jeunghoon / Pensack, Ryan D / Yurke, Bernard / Knowlton, William B / Melinger, Joseph S / Medintz, Igor L

ACS omega

2022 Volume 7, Issue 13, Page(s) 11002–11016

Abstract: Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in ... ...

Abstract	Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in particular is that of accessing exciton delocalization in designer DNA dye aggregate structures for potential development of light-harvesting devices and room-temperature quantum computers. Tuning the hydrophilicity/hydrophobicity of Cy5 dyes in such DNA structures should influence the strength of their excitonic coupling; however, the requisite commercial Cy5 derivatives available for direct incorporation into DNA are nonexistent. Here, we prepare a series of Cy5 derivatives that possess different 5,5'-substituents and detail their incorporation into a set of DNA sequences. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5'-substituents, including hexyloxy, triethyleneglycol monomethyl ether,
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.1c06921
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction.

Mass, Olga A / Basu, Shibani / Patten, Lance K / Terpetschnig, Ewald A / Krivoshey, Alexander I / Tatarets, Anatoliy L / Pensack, Ryan D / Yurke, Bernard / Knowlton, William B / Lee, Jeunghoon

The journal of physical chemistry letters

2022 Volume 13, Issue 46, Page(s) 10688–10696

Abstract: While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs ... ...

Abstract	While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.
MeSH term(s)	DNA, Cruciform ; Coloring Agents ; DNA ; Circular Dichroism ; Stereoisomerism
Chemical Substances	DNA, Cruciform ; Coloring Agents ; DNA (9007-49-2)
Language	English
Publishing date	2022-11-10
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.2c02721
Database	MEDical Literature Analysis and Retrieval System OnLINE

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