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Roy S, Mass OA, Kellis DL, Wilson CK, Hall JA, Yurke B, Knowlton WB. Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates. J Phys Chem B 2021; 125:13670-13684. [PMID: 34894675 PMCID: PMC8713290 DOI: 10.1021/acs.jpcb.1c07602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/04/2021] [Indexed: 11/28/2022]
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.
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Affiliation(s)
- Simon
K. Roy
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A. Mass
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Donald L. Kellis
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - John A. Hall
- Division
of Research and Economic Development, Boise
State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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2
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Affiliation(s)
- Jennifer Frommer
- Institute for Biochemistry University Greifswald Felix Hausdorff Str. 4 17487 Greifswald Germany
- present address: School of Chemistry University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Sabine Müller
- Institute for Biochemistry University Greifswald Felix Hausdorff Str. 4 17487 Greifswald Germany
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3
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Frommer J, Müller S. Reductive Charge Transfer through an RNA Aptamer. Angew Chem Int Ed Engl 2020; 59:22999-23004. [PMID: 32852119 PMCID: PMC7756803 DOI: 10.1002/anie.202009430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/20/2020] [Indexed: 12/27/2022]
Abstract
The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non‐Watson–Crick base‐paired regions might be required. We here demonstrate distance‐dependent reductive charge transfer through RNA duplexes and through the non‐Watson–Crick base‐paired region of an RNA aptamer.
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Affiliation(s)
- Jennifer Frommer
- Institute for Biochemistry, University Greifswald, Felix Hausdorff Str. 4, 17487, Greifswald, Germany.,present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Felix Hausdorff Str. 4, 17487, Greifswald, Germany
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4
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Hu X, Lindner JO, Würthner F. Stepwise Folding and Self-Assembly of a Merocyanine Folda-Pentamer. J Am Chem Soc 2020; 142:3321-3325. [PMID: 32003980 DOI: 10.1021/jacs.9b12599] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we report a synthetic protocol toward a merocyanine (MC) pentamer 1 which represents the first merocyanine oligomer longer than a dimer. By continuously decreasing the solvent polarity, we demonstrate the stepwise folding from partially folded monomeric and dimeric MC subunits (in chloroform) up to the full pentamer π-stack (in 75% methylcyclohexane/25% chloroform) and a subsequent self-assembly of pentamer 1 into larger aggregates (in 80% methylcyclohexane/20% chloroform). This hierarchical structure formation process became possible due to the predominant dipole-dipole interactions among MC dyes that allowed for a precise modulation of the energy landscape by the solvent polarity. This unprecedented stepwise control of dye assembly via hierarchical dipole-dipole interactions opens the door for a more precise control of dye-dye interactions in artificial multichromophoric ensembles.
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Affiliation(s)
- Xiaobo Hu
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany
| | - Joachim O Lindner
- Center for Nanosystems Chemistry , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
| | - Frank Würthner
- Institut für Organische Chemie , Universität Würzburg , Am Hubland , 97074 Würzburg , Germany.,Center for Nanosystems Chemistry , Universität Würzburg , Theodor-Boveri-Weg , 97074 Würzburg , Germany
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7
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Murayama K, Yamano Y, Asanuma H. 8-Pyrenylvinyl Adenine Controls Reversible Duplex Formation between Serinol Nucleic Acid and RNA by [2 + 2] Photocycloaddition. J Am Chem Soc 2019; 141:9485-9489. [DOI: 10.1021/jacs.9b03267] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuuhei Yamano
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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8
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Bätzner E, Liang Y, Schweigert C, Unterreiner AN, Wagenknecht HA. Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs. Chemphyschem 2015; 16:1607-12. [PMID: 25784385 DOI: 10.1002/cphc.201500062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 02/05/2023]
Abstract
The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture.
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Affiliation(s)
- Effi Bätzner
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Yu Liang
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Caroline Schweigert
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany).
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany).
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Kim KT, Veedu RN, Seo YJ, Kim BH. Quencher-free molecular beacons as probes for oligonucleotides containing CAG repeat sequences. Chem Commun (Camb) 2014; 50:1561-3. [PMID: 24382518 DOI: 10.1039/c3cc48853e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have identified quencher-free molecular beacons that allow the sensitive probing of CAG repeat oligonucleotides, including mRNA fragments of trinucleotide repeat diseases, with significant increases in fluorescence intensity mediated by disruption of the stacking of their (Py)U units.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking. Angew Chem Int Ed Engl 2014; 53:11370-5. [PMID: 25167966 DOI: 10.1002/anie.201406022] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/11/2022]
Abstract
Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.
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Affiliation(s)
- Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Helligkeit durch lokale Rigidifizierung - LNA-verstärkte FIT-Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Patwa A, Salgado G, Dole F, Navailles L, Barthélémy P. Tuning molecular interactions in lipid-oligonucleotides assemblies via locked nucleic acid (LNA)-based lipids. Org Biomol Chem 2014; 11:7108-12. [PMID: 24065175 DOI: 10.1039/c3ob41707g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hybrid nucleotide-lipids containing locked nucleic acid (LNA) show enhanced hybridization properties with complementary single strand RNAs compared to DNA lipid analogues. The LNA adenosine lipid features unique binding properties with a high binding affinity for poly-uridine and the entropically driven formation of a stable complex (K(d) ≈ 43 nM). Enhanced hybridization properties of LNA-based lipids should be applicable for the development of oligonucleotide (ON) delivery systems or as small molecule binders to RNA for novel therapeutic strategies.
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Affiliation(s)
- Amit Patwa
- Univ. Bordeaux, ARNA laboratory, F-33076 Bordeaux, France.
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13
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Kratochvílová I, Vala M, Weiter M, Špérová M, Schneider B, Páv O, Šebera J, Rosenberg I, Sychrovský V. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies. Biophys Chem 2013; 180-181:127-34. [DOI: 10.1016/j.bpc.2013.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 12/31/2022]
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14
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Salvatore P, Zeng D, Karlsen KK, Chi Q, Wengel J, Ulstrup J. Electrochemistry of single metalloprotein and DNA-based molecules at Au(111) electrode surfaces. Chemphyschem 2013; 14:2101-11. [PMID: 23788363 DOI: 10.1002/cphc.201300299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 11/10/2022]
Abstract
We have briefly overviewed recent efforts in the electrochemistry of single transition metal complex, redox metalloprotein, and redox-marked oligonucleotide (ON) molecules. We have particularly studied self-assembled molecular monolayers (SAMs) of several 5'-C6-SH single- (ss) and double-strand (ds) ONs immobilized on Au(111) electrode surfaces via Au-S bond formation, using a combination of nucleic acid chemistry, electrochemistry and electrochemically controlled scanning tunnelling microscopy (in situ STM). Ds ONs stabilized by multiply charged cations and locked nucleic acid (LNA) monomers have been primary targets, with a view on stabilizing the ds-ONs and improving voltammetric signals of intercalating electrochemical redox probes. Voltammetric signals of the intercalator anthraquinone monosulfonate (AQMS) at ds-DNA/Au(111) surfaces diluted by mercaptohexanol are significantly sharpened and more robust in the presence than in the absence of [Co(NH3)6](3+). AQMS also displays robust Faradaic voltammetric signals specific to the ds form on binding to similar LNA/Au(111) surfaces, but this signal only evolves after successive voltammetric scanning into negative potential ranges. Triply charged spermidine (Spd) invokes itself a strong voltammetric signal, which is specific to the ds form and fully matched sequences. This signal is of non-Faradaic, capacitive origin but appears in the same potential range as the Faradaic AQMS signal. In situ STM shows that molecular scale structures of the size of Spd-stabilized ds-ONs are densely packed over the Au(111) surface in potential ranges around the capacitive peak potential.
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Affiliation(s)
- Princia Salvatore
- Department of Chemistry, Kemitorvet, Building 207, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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15
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Abstract
In the past few decades, charge transfer in DNA has attracted considerable
attention from researchers in a wide variety of fields ranging from bioscience
and physical chemistry to nanotechnology. Charge transfer in DNA has been
investigated using various techniques. Among them, time-resolved spectroscopic
methods have provided information on charge-transfer dynamics in DNA, an
important basis for therapy applications, nanomaterials, and so on. In charge
transfer in DNA, holes and excess electrons act as positive and negative charge
carriers, respectively. Hole-transfer (HT) dynamics have been investigated in
detail, while the dynamics of excess electron transfer (EET) have only become
clear rather recently. In the present paper, we summarize studies on the
dynamics of HT and EET by several groups including ourselves.
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Affiliation(s)
- Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Thazhathveetil AK, Vura-Weis J, Trifonov A, Wasielewski MR, Lewis FD. Dynamics and efficiency of hole transport in LNA:DNA hybrid diblock oligomers. J Am Chem Soc 2012; 134:16434-40. [PMID: 22958189 DOI: 10.1021/ja307989t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report here the effect of replacing one or both of the purine or pyrimidine blocks of a diblock stilbene donor-acceptor capped hairpin with locked nucleic acid (LNA) bases on the dynamics and efficiency of hole transport. The structures of the DNA and LNA:DNA hybrids are tentatively assigned to B- or A-type structures on the basis of their circular dichroism spectra. Replacing the bases in either the A-block or the G-block of the diblock DNA hairpin with LNA bases results in a modest decrease in the base-to-base hopping rate constant and quantum yield for charge separation. Somewhat larger decreases are observed when all of the purine or pyrimidine bases are replaced by LNA bases.
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Affiliation(s)
- Arun K Thazhathveetil
- Department of Chemistry and Argonne-Northwestern Solar Energy Research Center, Northwestern University, Evanston, Illinois 60208, USA
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