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Zarandi MA, Pathak P, Beltrami N, Walker JN, Zhang F, Brodbelt JS, Schmehl R, Jayawickramarajah J. Heteromeric guanosine (G)-quadruplex derived antenna modules with directional energy transfer. NANOSCALE 2023; 15:19069-19073. [PMID: 37990645 DOI: 10.1039/d3nr04086k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
A heteromeric guanosine (G)-quadruplex centered self-assembly approach is developed to prepare compact light-harvesting antenna modules featuring multiple donor dyes and a single toehold region. Due to the mix-and-match nature of our approach, the number and placement of donor dyes can be readily fine-tuned via quadruplex assembly. Moreover, hybridization of the toehold with an acceptor containing sequence results in directional energy transfer ensembles with effective absorption coefficients in the 105 M-1 cm-1 range. These compact antennas exhibit system efficiencies that are comparable to much larger and elaborate DNA architectures containing numerous DNA strands.
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Affiliation(s)
| | - Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fengqi Zhang
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Russell Schmehl
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
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2
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Hirashima S, Park S, Sugiyama H. Evaluation by Experimentation and Simulation of a FRET Pair Comprising Fluorescent Nucleobase Analogs in Nucleosomes. Chemistry 2023; 29:e202203961. [PMID: 36700521 PMCID: PMC10332638 DOI: 10.1002/chem.202203961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/27/2023]
Abstract
Förster resonance energy transfer (FRET) is an attractive tool for understanding biomolecular dynamics. FRET-based analysis of nucleosomes has the potential to fill the knowledge gaps between static structures and dynamic cellular behaviors. Compared with typical FRET pairs using bulky fluorophores introduced by flexible linkers, fluorescent nucleoside-based FRET pair has great potential since it can be fitted within the helical structures of nucleic acids. Herein we report on the construction of nucleosomes containing a nucleobase FRET pair and the investigation of experimental and theoretical FRET efficiencies through steady-state fluorescence spectroscopy and calculation based on molecular dynamics simulations, respectively. Distinguishable experimental FRET efficiencies were observed depending on the positions of FRET pairs in nucleosomal DNA. The tendency could be supported by theoretical study. This work suggests the possibility of our approach to analyze structural changes of nucleosomes by epigenetic modifications or internucleosomal interactions.
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Affiliation(s)
- Shingo Hirashima
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo, Kyoto, 606-8502, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University Yamadaoka, Suita, 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University Sakyo, Kyoto, 606-8501, Japan
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3
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. A DNA‐Based Two‐Component Excitonic Switch Utilizing High‐Performance Diarylethenes. Angew Chem Int Ed Engl 2022; 61:e202117735. [PMID: 35076154 PMCID: PMC9305942 DOI: 10.1002/anie.202117735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 11/13/2022]
Abstract
Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2′‐deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non‐nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all‐optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double‐methylated 2′‐deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster‐Resonance‐Energy‐Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance‐ and orientation‐dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.
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Affiliation(s)
- Simon M. Büllmann
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Nicolas F. Zorn
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Jana Zaumseil
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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4
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. Ein DNA‐basierter exzitonischer Zweikomponenten‐Schalter auf der Grundlage von Hochleistungs‐Diarylethenen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simon M. Büllmann
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Theresa Kolmar
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Nicolas F. Zorn
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Jana Zaumseil
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Andres Jäschke
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
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5
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Muraru S, Muraru S, Nitu FR, Ionita M. Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods. J Chem Inf Model 2022; 62:232-239. [PMID: 35014791 DOI: 10.1021/acs.jcim.1c00957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computational methods can greatly aid nucleic acid fluorescence experiments by either offering fully detailed atomic insights into the conformations and interactions present in the studied system or by providing accurate simulations of the fundamental parameters. Fluorescence-based optical biosensors show great potential for clinical diagnosis of life-altering diseases with a very high specificity. Many of the designs for such rely on the concept of Förster resonance energy transfer (FRET). Currently, the methods used experimentally make use of theoretical assumptions which fundamentally affect the results. Having a detailed atomistic overview or significant simulated parameters could improve the understanding of the calculations and provide much more accurate outcomes. However, there are many challenges that need to be addressed before standardized computational protocols can be employed. This review is meant to highlight the progress made for computational methods used to simulate FRET experiments for nucleic acid probes. Recent advances have been made in computational tools, such as force field parametrizations and improved protocols. Complementary simulations to experimental data are also comprised in the this review.
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Affiliation(s)
- Sorin Muraru
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Sebastian Muraru
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Florentin Romeo Nitu
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Mariana Ionita
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania.,Advanced Polymer Materials Group, University Polithenica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
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6
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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7
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Pant P, Pathak A, Jayaram B. Symmetric Nucleosides as Potent Purine Nucleoside Phosphorylase Inhibitors. J Phys Chem B 2021; 125:2856-2862. [PMID: 33715357 DOI: 10.1021/acs.jpcb.0c10553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nucleic acids are one of the most enigmatic biomolecules crucial to several biological processes. Nucleic acid-protein interactions are vital for the coordinated and controlled functioning of a cell, leading to the design of several nucleoside/nucleotide analogues capable of mimicking these interactions and hold paramount importance in the field of drug discovery. Purine nucleoside phosphorylase is a well-established drug target due to its association with numerous immunodeficiency diseases. Here, we study the binding of human purine nucleoside phosphorylase (PNP) to some bidirectional symmetric nucleosides, a class of nucleoside analogues that are more flexible due to the absence of sugar pucker restraints. We compared the binding energies of PNP-symmetric nucleosides to the binding energies of PNP-inosine/Imm-H (a transition-state analogue), by means of 200 ns long all-atom explicit-solvent Gaussian accelerated molecular dynamics simulations followed by energetics estimation using the MM-PBSA methodology. Quite interestingly, we observed that a few symmetric nucleosides, namely, ν3 and ν4, showed strong binding with PNP (-14.1 and -12.6 kcal/mol, respectively), higher than inosine (-6.3 kcal/mol) and Imm-H (-9.6 kcal/mol). This is rationalized by an enhanced hydrogen-bond network for symmetric nucleosides compared to inosine and Imm-H while maintaining similar van der Waals contacts. We note that the chemical structures of both ν3 and ν4, due to an additional unsaturation in them, resemble enzymatic transition states and fall in the category of transition-state analogues (TSAs), which are quite popular.
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Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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