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Safar M, Saurabh A, Sarkar B, Fazel M, Ishii K, Tahara T, Sgouralis I, Pressé S. Single-photon smFRET. III. Application to pulsed illumination. BIOPHYSICAL REPORTS 2022; 2:100088. [PMID: 36530182 PMCID: PMC9747580 DOI: 10.1016/j.bpr.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single-photon, single-molecule FRET (smFRET) data analysis under pulsed illumination including 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; and 3) taking into account detector noise sources such as cross talk and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion article that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.
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Affiliation(s)
- Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, Japan
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennessee
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
- School of Molecular Sciences, Arizona State University, Phoenix, Arizona
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2
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Wan L, Lam SL, Lee HK, Guo P. Rational design of a reversible Mg 2+/EDTA-controlled molecular switch based on a DNA minidumbbell. Chem Commun (Camb) 2021; 56:10127-10130. [PMID: 32870195 DOI: 10.1039/d0cc03774e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we report that incorporation of an abasic site to DNA minidumbbells formed by natural sequences can lead to significant enhancements in their thermodynamic stability. Based on these stable minidumbbells, the first metal ion-controlled molecular switch which can regulate instant and reversible DNA duplex formation and dissociation has been constructed.
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Affiliation(s)
- Liqi Wan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
| | - Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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Halder A, Roy R, Bhattacharyya D, Mitra A. Consequences of Mg2+ binding on the geometry and stability of RNA base pairs. Phys Chem Chem Phys 2018; 20:21934-21948. [DOI: 10.1039/c8cp03602k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantum chemical calculations reveal the role of magnesium in stabilizing the geometries of intrinsically unstable RNA base pairs.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Rohit Roy
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | | | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
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4
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Campos R, Zhang S, Majikes JM, Ferraz LCC, LaBean TH, Dong MD, Ferapontova EE. Electronically addressable nanomechanical switching of i-motif DNA origami assembled on basal plane HOPG. Chem Commun (Camb) 2015; 51:14111-4. [DOI: 10.1039/c5cc04678e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, a pH-induced nanomechanical switching of i-motif structures incorporated into DNA origami bound onto cysteamine-modified basal plane HOPG was electronically addressed, demonstrating for the first time the electrochemical read-out of the nanomechanics of DNA origami.
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Affiliation(s)
- R. Campos
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - S. Zhang
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - J. M. Majikes
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - L. C. C. Ferraz
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - T. H. LaBean
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - M. D. Dong
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - E. E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
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5
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Wang R, Xu L, Li Y. Bio-nanogate controlled enzymatic reaction for virus sensing. Biosens Bioelectron 2014; 67:400-7. [PMID: 25212377 DOI: 10.1016/j.bios.2014.08.071] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 12/20/2022]
Abstract
The objective of this study was to develop an aptamer-based bifunctional bio-nanogate, which could selectively respond to target molecules, and control enzymatic reaction for electrochemical measurements. It was successfully applied for sensitive, selective, rapid, quantitative, and label-free detection of avian influenza viruses (AIV) H5N1. A nanoporous gold film with pore size of ~20 nm was prepared by a metallic corrosion method, and the purity was checked by energy-dispersive X-ray spectroscopy (EDS) study. To improve the performance of the bio-nanogate biosensor, its main analytical parameters were studied and optimized. We demonstrated that the developed bio-nanogate was capable of controlling enzymatic reaction for AIV H5N1 sensing within 1h with a detection limit of 2(-9)HAU (hemagglutination units). The enzymatic reaction was able to cause significant current change due to the presence of target AIV. A linear relationship was found in the virus titer range of 2(-10)-2(2)HAU. No interference was observed from non-target AIV subtypes such as H1N1, H2N2, H4N8 and H7N2. The developed approach could be adopted for sensing of other viruses.
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Affiliation(s)
- Ronghui Wang
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lizhou Xu
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310068, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310068, China; Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
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6
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Abi A, Lin M, Pei H, Fan C, Ferapontova EE, Zuo X. Electrochemical switching with 3D DNA tetrahedral nanostructures self-assembled at gold electrodes. ACS APPLIED MATERIALS & INTERFACES 2014; 6:8928-8931. [PMID: 24802004 DOI: 10.1021/am501823q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanomechanical switching of functional three-dimensional (3D) DNA nanostructures is crucial for nanobiotechnological applications such as nanorobotics or self-regulating sensor and actuator devices. Here, DNA tetrahedral nanostructures self-assembled onto gold electrodes were shown to undergo the electronically addressable nanoswitching due to their mechanical reconfiguration upon external chemical stimuli. That enables construction of robust surface-tethered electronic nanodevices based on 3D DNA tetrahedra. One edge of the tetrahedron contained a partially self-complementary region with a stem-loop hairpin structure, reconfigurable upon hybridization to a complementary DNA (stimulus DNA) sequence. A non-intercalative ferrocene (Fc) redox label was attached to the reconfigurable tetrahedron edge in such a way that reconfiguration of this edge changed the distance between the electrode and Fc.
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Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, ‡Center for DNA Nanotechnology (CDNA) at iNANO, and §Sino-Danish Centre for Education and Research (SDC) at iNANO, Aarhus University , Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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8
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Papadakis G, Tsortos A, Gizeli E. Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction. NANO LETTERS 2010; 10:5093-5097. [PMID: 21038866 DOI: 10.1021/nl103491v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion, Greece
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Abstract
We introduce ultra-fast tunable nanoswitches based on the transition between states of nanoparticle meta-molecules. These molecules are formed (activated) when hybrid systems consisting of metallic nanoparticles and semiconductor quantum dots interact with coherent light sources (laser fields). The switching process occurs via minuscule changes of the refractive index of the environment or the distance between the quantum dots and metallic nanoparticles. These changes stimulate the transition between the states of the meta-molecules in nanosecond timescales, setting up dramatic optical events that can be observed easily. These nanoswitches can be tuned by varying the intensity of the activating laser field, allowing us to adjust the switching process to occur at different values of refractive indices. The results open a new horizon for chemically, biologically, or physically triggered optical nanoswitches and nanosensors that are sensitive to ultra-small changes in the environment.
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Affiliation(s)
- S M Sadeghi
- Department of Physics, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Condensed DNA: condensing the concepts. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 105:208-22. [PMID: 20638406 DOI: 10.1016/j.pbiomolbio.2010.07.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/11/2010] [Indexed: 01/09/2023]
Abstract
DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.
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Ferapontova EE, Hansen MN, Saunders AM, Shipovskov S, Sutherland DS, Gothelf KV. Electrochemical DNA sandwich assay with a lipase label for attomole detection of DNA. Chem Commun (Camb) 2010; 46:1836-8. [PMID: 20198225 DOI: 10.1039/b924627d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fast and sensitive electrochemical lipase-based sandwich hybridization assay for detection of attomole levels of DNA has been developed. A combination of magnetic beads, used for pre-concentration and bioseparation of the analyte with a lipase catalyst label allowed detection of DNA with a limit of 20 amol.
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Affiliation(s)
- Elena E Ferapontova
- Centre for DNA Nanotechnology, Department of Chemistry and iNANO, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
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12
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Beales PA, Vanderlick TK. Partitioning of Membrane-Anchored DNA between Coexisting Lipid Phases. J Phys Chem B 2009; 113:13678-86. [DOI: 10.1021/jp9006735] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Paul A. Beales
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, and Department of Chemical Engineering, Yale University, New Haven, Connecticut 06511
| | - T. Kyle Vanderlick
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, and Department of Chemical Engineering, Yale University, New Haven, Connecticut 06511
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