1
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Hao J, Cao D, Zhao Q, Zhang D, Wang H. Intramolecular Folding of PolyT Oligonucleotides Induced by Cooperative Binding of Silver(I) Ions. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227842. [PMID: 36431941 PMCID: PMC9694225 DOI: 10.3390/molecules27227842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Ag+-bridged T-Ag+-T was recently discovered in a Ag+-DNA nanowire crystal, but it was reported that Ag+ had little to no affinity to T nucleobases and T-rich oligonucleotides in solution. Therefore, the binding mode for the formation of this type of novel metallo base pair in solution is elusive. Herein, we demonstrate that Ag+ can interact with polyT oligonucleotides once the concentration of Ag+ in solution exceeds a threshold value. The threshold value is independent of the concentration of the polyT oligonucleotide but is inversely proportional to the length of the polyT oligonucleotide. The polyT oligonucleotides are intramolecularly folded due to their positively cooperative formation and the stack of T-Ag+-T base pairs, resulting in the 5'- and 3'-ends being in close proximity to each other. The intramolecular Ag+-folded polyT oligonucleotide has a higher thermal stability than the duplex and can be reversibly modulated by cysteine.
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Affiliation(s)
- Jinghua Hao
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qiang Zhao
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dapeng Zhang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-62849611; Fax: +86-10-62849600
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Yeou S, Lee NK. Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability. Mol Cells 2022; 45:33-40. [PMID: 34470919 PMCID: PMC8819492 DOI: 10.14348/molcells.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022] Open
Abstract
The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.
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Affiliation(s)
- Sanghun Yeou
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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3
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Valli J, Garcia-Burgos A, Rooney LM, Vale de Melo E Oliveira B, Duncan RR, Rickman C. Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique. J Biol Chem 2021; 297:100791. [PMID: 34015334 PMCID: PMC8246591 DOI: 10.1016/j.jbc.2021.100791] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| | - Adrian Garcia-Burgos
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Liam M Rooney
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Beatriz Vale de Melo E Oliveira
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Rory R Duncan
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Colin Rickman
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
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4
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Simple, rapid, and sensitive on-site detection of Hg 2+ in water samples through combining portable evanescent wave optofluidic biosensor and fluorescence resonance energy transfer principle. Anal Chim Acta 2021; 1155:338351. [PMID: 33766323 DOI: 10.1016/j.aca.2021.338351] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022]
Abstract
Rapid and sensitive detection of Hg2+ in the environment and drinking water is vital because of its non-degradability, bioaccumulation, and high toxicity. Herein, we report a portable evanescent wave optofluidic biosensor (EWOB) for simple sensitive detection of Hg2+ using fluorescence labeled poly-A DNA strand (CY-A14) and quencher labeled poly-T DNA strand (BQ-T14) as signal reporter and biorecognition element, respectively. Both CY-A14 and Hg2+ can competitively bind with BQ-T14 based on DNA hybridization and the specifical binding of Hg2+ and T bases of DNA to form T-Hg2+-T mismatch structure, respectively. Higher concentration of Hg2+ lead to less CY-A14 bound to BQ-T14 and thus a higher fluorescence intensity. The influence of several key environmental factors on Hg2+ biosensor, such as pH, temperature, and ionic strength, was investigated in details because they were essential for practical applications of Hg2+ biosensor. Under optimal conditions, a detection cycle for a single sample, including the measurement and regeneration, was less than 10 min with a Hg2+ detection limit of 8.5 nM. The high selectivity of the biosensor was showed by evaluating its response to various potentially interfering metal ions. Our results clearly demonstrated that the portable EWOB could serve as a powerful tool for rapid and sensitive on-site detection of Hg2+ in real water samples. The EWOB is also potentially applicable to detect other heavy metal ions or small molecule targets for which DNA/aptamers could be applied as specific biosensing probes.
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5
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Oweida TJ, Kim HS, Donald JM, Singh A, Yingling YG. Assessment of AMBER Force Fields for Simulations of ssDNA. J Chem Theory Comput 2021; 17:1208-1217. [PMID: 33434436 DOI: 10.1021/acs.jctc.0c00931] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.
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Affiliation(s)
- Thomas J Oweida
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ho Shin Kim
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Johnny M Donald
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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6
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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7
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Mondal S, Mishra PP. Direct observation of effect of crowding induced macromolecular hydration on molecular breathing in the stem of Fork-DNA by single-molecule FRET microspectroscopy. Int J Biol Macromol 2020; 167:559-569. [PMID: 33278436 DOI: 10.1016/j.ijbiomac.2020.11.197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 11/15/2022]
Abstract
The perpetually changing cellular conditions, nucleotide sequence, and environmental effects including osmotic stress have multiple effects on DNA, leading to several conformational alternations and subsequently influencing their activity, too. In this work, single-molecule FRET microspectroscopy has been employed to monitor the breathing dynamics as an effect of molecular crowding in the stem region of Fork-DNA. The structural integrity greatly alters with the presence or absence of nucleotide overhangs and on the nature and concentration of the crowding agent, thus affecting the stability of the stem region and hence the forked DNA. The multiple hydrogen bonds and hydrophobic interactions between the polynucleotide strands appear to be altered with osmotic crowding. This induces increased flexibility in the double helix and allows DNA to breath. The conformational alternation of the DNA happens in nanometer resolution, that is been monitored by the change in the FRET efficiency between the dyes attached to two different strands of the DNA. The nature and molecular weight of crowding agents control the degree of spatial breathing in the stem of Fork-DNA. These constant fluctuations between the entropically favorable partially folded structures to an enthalpically favorable folded structure are not only valuable for elucidating nucleic acid structure but might play an important role in enzyme kinetics.
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Affiliation(s)
- Soma Mondal
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India.
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8
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Paoletti F, El-Sagheer AH, Allard J, Brown T, Dushek O, Esashi F. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. EMBO J 2020; 39:e103002. [PMID: 31943278 PMCID: PMC7110135 DOI: 10.15252/embj.2019103002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/21/2019] [Accepted: 12/16/2019] [Indexed: 12/23/2022] Open
Abstract
The timely activation of homologous recombination is essential for the maintenance of genome stability, in which the RAD51 recombinase plays a central role. Biochemically, human RAD51 polymerises faster on single‐stranded DNA (ssDNA) compared to double‐stranded DNA (dsDNA), raising a key conceptual question: how does it discriminate between them? In this study, we tackled this problem by systematically assessing RAD51 binding kinetics on ssDNA and dsDNA differing in length and flexibility using surface plasmon resonance. By directly fitting a mechanistic model to our experimental data, we demonstrate that the RAD51 polymerisation rate positively correlates with the flexibility of DNA. Once the RAD51‐DNA complex is formed, however, RAD51 remains stably bound independent of DNA flexibility, but rapidly dissociates from flexible DNA when RAD51 self‐association is perturbed. This model presents a new general framework suggesting that the flexibility of DNA, which may increase locally as a result of DNA damage, plays an important role in rapidly recruiting repair factors that multimerise at sites of DNA damage.
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Affiliation(s)
- Federico Paoletti
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Oxford, UK.,Department of Science and Mathematics, Suez University, Suez, Egypt
| | - Jun Allard
- Department of Mathematics, University of California, Irvine, CA, USA
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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9
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Zhu B, Guo J, Zhang L, Pan M, Jing X, Wang L, Liu X, Zuo X. In-Situ Configuration Studies on Segmented DNA Origami Nanotubes. Chembiochem 2019; 20:1508-1513. [PMID: 30702811 DOI: 10.1002/cbic.201800727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Indexed: 11/09/2022]
Abstract
One-dimensional nanotubes are of considerable interest in materials and biochemical sciences. A particular desire is to create DNA nanotubes with user-defined structural features and biological relevance, which will facilitate the application of these nanotubes in the controlled release of drugs, templating of other materials into linear arrays and the construction of artificial membrane channels. However, little is known about the structures of assembled DNA nanotubes in solution. Here we report an in situ exploration of segmented DNA nanotubes, composed of multiple units with set length distributions, by using synchrotron small-angle X-ray scattering (SAXS). Through joint experimental and theoretical studies, we show that the SAXS data are highly informative in the context of heterogeneous mixtures of DNA nanotubes. The structural parameters obtained by SAXS are in good agreement with those determined by atomic force microscopy (AFM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). In particular, the SAXS data revealed important structural information on these DNA nanotubes, such as the in-solution diameters (≈25 nm), which could be obtained only with difficulty by use of other methods. Our results establish SAXS as a reliable structural analysis method for long DNA nanotubes and could assist in the rational design of these structures.
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Affiliation(s)
- Bowen Zhu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jingyang Guo
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lixia Zhang
- Jiading District Central Hospital, Shanghai, 201800, China
| | - Muchen Pan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xinxin Jing
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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10
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Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength. Int J Mol Sci 2018; 19:ijms19103230. [PMID: 30347651 PMCID: PMC6214132 DOI: 10.3390/ijms19103230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH2, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl2 or MgSO4 cations. At 10 mM MgCl2 or MgSO4, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH2. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH2, MgCl2 and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.
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11
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Kim N, Kwon J, Lim Y, Kang J, Bae S, Kim SK. Incorporation of STED technique into single-molecule spectroscopy to break the concentration limit of diffusing molecules in single-molecule detection. Chem Commun (Camb) 2018; 54:9667-9670. [DOI: 10.1039/c8cc05726e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Incorporation of STED into ALEX-FRET increases the concentration limit of single-molecule detection by 100-fold to 5 nM.
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Affiliation(s)
- Namdoo Kim
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Jiwoong Kwon
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Korea
| | - Youngbin Lim
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Korea
| | - Jooyoun Kang
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Sohyeon Bae
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Seong Keun Kim
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
- Department of Biophysics and Chemical Biology
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12
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Lomzov AA, Vorobjev YN, Pyshnyi DV. Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation. J Phys Chem B 2015; 119:15221-34. [PMID: 26569147 DOI: 10.1021/acs.jpcb.5b09645] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular dynamics simulation approach was applied for the prediction of the thermal stability of oligonucleotide duplexes. It was shown that the enthalpy of the DNA/DNA complex formation could be calculated using this approach. We have studied the influence of various simulation parameters on the secondary structure and the hybridization enthalpy value of Dickerson-Drew dodecamer. The optimal simulation parameters for the most reliable prediction of the enthalpy values were determined. The thermodynamic parameters (enthalpy and entropy changes) of a duplex formation were obtained experimentally for 305 oligonucleotides of various lengths and GC-content. The resulting database was studied with molecular dynamics (MD) simulation using the optimized simulation parameters. Gibbs free energy changes and the melting temperatures were evaluated using the experimental correlation between enthalpy and entropy changes of the duplex formation and the enthalpy values calculated by the MD simulation. The average errors in the predictions of enthalpy, the Gibbs free energy change, and the melting temperature of oligonucleotide complexes were 11%, 10%, and 4.4 °C, respectively. We have shown that the molecular dynamics simulation gives a possibility to calculate the thermal stability of native DNA/DNA complexes a priori with an unexpectedly high accuracy.
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Affiliation(s)
- Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Yury N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
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13
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Armstrong RE, Riskowski RA, Strouse GF. Nanometal Surface Energy Transfer Optical Ruler for Measuring a Human Telomere Structure. Photochem Photobiol 2015; 91:732-8. [DOI: 10.1111/php.12423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/01/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Rachel E. Armstrong
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
| | - Ryan A. Riskowski
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
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