1
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Smith SS. The bisulfite reaction with cytosine and genomic DNA structure. Anal Biochem 2024; 691:115532. [PMID: 38609028 DOI: 10.1016/j.ab.2024.115532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The bisulfite reaction with native DNA has been extensively employed in the detection of non-B DNA structures that can form spontaneously in DNA. These sequences are dynamic in that they can adopt both normal Watson-Crick paired B-DNA or unusual structures like the Triplex, G-Quadruplex, i-motif and Cruciform or Hairpin. Considerable evidence now suggests that these dynamic sequences play roles in both epigenetics and mutagenesis. The bisulfite reaction with native DNA offers a key approach to their detection. In this application whole cells, isolated nuclei or isolated DNA are treated with bisulfite under non-denaturing conditions in order to detect bisulfite accessible regions DNA that are associated with these structures. Here I review the stereochemistry of the bisulfite reaction, the electronic structure of its DNA cytosine substrates and its application in the detection of unusual structures in native DNA.
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Affiliation(s)
- Steven S Smith
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
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2
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Lallemang M, Akintayo CO, Wenzel C, Chen W, Sielaff L, Ripp A, Jessen HJ, Balzer BN, Walther A, Hugel T. Hierarchical Mechanical Transduction of Precision-Engineered DNA Hydrogels with Sacrificial Bonds. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59714-59721. [PMID: 38095074 DOI: 10.1021/acsami.3c15135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Engineering the response to external signals in mechanically switchable hydrogels is important to promote smart materials applications. However, comparably little attention has focused on embedded precision mechanisms for autonomous nonlinear response in mechanical profiles in hydrogels, and we lack understanding of how the behavior from the molecular scale transduces to the macroscale. Here, we design a nonlinear stress-strain response into hydrogels by engineering sacrificial DNA hairpin loops into model network hydrogels formed from star-shaped building blocks. We characterize the force-extension response of single DNA hairpins and are able to describe how the specific topology influences the nonlinear mechanical behavior at different length scales. For this purpose, we utilize force spectroscopy as well as microscopic and macroscopic deformation tests. This study contributes to a better understanding of designing nonlinear strain-adaptive features into hydrogel materials.
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Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Cecilia Oluwadunsin Akintayo
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Weixiang Chen
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
| | - Lucca Sielaff
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Alexander Ripp
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Henning J Jessen
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Freiburg 79104, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
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3
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Wang W, Chen W, Wu C, Zhang C, Feng J, Liu P, Hu Y, Li H, Sun F, Jiang K, Zhang X, Liu Z. Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing. Nat Methods 2023; 20:1780-1789. [PMID: 37798478 DOI: 10.1038/s41592-023-02037-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Extracellular matrix (ECM) rigidity serves as a crucial mechanical cue impacting diverse biological processes. However, understanding the molecular mechanisms of rigidity sensing has been limited by the spatial resolution and force sensitivity of current cellular force measurement techniques. Here we developed a method to functionalize DNA tension probes on soft hydrogel surfaces in a controllable and reliable manner, enabling molecular tension fluorescence microscopy for rigidity sensing studies. Our findings showed that fibroblasts respond to substrate rigidity by recruiting more force-bearing integrins and modulating integrin sampling frequency of the ECM, rather than simply overloading the existing integrin-ligand bonds, to promote focal adhesion maturation. We also demonstrated that ECM rigidity positively regulates the pN force of T cell receptor-ligand bond and T cell receptor mechanical sampling frequency, promoting T cell activation. Thus, hydrogel-based molecular tension fluorescence microscopy implemented on a standard confocal microscope provides a simple and effective means to explore detailed molecular force information for rigidity-dependent biological processes.
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Affiliation(s)
- Wenxu Wang
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Wei Chen
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Chaoyang Wu
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Chen Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Jingjing Feng
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Pengxiang Liu
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Yuru Hu
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Hongyun Li
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Feng Sun
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Kai Jiang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China
| | - Xinghua Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Zheng Liu
- TaiKang Center for Life and Medical Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan, China.
- College of Life Sciences, Wuhan University, Wuhan, China.
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4
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Koo J, Gurusamy D, Palli SR. Inefficient uptake of small interfering RNAs is responsible for their inability to trigger RNA interference in Colorado potato beetle cells. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-12. [PMID: 37452750 PMCID: PMC10528746 DOI: 10.1002/arch.22036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
There has been limited success in the usage of exogenous small interference RNA (siRNA) or small hairpin RNA (shRNA) to trigger RNA interference (RNAi) in insects. Instead, long double-stranded RNAs (dsRNA) are used to induce knockdown of target genes in insects. Here, we compared the potency of si/sh RNAs and dsRNA in Colorado potato beetle (CPB) cells. CPB cells showed highly efficient RNAi response to dsRNA. However, si/sh RNAs were inefficient in triggering RNAi in CPB cells. Confocal microscopy observations of Cy3 labeled-si/sh RNA cellular uptake revealed reduced si/sh RNA uptake compared to dsRNA. si/sh RNAs were stable in the conditioned media of CPB cells. Although in a small amount, when internalized by CPB cells, the si/sh RNAs were processed by the Dicer enzyme. Lipid-mediated transfection and chimeric dsRNA approaches were used to improve the delivery of si/sh RNAs. Our results suggest that the uptake of si/sh RNAs is inefficient in CPB cells, resulting in ineffective RNAi response. However, with the help of effective delivery methods, si/sh RNA could be a useful option for developing target-specific RNAi-mediated biopesticides.
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Affiliation(s)
- Jinmo Koo
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
| | - Dhandapani Gurusamy
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
- Current address, Department of Botany, Kongunadu Arts and Science College (Autonomous), Bharathiar University, Coimbatore, India
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
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5
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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6
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Ordóñez C, Martínez-Zapata D, Santamaria R. Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study. J Biomol Struct Dyn 2022; 40:13207-13217. [PMID: 34629032 DOI: 10.1080/07391102.2021.1987988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cristian Ordóñez
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Daniel Martínez-Zapata
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ruben Santamaria
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
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7
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Carey TR, Kozminsky M, Hall J, Vargas-Zapata V, Geiger K, Coscoy L, Sohn LL. Detecting Intact Virus Using Exogenous Oligonucleotide Labels. Anal Chem 2022; 94:7619-7627. [PMID: 35584293 DOI: 10.1021/acs.analchem.2c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has revealed how an emerging pathogen can cause a sudden and dramatic increase in demand for viral testing. Testing pooled samples could meet this demand; however, the sensitivity of reverse transcription quantitative polymerase chain reaction (RT-qPCR), the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce detection of intact virus by exogenous-nucleotide reaction (DIVER), a method that quantifies intact virus and is robust to sample dilution. As demonstrated using two models of severe acute respiratory syndrome coronavirus 2, DIVER first tags membraned particles with exogenous oligonucleotides, then captures the tagged particles on beads functionalized with a virus-specific capture agent (in this instance, angiotensin-converting enzyme 2), and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and spike-pseudotyped lentivirus, we show that DIVER can detect 1 × 105 liposomes and 100 plaque-forming units of lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well positioned for efficient sample pooling and clinical validation.
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Affiliation(s)
- Thomas R Carey
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
| | - Molly Kozminsky
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California 94720, United States
| | - Jennifer Hall
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Valerie Vargas-Zapata
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Kristina Geiger
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Laurent Coscoy
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Lydia L Sohn
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States.,Department of Mechanical Engineering, University of California, Berkeley, 5118 Etcheverry Hall, Berkeley, California 94720, United States
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8
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Altun A, Garcia-Ratés M, Neese F, Bistoni G. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex. Chem Sci 2021; 12:12785-12793. [PMID: 34703565 PMCID: PMC8494058 DOI: 10.1039/d1sc03868k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023] Open
Abstract
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
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9
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Martinez GS, de Ávila e Silva S, Kumar A, Pérez-Rueda E. DNA structural and physical properties reveal peculiarities in promoter sequences of the bacterium Escherichia coli K-12. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04713-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
AbstractThe gene transcription of bacteria starts with a promoter sequence being recognized by a transcription factor found in the RNAP enzyme, this process is assisted through the conservation of nucleotides as well as other factors governing these intergenic regions. Faced with this, the coding of genetic information into physical aspects of the DNA such as enthalpy, stability, and base-pair stacking could suggest promoter activity as well as protrude differentiation of promoter and non-promoter data. In this work, a total of 3131 promoter sequences associated to six different sigma factors in the bacterium E. coli were converted into numeric attributes, a strong set of control sequences referring to a shuffled version of the original sequences as well as coding regions is provided. Then, the parameterized genetic information was normalized, exhaustively analyzed through statistical tests. The results suggest that strong signals in the promoter sequences match the binding site of transcription factor proteins, indicating that promoter activity is well represented by its conversion into physical attributes. Moreover, the features tested in this report conveyed significant variances between promoter and control data, enabling these features to be employed in bacterial promoter classification. The results produced here may aid in bacterial promoter recognition by providing a robust set of biological inferences.
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10
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Adam T, Dhahi TS, Gopinath SCB, Hashim U, Uda MNA. Recent advances in techniques for fabrication and characterization of nanogap biosensors: A review. Biotechnol Appl Biochem 2021; 69:1395-1417. [PMID: 34143905 DOI: 10.1002/bab.2212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Nanogap biosensors have fascinated researchers due to their excellent electrical properties. Nanogap biosensors comprise three arrays of electrodes that form nanometer-size gaps. The sensing gaps have become the major building blocks of several sensing applications, including bio- and chemosensors. One of the advantages of nanogap biosensors is that they can be fabricated in nanoscale size for various downstream applications. Several studies have been conducted on nanogap biosensors, and nanogap biosensors exhibit potential material properties. The possibilities of combining these unique properties with a nanoscale-gapped device and electrical detection systems allow excellent and potential prospects in biomolecular detection. However, their fabrication is challenging as the gap is becoming smaller. It includes high-cost, low-yield, and surface phenomena to move a step closer to the routine fabrications. This review summarizes different feasible techniques in the fabrication of nanogap electrodes, such as preparation by self-assembly with both conventional and nonconventional approaches. This review also presents a comprehensive analysis of the fabrication, potential applications, history, and the current status of nanogap biosensors with a special focus on nanogap-mediated bio- and chemical sonsors.
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Affiliation(s)
- Tijjani Adam
- Faculty of Electronic Engineering Technology, Universiti Malaysia Perlis, Kampus Uniciti Alam Sg. Chuchuh, Padang Besar (U), Perlis, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Th S Dhahi
- Physics Department, University of Basrah, Basra, Iraq.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - U Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - M N A Uda
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
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11
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Gravina NM, Gumbart JC, Kim HD. Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. J Phys Chem B 2021; 125:4016-4024. [PMID: 33870695 DOI: 10.1021/acs.jpcb.1c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, τb. We specify the orientation of the dsDNA segments with three parameters: θ, which measures the angle between the helical axes, and ϕ1 and ϕ2, which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both θ and ϕ2: ∼20-fold change with θ and 10-fold change with ϕ2. The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.
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Affiliation(s)
- Nicholas M Gravina
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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12
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Beiranvand N, Freindorf M, Kraka E. Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study. Molecules 2021; 26:2268. [PMID: 33919989 PMCID: PMC8071019 DOI: 10.3390/molecules26082268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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Affiliation(s)
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA; (N.B.); (M.F.)
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13
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Carey TR, Kozminsky M, Hall J, Vargas-Zapata V, Geiger K, Coscoy L, Sohn LL. Toward Community Surveillance: Detecting Intact SARS-CoV-2 Using Exogeneous Oligonucleotide Labels. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.23.21254201. [PMID: 33791715 PMCID: PMC8010747 DOI: 10.1101/2021.03.23.21254201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The persistence of the COVID-19 pandemic demands a dramatic increase in testing efficiency. Testing pooled samples for SARS-CoV-2 could meet this need; however, the sensitivity of RT-qPCR, the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce DIVER, a method that quantifies intact virus and is robust to sample dilution. DIVER first tags viral particles with exogeneous oligonucleotides, then captures the tagged particles on ACE2-functionalized beads, and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and Spike-pseudotyped lentivirus as SARS-CoV-2 models, we show that DIVER can detect 1×10 5 liposomes and 100 pfu lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well-positioned for efficient sample pooling and expanded community surveillance.
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14
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Label-Free Oligonucleotide-Based SPR Biosensor for the Detection of the Gene Mutation Causing Prothrombin-Related Thrombophilia. SENSORS 2020; 20:s20216240. [PMID: 33142935 PMCID: PMC7663036 DOI: 10.3390/s20216240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022]
Abstract
Prothrombin-related thrombophilia is a genetic disorder produced by a substitution of a single DNA base pair, replacing guanine with adenine, and is detected mainly by polymerase chain reaction (PCR). A suitable alternative that could detect the single point mutation without requiring sample amplification is the surface plasmon resonance (SPR) technique. SPR biosensors are of great interest: they offer a platform to monitor biomolecular interactions, are highly selective, and enable rapid analysis in real time. Oligonucleotide-based SPR biosensors can be used to differentiate complementary sequences from partially complementary or noncomplementary strands. In this work, a glass chip covered with an ultrathin (50 nm) gold film was modified with oligonucleotide strands complementary to the mutated or normal (nonmutated) DNA responsible for prothrombin-related thrombophilia, forming two detection platforms called mutated thrombophilia (MT) biosensor and normal thrombophilia (NT) biosensor. The results show that the hybridization response is obtained in 30 min, label free and with high reproducibility. The sensitivity obtained in both systems was approximately 4 ΔμRIU/nM. The dissociation constant and limits of detection calculated were 12.2 nM and 20 pM (3 fmol), respectively, for the MT biosensor, and 8.5 nM and 30 pM (4.5 fmol) for the NT biosensor. The two biosensors selectively recognize their complementary strand (mutated or normal) in buffer solution. In addition, each platform can be reused up to 24 times when the surface is regenerated with HCl. This work contributes to the design of the first SPR biosensor for the detection of prothrombin-related thrombophilia based on oligonucleotides with single point mutations, label-free and without the need to apply an amplification method.
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15
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Wack M, Wiegand T, Frischknecht F, Cavalcanti-Adam EA. An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens. Bio Protoc 2020; 10:e3733. [PMID: 33659394 DOI: 10.21769/bioprotoc.3733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 11/02/2022] Open
Abstract
Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligand-receptor adhesions helps to unravel the molecular mechanisms driving migration. Traction force microscopy or optical tweezers are typically used to measure the cellular forces exerted by cells on a substrate. However, the spatial resolution of traction force microscopy is limited to ~2 µm and performing experiments with optical traps is very time-consuming. Here we present the production of biomimetic surfaces that enable specific cell adhesion via synthetic ligands and at the same time monitor the transmitted forces by using molecular tension sensors. The ligands were coupled to double-stranded DNA probes with defined force thresholds for DNA unzipping. Receptor-mediated forces in the pN range are thereby semi-quantitatively converted into fluorescence signals, which can be detected by standard fluorescence microscopy at the resolution limit (~0.2 µm). The modular design of the assay allows to vary the presented ligands and the mechanical strength of the DNA probes, which provides a number of possibilities to probe the adhesion of different eukaryotic cell types and pathogens and is exemplified here with osteosarcoma cells and Plasmodium berghei Sporozoites.
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Affiliation(s)
- Maurizio Wack
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Tina Wiegand
- Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute for Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - E Ada Cavalcanti-Adam
- Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute for Physical Chemistry, Heidelberg University, Heidelberg, Germany
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16
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Lansakara TI, Morris HS, Singh P, Kohen A, Tivanski AV. Rigid Double-Stranded DNA Linkers for Single Molecule Enzyme-Drug Interaction Measurements Using Molecular Recognition Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4174-4183. [PMID: 32233509 DOI: 10.1021/acs.langmuir.9b03495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-molecule studies can reveal the distribution of states and interactions between ligand-enzyme complexes not accessible for most studies that measure a large ensemble average response of many molecules. Furthermore, in some biological applications, the information regarding the outliers, not the average of measured properties, can be more important. The high spatial and force resolution provided by atomic force microscopy (AFM) under physiological conditions has been utilized in this study to quantify the force-distance relations of enzyme-drug interactions. Different immobilization techniques of the protein to a surface and the drug to AFM tip were quantitatively compared to improve the accuracy and precision of the measurement. Protein that is directly bound to the surface, forming a monolayer, was compared to enzyme molecules bound to the surface with rigid double-stranded (ds) DNA spacers. These surfaces immobilization techniques were studied with the drug bound directly to the AFM tip and drug bound via flexible poly(ethylene glycol) and rigid dsDNA linkers. The activity of the enzyme was found to be not significantly altered by immobilization methods relative to its activity in solution. The findings indicate that the approach for studying drug-enzyme interaction based on rigid dsDNA linker on the surface and either flexible or rigid linker on the tip affords straightforward, highly specific, reproducible, and accurate force measurements with a potential for single-molecule level studies. The method could facilitate in-depth examination of a broad spectrum of biological targets and potential drugs.
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Affiliation(s)
| | - Holly S Morris
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexei V Tivanski
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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17
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Zhang L, Xiao M, Zhou J, Yu J. Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA). Bioinformatics 2018; 34:3624-3630. [DOI: 10.1093/bioinformatics/bty392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Ming Xiao
- School of Computer and Information Science, Southwest University, Chongqing, China
- College of Mobile Telecommunications, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jingsong Zhou
- College of Computer Science, Sichuan University, Chengdu, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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18
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Ren W, Zheng K, Liao C, Yang J, Zhao J. Charge evolution during the unfolding of a single DNA i-motif. Phys Chem Chem Phys 2018; 20:916-924. [PMID: 29230450 DOI: 10.1039/c7cp06235d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effective charge and evolution of single chains of a DNA i-motif during its unfolding process are investigated at the single molecule level. Using fluorescence correlation spectroscopy and photon counting histograms, the single chain dimensions and electrical potential of cytosine-rich human telomeric oligonucleotides are monitored, during their unfolding from the i-motif to the random coil state. It is discovered that the effective charge density of the DNA chain is very sensitive to conformation changes and the results remarkably expose the existence of an intermediate state of the unfolding process. A huge difference in pH value exists in the vicinity of the DNA chain and the bulk solution, depending on the salt concentration, as reflected by a down-shift in the pH value of unfolding. The presence of an external salt in the solution helps to stabilize the i-motif structure at low pH values due to the reduction of the effective charge density. It can also destabilize the folded structure in the pH range of the conformation transition due to the elevation of the local pH value, encouraging the deprotonation of the cytosine groups. These results provide new information for understanding the structure and stability of i-motif DNA, and its biological function, as well as the building blocks for smart nanomaterials.
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Affiliation(s)
- Weibin Ren
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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19
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Electronic properties of DNA: Description of weak interactions in TATA-box-like chains. Biophys Chem 2017; 233:26-35. [PMID: 29287183 DOI: 10.1016/j.bpc.2017.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 11/23/2022]
Abstract
DNA is one of the most important biomolecules since it contains all the genetic information about an organism. The tridimensional structure of DNA is a determinant factor that influences the physiological and biochemical mechanisms by which this molecule carries out its biological functions. It is believed that hydrogen bonds and π-π stacking are the most relevant non-covalent interactions regarding DNA stability. Due to its importance, several theoretical works have been made to describe these interactions, however, most of them often consider only the presence of two nitrogenous bases, having a limited overview of the participation of these in B-DNA stabilization. Furthermore, due to the complexity of the system, there are discrepancies between which involved interaction is more important in duplex stability. Therefore, in this project we describe these interactions considering the effect of chain length on the energy related to both hydrogen bonds and π-π stacking, using as model TATA-box-like chains with n base pairs (n=1 to 14) and taking into consideration two different models: ideal and optimized B-DNA. We have found that there is a cooperative effect on hydrogen bond and π-π stacking mean energies when the presence of other base pairs is considered. In addition, it was found that hydrogen bonds contribute more importantly than π-π stacking to B-DNA stability; nevertheless, the participation of π-π stacking is not negligible: when B-DNA looks for a conformation of lower energy, π-π stacking interaction are the first to be optimized. All work was realized under the framework of DFT using the DMol3 code (M06-L/DNP).
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21
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Landuzzi F, Palla PL, Cleri F. Stability of radiation-damaged DNA after multiple strand breaks. Phys Chem Chem Phys 2017; 19:14641-14651. [DOI: 10.1039/c7cp02266b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Radiation induced double-strand breaks in DNA are more stable against thermal and mechanical stress than usually thought.
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Affiliation(s)
- Fabio Landuzzi
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Pier Luca Palla
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Fabrizio Cleri
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
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Choi S, Lee G, Park IS, Son M, Kim W, Lee H, Lee SY, Na S, Yoon DS, Bashir R, Park J, Lee SW. Detection of Silver Ions Using Dielectrophoretic Tweezers-Based Force Spectroscopy. Anal Chem 2016; 88:10867-10875. [DOI: 10.1021/acs.analchem.6b00107] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seungyeop Choi
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Gyudo Lee
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
- School
of Public Health, Harvard University, Boston, Massachusetts 02115, United States
| | - In Soo Park
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Myeonggu Son
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Woong Kim
- Department
of Control and Instrumentation Engineering, Korea University, Sejong 30019, Republic of Korea
| | - Hyungbeen Lee
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Sei-Young Lee
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Sungsoo Na
- Department
of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dae Sung Yoon
- Department
of Bio-convergence Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Rashid Bashir
- Department
of Bioengineering, University Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jinsung Park
- Department
of Control and Instrumentation Engineering, Korea University, Sejong 30019, Republic of Korea
| | - Sang Woo Lee
- Department
of Biomedical Engineering, Yonsei University, Wonju 26493, Republic of Korea
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