1
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Filliaux S, Sun Z, Lyubchenko YL. Nanoscale Structure, Interactions, and Dynamics of Centromere Nucleosomes. Biomacromolecules 2024. [PMID: 38959412 DOI: 10.1021/acs.biomac.3c01440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Centromeres are specific segments of chromosomes comprising two types of nucleosomes: canonical nucleosomes containing an octamer of H2A, H2B, H3, and H4 histones and CENP-A nucleosomes in which H3 is replaced with its analogue CENP-A. This modification leads to a difference in DNA wrapping (∼121 bp), considerably less than 147 bp in canonical nucleosomes. We used atomic force microscopy (AFM) and high-speed AFM (HS-AFM) to characterize nanoscale features and dynamics for both types of nucleosomes. For both nucleosomes, spontaneous asymmetric unwrapping of DNA was observed, and this process occurs via a transient state with ∼100 bp DNA wrapped around the core, followed by a rapid dissociation of DNA. Additionally, HS-AFM revealed higher stability of CENP-A nucleosomes compared with H3 nucleosomes in which dissociation of the histone core occurs prior to the nucleosome dissociation. These results help elucidate the differences between these nucleosomes and the potential biological necessity for CENP-A nucleosomes.
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Affiliation(s)
- Shaun Filliaux
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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2
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Neyra K, Everson HR, Mathur D. Dominant Analytical Techniques in DNA Nanotechnology for Various Applications. Anal Chem 2024; 96:3687-3697. [PMID: 38353660 PMCID: PMC11261746 DOI: 10.1021/acs.analchem.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
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3
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Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE, Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim SJ, Karpova T, Wang YX, Lee KS. Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 2023; 6:712. [PMID: 37433832 PMCID: PMC10336005 DOI: 10.1038/s42003-023-05067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Proper organization of intracellular assemblies is fundamental for efficient promotion of biochemical processes and optimal assembly functionality. Although advances in imaging technologies have shed light on how the centrosome is organized, how its constituent proteins are coherently architected to elicit downstream events remains poorly understood. Using multidisciplinary approaches, we showed that two long coiled-coil proteins, Cep63 and Cep152, form a heterotetrameric building block that undergoes a stepwise formation into higher molecular weight complexes, ultimately generating a cylindrical architecture around a centriole. Mutants defective in Cep63•Cep152 heterotetramer formation displayed crippled pericentriolar Cep152 organization, polo-like kinase 4 (Plk4) relocalization to the procentriole assembly site, and Plk4-mediated centriole duplication. Given that the organization of pericentriolar materials (PCM) is evolutionarily conserved, this work could serve as a model for investigating the structure and function of PCM in other species, while offering a new direction in probing the organizational defects of PCM-related human diseases.
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Affiliation(s)
- Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liang Zhang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lingjun Meng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, P R China
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tatiana Karpova
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Xu L, Halma MTJ, Wuite GJL. Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches. Int J Mol Sci 2023; 24:ijms24032806. [PMID: 36769124 PMCID: PMC9917605 DOI: 10.3390/ijms24032806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins' activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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5
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Hu WP, Wu YM, Vu CA, Chen WY. Ultrasensitive Detection of Interleukin 6 by Using Silicon Nanowire Field-Effect Transistors. SENSORS (BASEL, SWITZERLAND) 2023; 23:625. [PMID: 36679421 PMCID: PMC9865274 DOI: 10.3390/s23020625] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Interleukin 6 (IL-6) has been regarded as a biomarker that can be applied as a predictor for the severity of COVID-19-infected patients. The IL-6 level also correlates well with respiratory dysfunction and mortality risk. In this work, three silanization approaches and two types of biorecognition elements were used on the silicon nanowire field-effect transistors (SiNW-FETs) to investigate and compare the sensing performance on the detection of IL-6. Experimental data revealed that the mixed-SAMs-modified silica surface could have superior surface morphology to APTES-modified and APS-modified silica surfaces. According to the data on detecting various concentrations of IL-6, the detection range of the aptamer-functionalized SiNW-FET was broader than that of the antibody-functionalized SiNW-FET. In addition, the lowest concentration of valid detection for the aptamer-functionalized SiNW-FET was 2.1 pg/mL, two orders of magnitude lower than the antibody-functionalized SiNW-FET. The detection range of the aptamer-functionalized SiNW-FET covered the concentration of IL-6, which could be used to predict fatal outcomes of COVID-19. The detection results in the buffer showed that the anti-IL-6 aptamer could produce better detection results on the SiNW-FETs, indicating its great opportunity in applications for sensing clinical samples.
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Affiliation(s)
- Wen-Pin Hu
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Yu-Ming Wu
- Department of Chemical and Materials Engineering, National Central University, Taoyuan City 32001, Taiwan
| | - Cao-An Vu
- Department of Chemical and Materials Engineering, National Central University, Taoyuan City 32001, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Taoyuan City 32001, Taiwan
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6
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Ding J. High-Resolution Atomic Force Microscopy Imaging of RNA Molecules in Solution. Methods Mol Biol 2023; 2568:133-145. [PMID: 36227566 DOI: 10.1007/978-1-0716-2687-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Atomic force microscopy (AFM) is an important and versatile technique to investigate the structures and dynamics of biomolecules under physiologically relevant conditions at the single-molecule level. Recent progresses in high-resolution AFM imaging of nucleic acids have expanded this technique from simple characterization of double-stranded DNA or RNA to detailed analyses of the structure and dynamics of large functional RNAs with complex folds. Several technical developments, such as sharper probes and more stable instruments with novel imaging modes, AFM is capable of directly visualizing RNA conformational heterogeneity in solution in real time. Here, we introduce a comprehensive method for recording high-resolution images of RNA molecules, including sample preparation, instrument setup, data acquisition, and image processing.
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Affiliation(s)
- Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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7
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Kodera N, Ando T. Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy. Methods 2022; 207:44-56. [PMID: 36055623 DOI: 10.1016/j.ymeth.2022.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are partially or entirely disordered. Their intrinsically disordered regions (IDRs) dynamically explore a wide range of structural space by their highly flexible nature. Due to this distinct feature largely different from structured proteins, conventional structural analyses relying on ensemble averaging is unsuitable for characterizing the dynamic structure of IDPs. Therefore, single-molecule measurement tools have been desired in IDP studies. High-speed atomic force microscopy (HS-AFM) is a unique tool that allows us to directly visualize single biomolecules at 2-3 nm lateral and ∼ 0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution under near physiological conditions, without any chemical labeling. HS-AFM has been successfully used not only to characterize the shape and motion of IDP molecules but also to visualize their function-related dynamics. In this article, after reviewing the principle and current performances of HS-AFM, we describe experimental considerations in the HS-AFM imaging of IDPs and methods to quantify molecular features from captured images. Finally, we outline recent HS-AFM imaging studies of IDPs.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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8
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Zagorski K, Stormberg T, Hashemi M, Kolomeisky AB, Lyubchenko YL. Nanorings to Probe Mechanical Stress of Single-Stranded DNA Mediated by the DNA Duplex. Int J Mol Sci 2022; 23:12916. [PMID: 36361704 PMCID: PMC9655958 DOI: 10.3390/ijms232112916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 01/11/2024] Open
Abstract
The interplay between the mechanical properties of double-stranded and single-stranded DNA is a phenomenon that contributes to various genetic processes in which both types of DNA structures coexist. Highly stiff DNA duplexes can stretch single-stranded DNA (ssDNA) segments between the duplexes in a topologically constrained domain. To evaluate such an effect, we designed short DNA nanorings in which a DNA duplex with 160 bp is connected by a 30 nt single-stranded DNA segment. The stretching effect of the duplex in such a DNA construct can lead to the elongation of ssDNA, and this effect can be measured directly using atomic force microscopy (AFM) imaging. In AFM images of the nanorings, the ssDNA regions were identified, and the end-to-end distance of ssDNA was measured. The data revealed a stretching of the ssDNA segment with a median end-to-end distance which was 16% higher compared with the control. These data are in line with theoretical estimates of the stretching of ssDNA by the rigid DNA duplex holding the ssDNA segment within the nanoring construct. Time-lapse AFM data revealed substantial dynamics of the DNA rings, allowing for the formation of transient crossed nanoring formations with end-to-end distances as much as 30% larger than those of the longer-lived morphologies. The generated nanorings are an attractive model system for investigation of the effects of mechanical stretching of ssDNA on its biochemical properties, including interaction with proteins.
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Affiliation(s)
- Karen Zagorski
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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9
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3-Aminopropylsilatrane and Its Derivatives: A Variety of Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113549. [PMID: 35684486 PMCID: PMC9182167 DOI: 10.3390/molecules27113549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/26/2022]
Abstract
Silatranes arouse much research interest owing to their unique structure, unusual physical–chemical properties, and diverse biological activity. The application of some silatranes and their analogues has been discussed in several works. Meanwhile, a comprehensive review of the wide practical usage of silatranes is still absent in the literature. The ability of silatranes to mildly control hydrolysis allows them to form extremely stable and smooth siloxane monolayers almost on any surface. The high physiological activity of silatranes makes them prospective drug candidates. In the present review, based on the results of numerous previous studies, using the commercially available 3-aminopropylsilatrane and its hybrid derivatives, we have demonstrated the high potential of 1-organylsilatranes in various fields, including chemistry, biology, pharmaceuticals, medicine, agriculture, and industry. For example, these compounds can be employed as plant growth biostimulants, drugs, optical, catalytic, sorption, and special polymeric materials, as well as modern high-tech devices.
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10
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Dey S, Dorey A, Abraham L, Xing Y, Zhang I, Zhang F, Howorka S, Yan H. A reversibly gated protein-transporting membrane channel made of DNA. Nat Commun 2022; 13:2271. [PMID: 35484117 PMCID: PMC9051096 DOI: 10.1038/s41467-022-28522-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/14/2022] [Indexed: 01/14/2023] Open
Abstract
Controlled transport of biomolecules across lipid bilayer membranes is of profound significance in biological processes. In cells, cargo exchange is mediated by dedicated channels that respond to triggers, undergo a nanomechanical change to reversibly open, and thus regulate cargo flux. Replicating these processes with simple yet programmable chemical means is of fundamental scientific interest. Artificial systems that go beyond nature's remit in transport control and cargo are also of considerable interest for biotechnological applications but challenging to build. Here, we describe a synthetic channel that allows precisely timed, stimulus-controlled transport of folded and functional proteins across bilayer membranes. The channel is made via DNA nanotechnology design principles and features a 416 nm2 opening cross-section and a nanomechanical lid which can be controllably closed and re-opened via a lock-and-key mechanism. We envision that the functional DNA device may be used in highly sensitive biosensing, drug delivery of proteins, and the creation of artificial cell networks.
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Affiliation(s)
- Swarup Dey
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Leeza Abraham
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Irene Zhang
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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11
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Sharafeldin M, Davis JJ. Characterising the biosensing interface. Anal Chim Acta 2022; 1216:339759. [DOI: 10.1016/j.aca.2022.339759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022]
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12
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Keshav A, Murarka P, Srivastava P. Bending is required for activation of dsz operon by the TetR family protein (DszGR). Gene 2022; 810:146061. [PMID: 34774682 DOI: 10.1016/j.gene.2021.146061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022]
Abstract
The dsz operon responsible for the biodesulfurization of organosulfurs is under the control of a 385 bp long promoter. Recently, a TetR family protein was identified which served as an activator of operon. Here we report that the TetR family protein (WP_058249973.1), named DszGR can specifically activate the dsz operon. Direct binding of the DszGR to DNA was observed at single molecule level by AFM. It was found that the binding of DszGR to the promoter DNA induces a bend by about ∼40-50° degrees which may not be enough for the activation of the promoter. Thus, bendability in the promoter sequence was analyzed. The results show that the promoter has a curvature at around -235 and -200 bp with respect to dszA start codon. On mutating this region, a decrease in activity of the promoter was observed. Our results suggest that the DszGR protein binds to the upstream sequences and induces a bend, which is facilitated by further bending of the DNA which is required for dsz promoter activity. IHF binding site present in the promoter, and a significant reduction in desulphurization activity in the absence of either IHF subunits, suggested role of IHF in regulation of the dsz operon.
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Affiliation(s)
- Aditi Keshav
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pooja Murarka
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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13
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Editorial. Methods 2021; 197:1-3. [PMID: 34637927 DOI: 10.1016/j.ymeth.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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Sil S, Singh S, Chemparathy DT, Chivero ET, Gordon L, Buch S. Astrocytes & Astrocyte derived Extracellular Vesicles in Morphine Induced Amyloidopathy: Implications for Cognitive Deficits in Opiate Abusers. Aging Dis 2021; 12:1389-1408. [PMID: 34527417 PMCID: PMC8407877 DOI: 10.14336/ad.2021.0406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
While opiates like morphine play a major role in the pharmacotherapy for the control of pain associated with various diseases, paradoxically, their long-term use is associated with cognitive impairments. Furthermore, morphine administration has been shown to result in neuronal synaptodendritic injury in rodent brains, leading to neurodegeneration. We recently reported the role of astrocytes as contributors of amyloidosis associated with HIV-associated neurological disorders. Herein we hypothesize that morphine could induce astrocytic amyloidosis, which, in turn, could be disseminated to various regions in the brain by astrocyte-derived EVs (ADEVs). In this study we demonstrate brain region-specific up-regulation of astrocytic amyloids in morphine dependendent rhesus macaques. In addition, herein we also demonstrate increased expression of β-site cleaving enzyme (BACE1), APP, and Aβ in human primary astrocytes (HPAs) exposed to morphine. Mechanisms involved in this process included the up-regulation of hypoxia-inducible factor (HIF-1α), its translocation and binding to the promoter of BACE1, leading to increased BACE1 activity and, generation of Aβ 1-42. Gene silencing approaches confirmed the regulatory role of HIF-1α in BACE1 mediated amyloidosis leading to astrocyte activation and neuroinflammation. We next sought to assess whether morphine-stimulated ADEVs could carry amyloid cargoes. Results showed that morphine exposure induced the release of morphine-ADEVs, carrying amyloids. Interestingly, silencing HIF-1α in astrocytes not only reduced the numbers of ADEV released, but also the packaging of amyloid cargos in the ADEVs. These findings were further validated in brain derived EVs (BEVs) isolated from macaques, wherein it was shown that BEVs from morphine-dependent macaques, carried varieties of amyloid cargoes including the cytokine IL-1β. This is the first report implicating the role of HIF-1α-BACE1 axis in morphine-mediated induction of astrocytic amyloidosis, leading, in turn, to neuroinflammation and release of the amyloid cargoes via ADEVs. These findings set the groundwork for the future development of therapeutic strategies for targeting cognitive deficits in chronic opiate users.
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Affiliation(s)
- Susmita Sil
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Seema Singh
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Divya T Chemparathy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Ernest T Chivero
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Lila Gordon
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
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15
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Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALB. Atomic force microscopy-A tool for structural and translational DNA research. APL Bioeng 2021; 5:031504. [PMID: 34286171 PMCID: PMC8272649 DOI: 10.1063/5.0054294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.
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Affiliation(s)
| | - James I. Provan
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - John A. Hartley
- UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
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16
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Prokhorov VV, Barinov NA, Prusakov KA, Dubrovin EV, Frank-Kamenetskii MD, Klinov DV. Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations. NANO-MICRO LETTERS 2021; 13:130. [PMID: 34138333 PMCID: PMC8141082 DOI: 10.1007/s40820-021-00626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.
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Affiliation(s)
- Valery V Prokhorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russian Federation.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Kirill A Prusakov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Lomonosov Moscow State University, Leninskie gory, 1-2, Moscow, 119991, Russian Federation
| | | | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation.
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17
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Rausch JW, Heinz WF, Payea MJ, Sherpa C, Gorospe M, Le Grice SFJ. Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Res 2021; 49:e35. [PMID: 33406226 DOI: 10.1093/nar/gkaa1256] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/27/2020] [Accepted: 12/18/2020] [Indexed: 01/10/2023] Open
Abstract
Just as eukaryotic circular RNA (circRNA) is a product of intracellular backsplicing, custom circRNA can be synthesized in vitro using a transcription template in which transposed halves of a split group I intron flank the sequence of the RNA to be circularized. Such permuted intron-exon (PIE) constructs have been used to produce circRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expression vectors for genetic engineering and vaccine development. One limitation of this approach is the obligatory incorporation of small RNA segments (E1 and E2) into nascent circRNA at the site of end-joining. This restriction may preclude synthesis of small circRNA therapeutics and RNA nanoparticles that are sensitive to extraneous sequence, as well as larger circRNA mimics whose sequences must precisely match those of the native species on which they are modelled. In this work, we used serial mutagenesis and in vitro selection to determine how varying E1 and E2 sequences in a thymidylate synthase (td) group I intron PIE transcription template construct affects circRNA synthesis yield. Based on our collective findings, we present guidelines for the design of custom-tailored PIE transcription templates from which synthetic circRNAs of almost any sequence may be efficiently synthesized.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Payea
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
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18
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Li H, Zhang K, Binzel DW, Shlyakhtenko LS, Lyubchenko YL, Chiu W, Guo P. RNA nanotechnology to build a dodecahedral genome of single-stranded RNA virus. RNA Biol 2021; 18:2390-2400. [PMID: 33845711 DOI: 10.1080/15476286.2021.1915620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The quest for artificial RNA viral complexes with authentic structure while being non-replicative is on its way for the development of viral vaccines. RNA viruses contain capsid proteins that interact with the genome during morphogenesis. The sequence and properties of the protein and genome determine the structure of the virus. For example, the Pariacoto virus ssRNA genome assembles into a dodecahedron. Virus-inspired nanotechnology has progressed remarkably due to the unique structural and functional properties of viruses, which can inspire the design of novel nanomaterials. RNA is a programmable biopolymer able to self-assemble sophisticated 3D structures with rich functionalities. RNA dodecahedrons mimicking the Pariacoto virus quasi-icosahedral genome structures were constructed from both native and 2'-F modified RNA oligos. The RNA dodecahedron easily self-assembled using the stable pRNA three-way junction of bacteriophage phi29 as building blocks. The RNA dodecahedron cage was further characterized by cryo-electron microscopy and atomic force microscopy, confirming the spontaneous and homogenous formation of the RNA cage. The reported RNA dodecahedron cage will likely provide further studies on the mechanisms of interaction of the capsid protein with the viral genome while providing a template for further construction of the viral RNA scaffold to add capsid proteins for the assembly of the viral nucleocapsid as a model. Understanding the self-assembly and RNA folding of this RNA cage may offer new insights into the 3D organization of viral RNA genomes. The reported RNA cage also has the potential to be explored as a novel virus-inspired nanocarrier.
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Affiliation(s)
- Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kaiming Zhang
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Lyudmila S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Wah Chiu
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA.,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.,College of Pharmacy, The Ohio State University, Columbus, OH, USA.,James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
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19
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Nishide G, Lim K, Mohamed MS, Kobayashi A, Hazawa M, Watanabe-Nakayama T, Kodera N, Ando T, Wong RW. High-Speed Atomic Force Microscopy Reveals Spatiotemporal Dynamics of Histone Protein H2A Involution by DNA Inchworming. J Phys Chem Lett 2021; 12:3837-3846. [PMID: 33852305 DOI: 10.1021/acs.jpclett.1c00697] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA-histone interaction is always perturbed by epigenetic regulators to regulate gene expression. Direct visualization of this interaction is yet to be achieved. By using high-speed atomic force microscopy (HS-AFM), we have observed the dynamic DNA-histone H2A interaction. HS-AFM movies demonstrate the globular core and disordered tail of H2A. DNA-H2A formed the classic "beads-on-string" conformation on poly-l-lysine (PLL) and lipid substrates. Notably, a short-linearized double-stranded DNA (dsDNA), resembling an inchworm, wrapped around a single H2A protein only observed on the lipid substrate. Such a phenomenon does not occur for plasmid DNA or linearized long dsDNA on the same substrate. Strong adsorption of PLL substrate resulted in poor dynamic DNA-H2A interaction. Nonetheless, short-linearized dsDNA-H2A formed stable wrapping with a "diamond ring" topology on the PLL substrate. Reversible liquid-liquid phase separation (LLPS) of the DNA-H2A aggregate was visualized by manipulating salt concentrations. Collectively, our study suggest that HS-AFM is feasible for investigating epigenetically modified DNA-histone interactions.
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Affiliation(s)
- Goro Nishide
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Keesiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Mahmoud Shaaban Mohamed
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | | | - Noriyuki Kodera
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Richard W Wong
- Division of Nano Life Science in the Graduate School of Frontier Science Initiative, WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- WPI-Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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20
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Oligonucleotide Delivery across the Caco-2 Monolayer: The Design and Evaluation of Self-Emulsifying Drug Delivery Systems (SEDDS). Pharmaceutics 2021; 13:pharmaceutics13040459. [PMID: 33800701 PMCID: PMC8066367 DOI: 10.3390/pharmaceutics13040459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/21/2023] Open
Abstract
Oligonucleotides (OND) represent a promising therapeutic approach. However, their instability and low intestinal permeability hamper oral bioavailability. Well-established for oral delivery, self-emulsifying drug delivery systems (SEDDS) can overcome the weakness of other delivery systems such as long-term instability of nanoparticles or complicated formulation processes. Therefore, the present study aims to prepare SEDDS for delivery of a nonspecific fluorescently labeled OND across the intestinal Caco-2 monolayer. The hydrophobic ion pairing of an OND and a cationic lipid served as an effective hydrophobization method using either dimethyldioctadecylammonium bromide (DDAB) or 1,2-dioleoyl-3-trimethylammonium propane (DOTAP). This strategy allowed a successful loading of OND-cationic lipid complexes into both negatively charged and neutral SEDDS. Subjecting both complex-loaded SEDDS to a nuclease, the negatively charged SEDDS protected about 16% of the complexed OND in contrast to 58% protected by its neutral counterpart. Furthermore, both SEDDS containing permeation-enhancing excipients facilitated delivery of OND across the intestinal Caco-2 cell monolayer. The negatively charged SEDDS showed a more stable permeability profile over 120 min, with a permeability of about 2 × 10-7 cm/s, unlike neutral SEDDS, which displayed an increasing permeability reaching up to 7 × 10-7 cm/s. In conclusion, these novel SEDDS-based formulations provide a promising tool for OND protection and delivery across the Caco-2 cell monolayer.
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21
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Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman HN, Wang YX. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 2021; 12:1762. [PMID: 33741910 PMCID: PMC7979858 DOI: 10.1038/s41467-021-21838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.
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Affiliation(s)
| | - Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jienyu Ding
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Ping Yu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Tzai Lee
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, USA.,Department of Chemistry and Physics, ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Suraj Pandey
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Marius Schmidt
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
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22
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Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 2021; 11:4518. [PMID: 33633170 PMCID: PMC7907199 DOI: 10.1038/s41598-021-83889-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/09/2021] [Indexed: 11/23/2022] Open
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos), which are the core of RNA interference. The best understood prokaryotic Ago (pAgo) proteins are full-length pAgos. They are composed of four major structural/functional domains (N, PAZ, MID, and PIWI) and thereby closely resemble eAgos. It was demonstrated that full-length pAgos function as prokaryotic antiviral systems, with the PIWI domain performing cleavage of invading nucleic acids. However, the majority of identified pAgos are shorter and catalytically inactive (encode just MID and inactive PIWI domains), thus their action mechanism and function remain unknown. In this work we focus on AfAgo, a short pAgo protein encoded by an archaeon Archaeoglobus fulgidus. We find that in all previously solved AfAgo structures, its two monomers form substantial dimerization interfaces involving the C-terminal β-sheets. Led by this finding, we have employed various biochemical and biophysical assays, including SEC-MALS, SAXS, single-molecule FRET, and AFM, to show that AfAgo is indeed a homodimer in solution, which is capable of simultaneous interaction with two DNA molecules. This finding underscores the diversity of prokaryotic Agos and broadens the range of currently known Argonaute-nucleic acid interaction mechanisms.
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23
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Green synthesis, in vivo and in vitro pharmacological studies of Tamarindus indica based gold nanoparticles. Bioprocess Biosyst Eng 2021; 44:1185-1192. [PMID: 33582887 DOI: 10.1007/s00449-020-02500-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
The current investigation aims to synthesize gold nanoparticles (AuNPs) from aqueous extract of Tamarindus indica and to evaluate the in vitro anti-bacterial and in vivo sedative and anelgescic activities of crude extract as well as synthesized AuNPs. Several methods have been reported to synthesize AuNPs; however, most of them were not ecofriendly. In the present study, the green synthesis of AuNPs has been carried out. Using the green synthesis method, AuNPs of T. indica were synthesized at room temperature (25 °C) by mixing 5 mL of HAuCl4 (1 mM) with 1 mL of T. indica seed extract solution. This extract solution was prepared by taking 5 gm dry seeds in 100 mL of double deionized water with continuous stirring for up to 24 h at 80 °C. The stability of AuNPs was confirmed with the help of relevant experimental techniques including ultraviolet-visible (UV/Vis) showing maximum absorbance at 535-540 nm, Fourier transform infrared showing a broad signal at 3464 cm-1 which can be attributed to either amide or hydroxyl functionalities and atomic force microscopy analysis showed that the biomaterial surrounding AuNPs was agglomerated which proves the formation of discrete nanostructutres. These AuNPs have been evaluated for their antibacterial potential. The results revealed good antibacterial activity of the samples against. Klebsiella pneumonia, Bacillus subtilis and Staphylococcus epidermidis with 10-12 mm zone of inhibition range. The AuNPs were also found stable at high temperature, over a range of pH and in 1 mM salt solution. Moreover, the crude extract and respective AuNPs also exhibited interesting sedative and analgesic activities. Hence, we focused on phytochemicals-mediated synthesis of AuNPs considered as greatest attention in the treatment of anti-bacterial, analgesic, and sedative.
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24
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Xiong X, Han J, Chen Y, Li S, Xiao W, Shi Q. DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment. NANOTECHNOLOGY 2021; 32:055601. [PMID: 33179606 DOI: 10.1088/1361-6528/abb507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The evolution of single-stranded DNA (ssDNA) assembly on octadecylamine (ODA) modified highly oriented pyrolytic graphite (HOPG) surface by heating and ultrasonic treatment has been studied for the first time. We have observed that DNA on the ODA coated HOPG surface underwent dramatic morphological changes as a function of heating and ultrasonic treatment. Ordered DNA firstly changed to random aggregates by heating and then changed to three-dimensional (3D) networks by ultrasonic treatment. This finding points to previously unknown factors that impact graphite-DNA interaction and opens new opportunities to control the deposition of DNA onto graphitic substrates. In this way, we built a cost-effective method to produce large-scale 3D ssDNA networks. All of these studies pave the way to understand the properties of DNA-solid interface, design novel nanomaterials, and improve the sensitivity of DNA biosensors.
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Affiliation(s)
- Xiaolu Xiong
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Junfeng Han
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Yu Chen
- Institute of High Energy Physics, CAS. 19B Yuquan Road, Shijingshan District, Beijing 100081, People's Republic of China
| | - Shanshan Li
- Department of Rheumatology, China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Wende Xiao
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
- Micronano Centre, Beijing Key Lab of Nanophotonics & Ultrafine Optoelectronic Systems, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Qingfan Shi
- Key laboratory of advanced optoelectronic quantum architecture and measurement, ministry of education, School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
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25
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Carter OWL, Xu Y, Sadler PJ. Minerals in biology and medicine. RSC Adv 2021; 11:1939-1951. [PMID: 35424161 PMCID: PMC8693805 DOI: 10.1039/d0ra09992a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
Natural minerals ('stone drugs') have been used in traditional Chinese medicines for over 2000 years, but there is potential for modern-day use of inorganic minerals to combat viral infections, antimicrobial resistance, and for other areas in need of new therapies and diagnostic aids. Metal and mineral surfaces on scales from milli-to nanometres, either natural or synthetic, are patterned or can be modified with hydrophilic/hydrophobic and ionic/covalent target-recognition sites. They introduce new strategies for medical applications. Such surfaces have novel properties compared to single metal centres. Moreover, 3D mineral particles (including hybrid organo-minerals) can have reactive cavities, and some minerals have dynamic movement of metal ions, anions, and other molecules within their structures. Minerals have a unique ability to interact with viruses, microbes and macro-biomolecules through multipoint ionic and/or non-covalent contacts, with potential for novel applications in therapy and biotechnology. Investigations of mineral deposits in biology, with their often inherent heterogeneity and tendency to become chemically-modified on isolation, are highly challenging, but new methods for their study, including in intact tissues, hold promise for future advances.
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Affiliation(s)
- Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- MAS CDT, Senate House, University of Warwick Coventry CV4 7AL UK
| | - Yingjian Xu
- GoldenKeys High-Tech Materials Co., Ltd, Building B, Innovation & Entrepreneurship Park Guian New Area Guizhou Province 550025 China
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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26
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Graf J, Kretz M. From structure to function: Route to understanding lncRNA mechanism. Bioessays 2020; 42:e2000027. [PMID: 33164244 DOI: 10.1002/bies.202000027] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/03/2020] [Indexed: 12/13/2022]
Abstract
RNAs have emerged as a major target for diagnostics and therapeutics approaches. Regulatory nonprotein-coding RNAs (ncRNAs) in particular display remarkable versatility. They can fold into complex structures and interact with proteins, DNA, and other RNAs, thus modulating activity, localization, or interactome of multi-protein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of regulatory control. Interestingly, long noncoding RNAs (lncRNAs) tend to acquire complex secondary and tertiary structures and their function-in many cases-is dependent on structural conservation rather than primary sequence conservation. Whereas for many proteins, structure and its associated function are closely connected, for lncRNAs, the structural domains that determine functionality and its interactome are still not well understood. Numerous approaches for analyzing the structural configuration of lncRNAs have been developed recently. Here, will provide an overview of major experimental approaches used in the field, and discuss the potential benefit of using combinatorial strategies to analyze lncRNA modes of action based on structural information.
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Affiliation(s)
- Johannes Graf
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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27
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Chillón I, Marcia M. The molecular structure of long non-coding RNAs: emerging patterns and functional implications. Crit Rev Biochem Mol Biol 2020; 55:662-690. [PMID: 33043695 DOI: 10.1080/10409238.2020.1828259] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts that regulate vital cellular processes and are crucially connected to diseases. Despite their unprecedented molecular complexity, it is emerging that lncRNAs possess distinct structural motifs. Remarkably, the 3D shape and topology of full-length, native lncRNAs have been visualized for the first time in the last year. These studies reveal that lncRNA structures dictate lncRNA functions. Here, we review experimentally determined lncRNA structures and emphasize that lncRNA structural characterization requires synergistic integration of computational, biochemical and biophysical approaches. Based on these emerging paradigms, we discuss how to overcome the challenges posed by the complex molecular architecture of lncRNAs, with the goal of obtaining a detailed understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
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28
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Pan Y, Shlyakhtenko LS, Lyubchenko YL. High-speed atomic force microscopy directly visualizes conformational dynamics of the HIV Vif protein in complex with three host proteins. J Biol Chem 2020; 295:11995-12001. [PMID: 32587092 PMCID: PMC7443491 DOI: 10.1074/jbc.ra120.014442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Indexed: 11/06/2022] Open
Abstract
Vif (viral infectivity factor) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of host APOBEC3 (apolipoprotein B mRNA-editing enzyme catalytic subunit 3) proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and core-binding factor subunit β, forming a four-protein complex called VCBC. The structure of VCBC-Cullin5 has recently been solved by X-ray crystallography, and, using molecular dynamics simulations, the dynamics of VCBC have been characterized. Here, we applied time-lapse high-speed atomic force microscopy to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of this complex, which we identified as the triangle, dumbbell, and globular structures. Moreover, we characterized the dynamics of each of these structures. Our data revealed the very dynamic behavior of all of them, with the triangle and dumbbell structures being the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and may support efforts to improve HIV treatment, because Vif is essential for virus survival in the cell.
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Affiliation(s)
- Yangang Pan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA.
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29
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Uroda T, Chillón I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M. Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques. Nat Protoc 2020; 15:2107-2139. [PMID: 32451442 DOI: 10.1038/s41596-020-0323-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered transcripts that regulate vital cellular processes, such as cellular differentiation and DNA replication, and are crucially connected to diseases. Although the 3D structures of lncRNAs are key determinants of their function, the unprecedented molecular complexity of lncRNAs has so far precluded their 3D structural characterization at high resolution. It is thus paramount to develop novel approaches for biochemical and biophysical characterization of these challenging targets. Here, we present a protocol that integrates non-denaturing lncRNA purification with in-solution hydrodynamic analysis and single-particle atomic force microscopy (AFM) imaging to produce highly homogeneous lncRNA preparations and visualize their 3D topology at ~15-Å resolution. Our protocol is suitable for imaging lncRNAs in biologically active conformations and for measuring structural defects of functionally inactive mutants that have been identified by cell-based functional assays. Once optimized for the specific target lncRNA of choice, our protocol leads from cloning to AFM imaging within 3-4 weeks and can be implemented using state-of-the-art biochemical and biophysical instrumentation by trained researchers familiar with RNA handling and supported by AFM and small-angle X-ray scattering (SAXS) experts.
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Affiliation(s)
- Tina Uroda
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.,Department of BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Marie Teulon
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Ombeline Pessey
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Luc Pellequer
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.
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30
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Heenan PR, Wang X, Gooding AR, Cech TR, Perkins TT. Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid. Nucleic Acids Res 2020; 48:2969-2981. [PMID: 32043141 DOI: 10.1093/nar/gkaa073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/20/2020] [Accepted: 01/25/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2 and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA's helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2's methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.
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Affiliation(s)
- Patrick R Heenan
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.,JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Anne R Gooding
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Thomas R Cech
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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31
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Spokoini-Stern R, Stamov D, Jessel H, Aharoni L, Haschke H, Giron J, Unger R, Segal E, Abu-Horowitz A, Bachelet I. Visualizing the structure and motion of the long noncoding RNA HOTAIR. RNA (NEW YORK, N.Y.) 2020; 26:629-636. [PMID: 32115425 PMCID: PMC7161352 DOI: 10.1261/rna.074633.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Long noncoding RNA molecules (lncRNAs) are estimated to account for the majority of eukaryotic genomic transcripts, and have been associated with multiple diseases in humans. However, our understanding of their structure-function relationships is scarce, with structural evidence coming mostly from indirect biochemical approaches or computational predictions. Here we describe direct visualization of the lncRNA HOTAIR (HOx Transcript AntIsense RNA) using atomic force microscopy (AFM) in nucleus-like conditions at 37°. Our observations reveal that HOTAIR has a discernible, although flexible, shape. Fast AFM scanning enabled the quantification of the motion of HOTAIR, and provided visual evidence of physical interactions with genomic DNA segments. Our report provides a biologically plausible description of the anatomy and intrinsic properties of HOTAIR, and presents a framework for studying the structural biology of lncRNAs.
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Affiliation(s)
- Rachel Spokoini-Stern
- Augmanity, Rehovot 7670308, Israel
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | | | | | | | | | - Ron Unger
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eran Segal
- Weizmann Institute of Science, Rehovot 7610001, Israel
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32
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Chen S, Xu J, Liu M, Rao ALN, Zandi R, Gill SS, Mohideen U. Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy. PLoS One 2020; 15:e0228036. [PMID: 32015565 PMCID: PMC6996966 DOI: 10.1371/journal.pone.0228036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates depending on the net charges carried. Gag and its complexes consist of monomers, dimers and tetramers, which was confirmed by gel electrophoresis. The addition of specific ΨRNA to Gag is found to increase Gag multimerization. Non-specific TARpolyA RNA was found not to lead to an increase in Gag multimerization. The addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent than ΨRNA. When both ΨRNA and PI(4,5)P2 are present Gag undergoes comformational changes and an even higher degree of multimerization.
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Affiliation(s)
- Shaolong Chen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Jun Xu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Mingyue Liu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - A. L. N. Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, California, United States of America
| | - Roya Zandi
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Sarjeet S. Gill
- Department of Cell Biology & Neuroscience, University of California, Riverside, California, United States of America
| | - Umar Mohideen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
- * E-mail:
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Zakrevsky P, Kasprzak WK, Heinz WF, Wu W, Khant H, Bindewald E, Dorjsuren N, Fields EA, de Val N, Jaeger L, Shapiro BA. Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates. NANOSCALE 2020; 12:2555-2568. [PMID: 31932830 DOI: 10.1039/c9nr08197f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA interference (RNAi) substrates, allowing multiple functional entities to be combined on a single particle in a programmable fashion. Rather than employing a completely bottom-up approach to scaffold design, here multiple copies of an existing synthetic supramolecular RNA nano-architecture serve as building blocks along with additional motifs for the design of a novel truncated tetrahedral RNA scaffold, demonstrating that rationally designed RNA assemblies can themselves serve as modular pieces in the construction of larger rationally designed structures. The resulting tetrahedral scaffold displays enhanced characteristics for RNAi-substrate delivery in comparison to similar RNA-based scaffolds, as evidenced by its increased functional capacity, increased cellular uptake and ultimately an increased RNAi efficacy of its adorned Dicer substrate siRNAs. The unique truncated tetrahedral shape of the nanoparticle core appears to contribute to this particle's enhanced function, indicating the physical characteristics of RNA scaffolds merit significant consideration when designing platforms for delivery of functional RNAs via RNA nanoparticles.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Htet Khant
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eric A Fields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA and Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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34
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Visser MJ, Pretorius E. Atomic Force Microscopy: The Characterisation of Amyloid Protein Structure in Pathology. Curr Top Med Chem 2020; 19:2958-2973. [DOI: 10.2174/1568026619666191121143240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
Abstract
:
Proteins are versatile macromolecules that perform a variety of functions and participate in
virtually all cellular processes. The functionality of a protein greatly depends on its structure and alterations
may result in the development of diseases. Most well-known of these are protein misfolding disorders,
which include Alzheimer’s and Parkinson’s diseases as well as type 2 diabetes mellitus, where
soluble proteins transition into insoluble amyloid fibrils. Atomic Force Microscopy (AFM) is capable of
providing a topographical map of the protein and/or its aggregates, as well as probing the nanomechanical
properties of a sample. Moreover, AFM requires relatively simple sample preparation, which presents
the possibility of combining this technique with other research modalities, such as confocal laser
scanning microscopy, Raman spectroscopy and stimulated emission depletion microscopy. In this review,
the basic principles of AFM are discussed, followed by a brief overview of how it has been applied
in biological research. Finally, we focus specifically on its use as a characterisation method to
study protein structure at the nanoscale in pathophysiological conditions, considering both molecules
implicated in disease pathogenesis and the plasma protein fibrinogen. In conclusion, AFM is a userfriendly
tool that supplies multi-parametric data, rendering it a most valuable technique.
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Affiliation(s)
- Maria J.E. Visser
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
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35
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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36
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Lunelli L, Caradonna F, Potrich C, Piotto C, Bettotti P, Vanzetti L, Pederzolli C, Guella G. A new silanizing agent tailored to surface bio-functionalization. Colloids Surf B Biointerfaces 2019; 181:166-173. [PMID: 31132608 DOI: 10.1016/j.colsurfb.2019.05.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/18/2019] [Accepted: 05/15/2019] [Indexed: 11/28/2022]
Abstract
Amino-terminated surfaces can be effectively obtained by means of silanizing agents, realizing surfaces suitable for the purification of biomarkers of several pathologies. Since the level of biomarkers, such as microRNAs and cell-free DNA, into circulation may be extremely low, new and ameliorated capturing molecules and protocols are highly required. In this work, a new silane, acetone-imine propyl trimethoxysilane (AIPTMS), is synthesized with a simple and elegant reaction, via the nucleophilic addition of the primary amino group to the carbonyl group of acetone. AIPTMS and APTMS were used to silanize silicon oxide surfaces, which were characterized chemically (XPS) and morphologically (AFM). The two types of surfaces were chemically similar, but behaved very differently both for surface morphology and functional properties. The AIPTMS-modified surface was indeed very smooth and homogeneous with respect to the APTMS-modified surface. Moreover, the AIPTMS surface captured larger amounts of nucleic acids almost immediately after preparation, while APTMS-based functional surfaces needed longer time to reach comparable efficiency. AIPTMS shows several advantages over standard aminosilanes, as it realizes a more homogeneous surface coverage that, in turn, produces an improved response towards the capture of nucleic acids. AIPTMS is a very promising reagent for the reliable and reproducible preparation of active biofunctional surfaces for the purification and analysis of circulating biomarkers.
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Affiliation(s)
- L Lunelli
- Fondazione Bruno Kessler, Center for Materials and Microsystems, Lab. Biomarker Studies and Structure Analysis for Health, via Sommarive 18, I-38123 Povo (Trento), Italy; CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via alla Cascata 56/C, I-38123 Povo (Trento), Italy
| | - F Caradonna
- Fondazione Bruno Kessler, Center for Materials and Microsystems, Lab. Biomarker Studies and Structure Analysis for Health, via Sommarive 18, I-38123 Povo (Trento), Italy; University of Trento, Department of Physics, Bioorgan Chem Lab, Via Sommarive 14, I-38123 Trento, Italy
| | - C Potrich
- Fondazione Bruno Kessler, Center for Materials and Microsystems, Lab. Biomarker Studies and Structure Analysis for Health, via Sommarive 18, I-38123 Povo (Trento), Italy; CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via alla Cascata 56/C, I-38123 Povo (Trento), Italy.
| | - C Piotto
- University of Trento, Department of Physics, Nanoscience Laboratory, Via Sommarive 14, I-38123 Trento, Italy
| | - P Bettotti
- University of Trento, Department of Physics, Nanoscience Laboratory, Via Sommarive 14, I-38123 Trento, Italy
| | - L Vanzetti
- Fondazione Bruno Kessler, Center for Materials and Microsystems, via Sommarive 18, I-38123 Povo, Trento, Italy
| | - C Pederzolli
- Fondazione Bruno Kessler, Center for Materials and Microsystems, Lab. Biomarker Studies and Structure Analysis for Health, via Sommarive 18, I-38123 Povo (Trento), Italy
| | - G Guella
- University of Trento, Department of Physics, Bioorgan Chem Lab, Via Sommarive 14, I-38123 Trento, Italy; CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via alla Cascata 56/C, I-38123 Povo (Trento), Italy
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Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway. Mol Cell 2019; 75:982-995.e9. [PMID: 31444106 PMCID: PMC6739425 DOI: 10.1016/j.molcel.2019.07.025] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 01/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures ("kissing loops"). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation in vivo and disrupt MEG3 folding in vitro. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function.
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38
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Li H, Wang S, Ji Z, Xu C, Shlyakhtenko LS, Guo P. Construction of RNA nanotubes. NANO RESEARCH 2019; 12:1952-1958. [PMID: 32153728 PMCID: PMC7062307 DOI: 10.1007/s12274-019-2463-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nanotubes are miniature materials with significant potential applications in nanotechnological, medical, biological and material sciences. The quest for manufacturing methods of nano-mechanical modules is in progress. For example, the application of carbon nanotubes has been extensively investigated due to the precise width control, but the precise length control remains challenging. Here we report two approaches for the one-pot self-assembly of RNA nanotubes. For the first approach, six RNA strands were used to assemble the nanotube by forming a 11 nm long hollow channel with the inner diameter of 1.7 nm and the outside diameter of 6.3 nm. For the second approach, six RNA strands were designed to hybridize with their neighboring strands by complementary base pairing and formed a nanotube with a six-helix hollow channel similar to the nanotube assembled by the first approach. The fabricated RNA nanotubes were characterized by gel electrophoresis and atomic force microscopy (AFM), confirming the formation of nanotube-shaped RNA nanostructures. Cholesterol molecules were introduced into RNA nanotubes to facilitate their incorporation into lipid bilayer. Incubation of RNA nanotube complex with the free-standing lipid bilayer membrane under applied voltage led to discrete current signatures. Addition of peptides into the sensing chamber revealed discrete steps of current blockage. Polyarginine peptides with different lengths can be detected by current signatures, suggesting that the RNA-cholesterol complex holds the promise of achieving single molecule sensing of peptides.
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Affiliation(s)
- Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Shaoying Wang
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Lyudmila S Shlyakhtenko
- UNMC Nanoimaging Core Facility, Department of Pharmaceutical Sciences, College of Pharmacy University of Nebraska Medical Center, Omaha, NE, 68182, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
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Stumme-Diers MP, Banerjee S, Hashemi M, Sun Z, Lyubchenko YL. Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A. Nucleic Acids Res 2019; 46:94-103. [PMID: 29040671 PMCID: PMC5758880 DOI: 10.1093/nar/gkx933] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/02/2017] [Indexed: 01/12/2023] Open
Abstract
In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, high-speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits upon unwrapping DNA, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere.
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Affiliation(s)
- Micah P Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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40
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Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS NANO 2019; 13:4220-4229. [PMID: 30938988 DOI: 10.1021/acsnano.8b09234] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl2 and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl2-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl2. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Physics , University of Colorado , Boulder , Colorado 80309 , United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Molecular, Cellular, and Developmental Biology , University of Colorado , Boulder , Colorado 80309 , United States
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41
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Moreno M, Vázquez L, López-Carrasco A, Martín-Gago J, Flores R, Briones C. Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy. RNA Biol 2019; 16:295-308. [PMID: 30734641 PMCID: PMC6380281 DOI: 10.1080/15476286.2019.1572436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 11/01/2022] Open
Abstract
Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.
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Affiliation(s)
- M. Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - L. Vázquez
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - A. López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - J.A. Martín-Gago
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - R. Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - C. Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
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42
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Stumme-Diers MP, Stormberg T, Sun Z, Lyubchenko YL. Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging. J Vis Exp 2019. [PMID: 30774135 DOI: 10.3791/58820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.
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Affiliation(s)
| | - Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center;
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43
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Roth E, Glick Azaria A, Girshevitz O, Bitler A, Garini Y. Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure. NANO LETTERS 2018; 18:6703-6709. [PMID: 30352164 DOI: 10.1021/acs.nanolett.8b02093] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.
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Affiliation(s)
- Efrat Roth
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Alex Glick Azaria
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Olga Girshevitz
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Arkady Bitler
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Yuval Garini
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
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44
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Hu G, Liao K, Niu F, Yang L, Dallon BW, Callen S, Tian C, Shu J, Cui J, Sun Z, Lyubchenko YL, Ka M, Chen XM, Buch S. Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:450-463. [PMID: 30388619 PMCID: PMC6202788 DOI: 10.1016/j.omtn.2018.09.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/31/2022]
Abstract
Impairment of microglial functions, such as phagocytosis and/or dysregulation of immune responses, has been implicated as an underlying factor involved in the pathogenesis of various neurodegenerative disorders. Our previous studies have demonstrated that long intergenic noncoding RNA (lincRNA)-Cox2 expression is influenced by nuclear factor κB (NF-κB) signaling and serves as a coactivator of transcriptional factors to regulate the expression of a vast array of immune-related genes in microglia. Extracellular vesicles (EVs) have been recognized as primary facilitators of cell-to-cell communication and cellular regulation. Herein, we show that EVs derived from astrocytes exposed to morphine can be taken up by microglial endosomes, leading, in turn, to activation of Toll-like receptor 7 (TLR7) with a subsequent upregulation of lincRNA-Cox2 expression, ultimately resulting in impaired microglial phagocytosis. This was further validated in vivo, wherein inhibition of microglial phagocytic activity was also observed in brain slices isolated from morphine-administrated mice compared with control mice. Additionally, we also showed that intranasal delivery of EVs containing lincRNA-Cox2 siRNA (small interfering RNA) was able to restore microglial phagocytic activity in mice administered morphine. These findings have ramifications for the development of EV-loaded RNA-based therapeutics for the treatment of various disorders involving functional impairment of microglia.
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Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA.
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Fang Niu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Lu Yang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Blake W Dallon
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Shannon Callen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Changhai Tian
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198-5850, USA
| | - Jiang Shu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Minhan Ka
- Center for Substance Abuse Pharmacology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA.
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45
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Mahata T, Chakraborty J, Kanungo A, Patra D, Basu G, Dutta S. Intercalator-Induced DNA Superstructure Formation: Doxorubicin and a Synthetic Quinoxaline Derivative. Biochemistry 2018; 57:5557-5563. [DOI: 10.1021/acs.biochem.8b00613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Tridib Mahata
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Jeet Chakraborty
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, WB, India
| | - Ajay Kanungo
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, WB, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 600113, India
| | - Dipendu Patra
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, WB, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 600113, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, WB, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 600113, India
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46
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Cavalcanti DP, de Souza W. The Kinetoplast of Trypanosomatids: From Early Studies of Electron Microscopy to Recent Advances in Atomic Force Microscopy. SCANNING 2018; 2018:9603051. [PMID: 30018700 PMCID: PMC6029474 DOI: 10.1155/2018/9603051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
The kinetoplast is a specialized region of the mitochondria of trypanosomatids that harbors the most complex and unusual mitochondrial DNA found in nature. Kinetoplast DNA (kDNA) is composed of thousands of circular molecules topologically interlocked to form a single network. Two types of DNA circles are present in the kinetoplast: minicircles (0.5-10 kb) and maxicircles (20-40 kb). Knowledge of kinetoplast architecture is crucial to understanding the replication and segregation of kDNA circles because the molecules involved in these processes are precisely positioned in functional domains throughout the kinetoplast. The fine structure of the kinetoplast was revealed in early electron microscopy (EM) studies. However, an understanding of the topological organization of kDNA was only demonstrated after the development of protocols to separate kDNA from nuclear DNA, followed by EM observations. Electron microscopy analysis of thin sections of trypanosomatids, spreading of isolated kDNA networks onto EM grids, deep-etching studies, and cytochemical and immunocytochemical approaches are examples of techniques that were useful for elucidating the structure and replication of the kinetoplast. Recently, atomic force microscopy has joined this set of techniques and improved our knowledge about the kDNA network and revealed new details about kDNA topology in trypanosomatids.
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Affiliation(s)
- Danielle Pereira Cavalcanti
- Laboratório de Microbiologia, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia-Inmetro, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem and Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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47
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Dutta S, Rivetti C, Gassman NR, Young CG, Jones BT, Scarpinato K, Guthold M. Analysis of single, cisplatin-induced DNA bends by atomic force microscopy and simulations. J Mol Recognit 2018; 31:e2731. [PMID: 29862590 DOI: 10.1002/jmr.2731] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/20/2022]
Abstract
Bent DNA, or DNA that is locally more flexible, is a recognition motif for many DNA binding proteins. These DNA conformational properties can thus influence many cellular processes, such as replication, transcription, and DNA repair. The importance of these DNA conformational properties is juxtaposed to the experimental difficulty to accurately determine small bends, locally more flexible DNA, or a combination of both (bends with increased flexibility). In essence, many current bulk methods use average quantities, such as the average end-to-end distance, to extract DNA conformational properties; they cannot access the additional information that is contained in the end-to-end distance distributions. We developed a method that exploits this additional information to determine DNA conformational parameters. The method is based on matching end-to-end distance distributions obtained experimentally by atomic force microscopy imaging to distributions obtained from simulations. We applied this method to investigate cisplatin GG biadducts. We found that cisplatin induces a bend angle of 36° and softens the DNA locally around the bend.
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Affiliation(s)
- Samrat Dutta
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Natalie R Gassman
- USA Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Carl G Young
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | - Bradley T Jones
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | - Karin Scarpinato
- Division of Research, Florida Atlantic University, Boca Raton, FL, USA
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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48
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Zhang Y, Hashemi M, Lv Z, Williams B, Popov KI, Dokholyan NV, Lyubchenko YL. High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. J Chem Phys 2018; 148:123322. [PMID: 29604892 PMCID: PMC5764752 DOI: 10.1063/1.5008874] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/26/2017] [Indexed: 11/14/2022] Open
Abstract
α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson's disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a "hinge". Monomers within dimers have a large interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Furthermore, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.
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Affiliation(s)
- Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
| | - Benfeard Williams
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 69198, USA
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49
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Sun Z, Hashemi M, Warren G, Bianco PR, Lyubchenko YL. Dynamics of the Interaction of RecG Protein with Stalled Replication Forks. Biochemistry 2018; 57:1967-1976. [PMID: 29432678 DOI: 10.1021/acs.biochem.7b01235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As a guardian of the bacterial genome, the RecG DNA helicase repairs DNA replication and rescues stalled replication. We applied atomic force microscopy (AFM) to directly visualize dynamics of RecG upon the interaction with replication fork substrates in the presence and absence of SSB using high-speed AFM. We directly visualized that RecG moves back and forth over dozens of base pairs in the presence of SSB. There is no RecG translocation in the absence of SSB. Computational modeling was performed to build models of Escherichia coli RecG in a free state and in complex with the fork. The simulations revealed the formation of complexes of RecG with the fork and identified conformational transitions that may be responsible for RecG remodeling that can facilitate RecG translocation along the DNA duplex. Such complexes do not form with the DNA duplex, which is in line with experimental data. Overall, our results provide mechanistic insights into the modes of interaction of RecG with the replication fork, suggesting a novel role of RecG in the repair of stalled DNA replication forks.
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Affiliation(s)
- Zhiqiang Sun
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Galina Warren
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Piero R Bianco
- Department of Microbiology and Immunology , University at Buffalo, State University of New York , Buffalo , New York 14214 , United States
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
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50
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Stumme-Diers MP, Banerjee S, Sun Z, Lyubchenko YL. Assembly of Centromere Chromatin for Characterization by High-Speed Time-Lapse Atomic Force Microscopy. Methods Mol Biol 2018; 1814:225-242. [PMID: 29956236 DOI: 10.1007/978-1-4939-8591-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) is an imaging technique that enables single molecule characterization of biological systems at nanometer resolution. Imaging in ambient conditions can provide details of the conformational states and interactions of a population of molecules which is well complemented by single-molecule imaging of the systems dynamics using time-lapse AFM imaging, in which images are capture at rates of 10-15 frames per second in an aqueous buffer. Here we describe the assembly and preparation of nucleosomes containing centromere protein A (CENP-A) for AFM imaging in both static and time-lapse modes. The AFM imaging and data analysis techniques described enable characterization of the extent of DNA wrapping around the histone core and time-resolved visualization of the systems intrinsic dynamic behaviors.
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Affiliation(s)
- Micah P Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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