1
|
Semenov K, Taraskin A, Yurchenko A, Baranovskaya I, Purvinsh L, Gyulikhandanova N, Vasin A. Uncertainty Estimation for Quantitative Agarose Gel Electrophoresis of Nucleic Acids. SENSORS (BASEL, SWITZERLAND) 2023; 23:1999. [PMID: 36850595 PMCID: PMC9966319 DOI: 10.3390/s23041999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
This paper considers the evaluation of uncertainty of quantitative gel electrophoresis. To date, such uncertainty estimation presented in the literature are based on the multiple measurements performed for assessing the intra- and interlaboratory reproducibility using standard samples. This paper shows how to estimate the uncertainty in cases where we cannot study scattering components of the results. The first point is dedicated to a case where we have standard samples (the direct expressions are shown). The second point considers the situation when standard samples are absent (the algorithm for estimating the lower bound for uncertainty is discussed). The role of the data processing algorithm is demonstrated.
Collapse
Affiliation(s)
- Konstantin Semenov
- Peter the Great St. Petersburg Polytechnic University, 29, Polytechnicheskaya Str., 195251 St. Petersburg, Russia
| | - Aleksandr Taraskin
- Peter the Great St. Petersburg Polytechnic University, 29, Polytechnicheskaya Str., 195251 St. Petersburg, Russia
- Smorodintsev Research Institute of Influenza, 15/17, Prof. Popov Str., 197376 St. Petersburg, Russia
| | - Alexandra Yurchenko
- Peter the Great St. Petersburg Polytechnic University, 29, Polytechnicheskaya Str., 195251 St. Petersburg, Russia
| | | | - Lada Purvinsh
- The University of Chicago, 947 E. 58th Str., Chicago, IL 60637, USA
| | - Natalia Gyulikhandanova
- Peter the Great St. Petersburg Polytechnic University, 29, Polytechnicheskaya Str., 195251 St. Petersburg, Russia
- Smorodintsev Research Institute of Influenza, 15/17, Prof. Popov Str., 197376 St. Petersburg, Russia
| | - Andrey Vasin
- Peter the Great St. Petersburg Polytechnic University, 29, Polytechnicheskaya Str., 195251 St. Petersburg, Russia
- Smorodintsev Research Institute of Influenza, 15/17, Prof. Popov Str., 197376 St. Petersburg, Russia
| |
Collapse
|
2
|
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.
Collapse
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
| | | |
Collapse
|
3
|
Sotres J, Boyd H, Gonzalez-Martinez JF. Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning. NANOSCALE 2021; 13:9193-9203. [PMID: 33885692 DOI: 10.1039/d1nr01109j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Scanning probe microscopies allow investigating surfaces at the nanoscale, in real space and with unparalleled signal-to-noise ratio. However, these microscopies are not used as much as it would be expected considering their potential. The main limitations preventing a broader use are the need of experienced users, the difficulty in data analysis and the time-consuming nature of experiments that require continuous user supervision. In this work, we addressed the latter and developed an algorithm that controlled the operation of an Atomic Force Microscope (AFM) that, without the need of user intervention, allowed acquiring multiple high-resolution images of different molecules. We used DNA on mica as a model sample to test our control algorithm, which made use of two deep learning techniques that so far have not been used for real time SPM automation. One was an object detector, YOLOv3, which provided the location of molecules in the captured images. The second was a Siamese network that could identify the same molecule in different images. This allowed both performing a series of images on selected molecules while incrementing the resolution, as well as keeping track of molecules already imaged at high resolution, avoiding loops where the same molecule would be imaged an unlimited number of times. Overall, our implementation of deep learning techniques brings SPM a step closer to full autonomous operation.
Collapse
Affiliation(s)
- Javier Sotres
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden and Biofilms-Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden.
| | - Hannah Boyd
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden and Biofilms-Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden.
| | - Juan F Gonzalez-Martinez
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden and Biofilms-Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden.
| |
Collapse
|
4
|
Lipiec E, Japaridze A, Szczerbiński J, Dietler G, Zenobi R. Preparation of Well-Defined DNA Samples for Reproducible Nanospectroscopic Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4821-4829. [PMID: 27434680 DOI: 10.1002/smll.201601711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Due to its well-defined topology and chemical structure, DNA could become a biological standard sample in the field of nanospectroscopy. Tip-enhanced Raman spectroscopy (TERS) provides new insights into individual DNA molecules immobilized on flat mica crystals. The high sensitivity of TERS is used to assess the chemical changes that appear in DNA upon different surface immobilization protocols.
Collapse
Affiliation(s)
- Ewelina Lipiec
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Krakow, Poland
| | - Aleksandre Japaridze
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Jacek Szczerbiński
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
| |
Collapse
|
5
|
Pang D, Thierry AR, Dritschilo A. DNA studies using atomic force microscopy: capabilities for measurement of short DNA fragments. Front Mol Biosci 2015; 2:1. [PMID: 25988169 PMCID: PMC4429637 DOI: 10.3389/fmolb.2015.00001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/02/2015] [Indexed: 01/05/2023] Open
Abstract
Short DNA fragments, resulting from ionizing radiation induced DNA double strand breaks (DSBs), or released from cells as a result of physiological processes and circulating in the blood stream, may play important roles in cellular function and potentially in disease diagnosis and early intervention. The size distribution of DNA fragments contribute to knowledge of underlining biological processes. Traditional techniques used in radiation biology for DNA fragment size measurements lack the resolution to quantify short DNA fragments. For the measurement of cell-free circulating DNA (ccfDNA), real time quantitative Polymerase Chain Reaction (q-PCR) provides quantification of DNA fragment sizes, concentration and specific gene mutation. A complementary approach, the imaging-based technique using Atomic Force Microscopy (AFM) provides direct visualization and measurement of individual DNA fragments. In this review, we summarize and discuss the application of AFM-based measurements of DNA fragment sizes. Imaging of broken plasmid DNA, as a result of exposure to ionizing radiation, as well as ccfDNA in clinical specimens offer an innovative approach for studies of short DNA fragments and their biological functions.
Collapse
Affiliation(s)
- Dalong Pang
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherche Médicale U896 Montpellier, France
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center Washington, DC, USA
| |
Collapse
|
6
|
Lipiec E, Sekine R, Bielecki J, Kwiatek WM, Wood BR. Molecular Characterization of DNA Double Strand Breaks with Tip-Enhanced Raman Scattering. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
7
|
Lipiec E, Sekine R, Bielecki J, Kwiatek WM, Wood BR. Molecular Characterization of DNA Double Strand Breaks with Tip-Enhanced Raman Scattering. Angew Chem Int Ed Engl 2013; 53:169-72. [DOI: 10.1002/anie.201307271] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 11/09/2022]
|
8
|
Spyratou E, Makropoulou M, Mourelatou E, Demetzos C. Biophotonic techniques for manipulation and characterization of drug delivery nanosystems in cancer therapy. Cancer Lett 2012; 327:111-22. [DOI: 10.1016/j.canlet.2011.12.039] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 12/21/2011] [Accepted: 12/24/2011] [Indexed: 12/20/2022]
|
9
|
Kalle W, Strappe P. Atomic force microscopy on chromosomes, chromatin and DNA: a review. Micron 2012; 43:1224-31. [PMID: 22633852 DOI: 10.1016/j.micron.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/06/2012] [Accepted: 04/08/2012] [Indexed: 01/19/2023]
Abstract
The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.
Collapse
Affiliation(s)
- Wouter Kalle
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia.
| | | |
Collapse
|
10
|
Aziz K, Nowsheen S, Pantelias G, Iliakis G, Gorgoulis VG, Georgakilas AG. Targeting DNA damage and repair: embracing the pharmacological era for successful cancer therapy. Pharmacol Ther 2011; 133:334-50. [PMID: 22197993 DOI: 10.1016/j.pharmthera.2011.11.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 12/19/2022]
Abstract
DNA is under constant assault from genotoxic agents which creates different kinds of DNA damage. The precise replication of the genome and the continuous surveillance of its integrity are critical for survival and the avoidance of carcinogenesis. Cells have evolved an arsenal of repair pathways and cell cycle checkpoints to detect and repair DNA damage. When repair fails, typically cell cycle progression is halted and apoptosis is initiated. Here, we review the different sources and types of DNA damage including DNA replication stress and oxidative stress, the repair pathways that cells utilize to repair damaged DNA, and discuss their biological significance, especially with reference to cancer induction and cancer therapy. We also describe the main methodologies currently used for the detection of DNA damage with their strengths and limitations. We conclude with an outline as to how this information can be used to identify novel pharmacological targets for DNA repair pathways or enhancers of DNA damage to develop improved treatment strategies that will benefit cancer patients.
Collapse
Affiliation(s)
- K Aziz
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA
| | | | | | | | | | | |
Collapse
|
11
|
Jiang Y, Rabbi M, Mieczkowski PA, Marszalek PE. Separating DNA with different topologies by atomic force microscopy in comparison with gel electrophoresis. J Phys Chem B 2010; 114:12162-5. [PMID: 20799746 DOI: 10.1021/jp105603k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy, which is normally used for DNA imaging to gain qualitative results, can also be used for quantitative DNA research, at a single-molecular level. Here, we evaluate the performance of AFM imaging specifically for quantifying supercoiled and relaxed plasmid DNA fractions within a mixture, and compare the results with the bulk material analysis method, gel electrophoresis. The advantages and shortcomings of both methods are discussed in detail. Gel electrophoresis is a quick and well-established quantification method. However, it requires a large amount of DNA, and needs to be carefully calibrated for even slightly different experimental conditions for accurate quantification. AFM imaging is accurate, in that single DNA molecules in different conformations can be seen and counted. When used carefully with necessary correction, both methods provide consistent results. Thus, AFM imaging can be used for DNA quantification, as an alternative to gel electrophoresis.
Collapse
Affiliation(s)
- Yong Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Jiangning, Nanjing, Jiangsu 211189, People's Republic of China.
| | | | | | | |
Collapse
|
12
|
Yoshikawa Y, Mori T, Suzuki M, Imanaka T, Yoshikawa K. Comparative study of kinetics on DNA double-strand break induced by photo- and gamma-irradiation: Protective effect of water-soluble flavonoids. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
13
|
Abstract
AFM (atomic force microscopy) analysis, both of fixed cells, and live cells in physiological environments, is set to offer a step change in the research of cellular function. With the ability to map cell topography and morphology, provide structural details of surface proteins and their expression patterns and to detect pico-Newton force interactions, AFM represents an exciting addition to the arsenal of the cell biologist. With the explosion of new applications, and the advent of combined instrumentation such as AFM-confocal systems, the biological application of AFM has come of age. The use of AFM in the area of biomedical research has been proposed for some time, and is one where a significant impact could be made. Fixed cell analysis provides qualitative and quantitative subcellular and surface data capable of revealing new biomarkers in medical pathologies. Image height and contrast, surface roughness, fractal, volume and force analysis provide a platform for the multiparameter analysis of cell and protein functions. Here, we review the current status of AFM in the field and discuss the important contribution AFM is poised to make in the understanding of biological systems.
Collapse
|
14
|
Brezeanu M, Träger F, Hubenthal F. Scanning force microscopy studies of X-ray-induced double-strand breaks in plasmid DNA. J Biol Phys 2009; 35:163-74. [PMID: 19669559 PMCID: PMC2669120 DOI: 10.1007/s10867-009-9137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 01/12/2009] [Indexed: 10/21/2022] Open
Abstract
We present an analysis of X-ray-induced damage in PhiX174 plasmid DNA, applying doses between D = 250 and 1,500 Gy. To analyse this damage in detail, the distribution of plasmid fragments after irradiation have been determined by scanning force microscopy. The results show that even for the lowest dose of D = 250 Gy, a significant amount of double-strand breaks are observed. For increasing dose, the percentage of small fragments increases and is accompanied by a shortening of the average fragment length from < L > = 1,400 nm for a dose of D = 250 Gy to < L > = 1,080 nm after irradiation with D = 1,500 Gy. The most crucial parameter, the average number of double-strand breaks per broken plasmid ( ) has been determined for the first time for the applied doses. The results show that the average number of DSBs per broken plasmid increases almost linearly from a value of = 1.3 after irradiation with D = 250 Gy to = 1.7 after exposure to D = 1,500 Gy. The presented results show that the amount of DSBs induced by X-ray radiation in plasmid DNA can be calculated with high accuracy by means of scanning force microscopy, providing relevant information regarding the interaction of X-rays with DNA molecules.
Collapse
Affiliation(s)
- M Brezeanu
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology-CINSaT, University of Kassel, 34132 Kassel, Germany.
| | | | | |
Collapse
|
15
|
Gan H, Tang K, Sun T, Hirtz M, Li Y, Chi L, Butz S, Fuchs H. Selective Adsorption of DNA on Chiral Surfaces: Supercoiled or Relaxed Conformation. Angew Chem Int Ed Engl 2009; 48:5282-6. [DOI: 10.1002/anie.200806295] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
16
|
Gan H, Tang K, Sun T, Hirtz M, Li Y, Chi L, Butz S, Fuchs H. Selective Adsorption of DNA on Chiral Surfaces: Supercoiled or Relaxed Conformation. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
17
|
Jiang Y, Rabbi M, Kim M, Ke C, Lee W, Clark RL, Mieczkowski PA, Marszalek PE. UVA generates pyrimidine dimers in DNA directly. Biophys J 2009; 96:1151-8. [PMID: 19186150 DOI: 10.1016/j.bpj.2008.10.030] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022] Open
Abstract
There is increasing evidence that UVA radiation, which makes up approximately 95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only approximately 60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA.
Collapse
Affiliation(s)
- Yong Jiang
- Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina, USA
| | | | | | | | | | | | | | | |
Collapse
|