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Koebley SR, Mikheikin A, Leslie K, Guest D, McConnell-Wells W, Lehman JH, Al Juhaishi T, Zhang X, Roberts CH, Picco L, Toor A, Chesney A, Reed J. Digital Polymerase Chain Reaction Paired with High-Speed Atomic Force Microscopy for Quantitation and Length Analysis of DNA Length Polymorphisms. ACS Nano 2020; 14:15385-15393. [PMID: 33169971 DOI: 10.1021/acsnano.0c05897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA length polymorphisms are found in many serious diseases, and assessment of their length and abundance is often critical for accurate diagnosis. However, measuring their length and frequency in a mostly wild-type background, as occurs in many situations, remains challenging due to their variable and repetitive nature. To overcome these hurdles, we combined two powerful techniques, digital polymerase chain reaction (dPCR) and high-speed atomic force microscopy (HSAFM), to create a simple, rapid, and flexible method for quantifying both the size and proportion of DNA length polymorphisms. In our approach, individual amplicons from each dPCR partition are imaged and sized directly. We focused on internal tandem duplications (ITDs) located within the FLT3 gene, which are associated with acute myeloid leukemia and often indicative of a poor prognosis. In an analysis of over 1.5 million HSAFM-imaged amplicons from cell line and clinical samples containing FLT3-ITDs, dPCR-HSAFM returned the expected variant length and variant allele frequency, down to 5% variant samples. As a high-throughput method with single-molecule resolution, dPCR-HSAFM thus represents an advance in HSAFM analysis and a powerful tool for the diagnosis of length polymorphisms.
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Affiliation(s)
- Sean R Koebley
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Andrey Mikheikin
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kevin Leslie
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Daniel Guest
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Wendy McConnell-Wells
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joshua H Lehman
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Taha Al Juhaishi
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Xiaojie Zhang
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Catherine H Roberts
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Loren Picco
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Amir Toor
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Alden Chesney
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Jason Reed
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Mikheikin A, Olsen A, Leslie K, Russell-Pavier F, Yacoot A, Picco L, Payton O, Toor A, Chesney A, Gimzewski JK, Mishra B, Reed J. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nat Commun 2017; 8:1665. [PMID: 29162844 PMCID: PMC5698298 DOI: 10.1038/s41467-017-01891-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 01/26/2023] Open
Abstract
Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches. Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.
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Affiliation(s)
- Andrey Mikheikin
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Anita Olsen
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Kevin Leslie
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Freddie Russell-Pavier
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.,Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Andrew Yacoot
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK
| | - Loren Picco
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Oliver Payton
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, 23284, VA, USA.,VCU Massey Cancer Center, Richmond, 23284, VA, USA
| | - Alden Chesney
- VCU Massey Cancer Center, Richmond, 23284, VA, USA.,Department of Pathology, VCU School of Medicine, Richmond, 23284, VA, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, 90095, CA, USA
| | - Bud Mishra
- Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, 10012, NY, USA
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA. .,VCU Massey Cancer Center, Richmond, 23284, VA, USA.
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Mikheikin A, Olsen A, Picco L, Payton O, Mishra B, Gimzewski JK, Reed J. High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems. Anal Chem 2016; 88:2527-32. [PMID: 26878668 DOI: 10.1021/acs.analchem.5b04023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrey Mikheikin
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Anita Olsen
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Loren Picco
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - Oliver Payton
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - Bud Mishra
- Departments
of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - James K. Gimzewski
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- California
NanoSystems Institute (CNSI) at the University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Jason Reed
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- VCU Massey Cancer Center, Richmond, Virginia 23298, United States
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Mikheikin A, Olsen A, Leslie K, Mishra B, Gimzewski J, Reed J. Atomic force microscopic detection enabling multiplexed low-cycle-number quantitative polymerase chain reaction for biomarker assays. Anal Chem 2014; 86:6180-3. [PMID: 24918650 PMCID: PMC4082389 DOI: 10.1021/ac500896k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023]
Abstract
Quantitative polymerase chain reaction is the current "golden standard" for quantification of nucleic acids; however, its utility is constrained by an inability to easily and reliably detect multiple targets in a single reaction. We have successfully overcome this problem with a novel combination of two widely used approaches: target-specific multiplex amplification with 15 cycles of polymerase chain reaction (PCR), followed by single-molecule detection of amplicons with atomic force microscopy (AFM). In test experiments comparing the relative expression of ten transcripts in two different human total RNA samples, we find good agreement between our single reaction, multiplexed PCR/AFM data, and data from 20 individual singleplex quantitative PCR reactions. This technique can be applied to virtually any analytical problem requiring sensitive measurement concentrations of multiple nucleic acid targets.
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Affiliation(s)
- Andrey Mikheikin
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Anita Olsen
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kevin Leslie
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bud Mishra
- Departments
of Computer Science and Mathematics, Courant Institute of Mathematical
Sciences, New York University, New York, New York 10012, United States
| | - James
K. Gimzewski
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute (CNSI) at University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jason Reed
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- VCU
Massey Cancer Center, Richmond, Virginia 23298, United States
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Tong Z, Mikheikin A, Krasnoslobodtsev A, Lv Z, Lyubchenko YL. Novel polymer linkers for single molecule AFM force spectroscopy. Methods 2013; 60:161-8. [PMID: 23624104 DOI: 10.1016/j.ymeth.2013.02.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/20/2013] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
Flexible polymer linkers play an important role in various imaging and probing techniques that require surface immobilization, including atomic force microscopy (AFM). In AFM force spectroscopy, polymer linkers are necessary for the covalent attachment of molecules of interest to the AFM tip and the surface. The polymer linkers tether the molecules and provide their proper orientation in probing experiments. Additionally, the linkers separate specific interactions from nonspecific short-range adhesion and serve as a reference point for the quantitative analysis of single molecule probing events. In this report, we present our results on the synthesis and testing of a novel polymer linker and the identification of a number of potential applications for its use in AFM force spectroscopy experiments. The synthesis of the linker is based on the well-developed phosphoramidate (PA) chemistry that allows the routine synthesis of linkers with predetermined lengths and PA composition. These linkers are homogeneous in length and can be terminated with various functional groups. PA linkers with different functional groups were synthesized and tested in experimental systems utilizing different immobilization chemistries. We probed interactions between complementary DNA oligonucleotides; DNA and protein complexes formed by the site-specific binding protein SfiI; and interactions between amyloid peptide (Aβ42). The results of the AFM force spectroscopy experiments validated the feasibility of the proposed approach for the linker design and synthesis. Furthermore, the properties of the tether (length, functional groups) can be adjusted to meet the specific requirements for different force spectroscopy experiments and system characteristics, suggesting that it could be used for a large number of various applications.
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Affiliation(s)
- Zenghan Tong
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198, USA
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Streltsov S, Sukhanova A, Mikheikin A, Grokhovsky S, Zhuze A, Kudelina I, Mochalov K, Oleinikov V, Jardillier JC, Nabiev I. Structural Basis of Topotecan−DNA Recognition Probed by Flow Linear Dichroism, Circular Dichroism, and Raman Spectroscopy. J Phys Chem B 2001. [DOI: 10.1021/jp0112166] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergei Streltsov
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Alyona Sukhanova
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Andrey Mikheikin
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Sergei Grokhovsky
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Alexei Zhuze
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Irina Kudelina
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Konstantin Mochalov
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Vladimir Oleinikov
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Jean-Claude Jardillier
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
| | - Igor Nabiev
- EA3306, Institut Fédératif de Recherche n°3 “Biomolécules”, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51100 Reims, France, Laboratory of DNA-Protein Recognition, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 117984, Russia, Center for Medical Studies, University of Oslo, Norway, and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia
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