1
|
Stadlbauer B, Mitscha-Baude G, Heitzinger C. Modeling single-molecule stochastic transport for DNA exo-sequencing in nanopore sensors. NANOTECHNOLOGY 2020; 31:075502. [PMID: 31652425 DOI: 10.1088/1361-6528/ab513e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a simulation framework for computing the probability that a single molecule reaches the recognition element in a nanopore sensor. The model consists of the Langevin equation for the diffusive motion of small particles driven by external forces and the Poisson-Nernst-Planck-Stokes equations to compute these forces. The model is applied to examine DNA exo-sequencing in α-hemolysin, whose practicability depends on whether isolated DNA monomers reliably migrate into the channel in their correct order. We find that, at moderate voltage, migration fails in the majority of trials if the exonuclease which releases monomers is located farther than 1 nm above the pore entry. However, by tuning the pore to have a higher surface charge, applying a high voltage of 1 V and ensuring the exonuclease stays close to the channel, success rates of over 95% can be achieved.
Collapse
Affiliation(s)
- Benjamin Stadlbauer
- Institute for Analysis and Scientific Computing, TU Vienna, A-1040 Vienna, Austria
| | | | | |
Collapse
|
2
|
Sampath G. DNA sequencing with stacked nanopores and exonuclease: A simulation-based analysis. Electrophoresis 2016; 37:2429-34. [DOI: 10.1002/elps.201600049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/03/2016] [Accepted: 06/09/2016] [Indexed: 12/16/2022]
|
3
|
Brady KT, Reiner JE. Improving the prospects of cleavage-based nanopore sequencing engines. J Chem Phys 2015; 143:074904. [DOI: 10.1063/1.4928647] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kyle T. Brady
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| |
Collapse
|
4
|
Abstract
An electrolytic cell with two nanopores in tandem and an exonuclease in between can efficiently and accurately sequence a single strand of DNA.
Collapse
|
5
|
Yuan M, Zhu Y, Lou X, Chen C, Wei G, Lan M, Zhao J. Sensitive label-free oligonucleotide-based microfluidic detection of mercury (II) ion by using exonuclease I. Biosens Bioelectron 2012; 31:330-6. [DOI: 10.1016/j.bios.2011.10.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 10/10/2011] [Accepted: 10/19/2011] [Indexed: 02/06/2023]
|
6
|
Lu D, Myers AR, George NP, Keck JL. Mechanism of Exonuclease I stimulation by the single-stranded DNA-binding protein. Nucleic Acids Res 2011; 39:6536-45. [PMID: 21572106 PMCID: PMC3159472 DOI: 10.1093/nar/gkr315] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bacterial single-stranded (ss) DNA-binding proteins (SSBs) bind and protect ssDNA intermediates formed during cellular DNA replication, recombination and repair reactions. SSBs also form complexes with an array of genome maintenance enzymes via their conserved C-terminal tail (SSB-Ct) elements. In many cases, complex formation with SSB stimulates the biochemical activities of its protein partners. Here, we investigate the mechanism by which Escherichia coli SSB stimulates hydrolysis of ssDNA by Exonuclease I (ExoI). Steady-state kinetic experiments show that SSB stimulates ExoI activity through effects on both apparent kcat and Km. SSB variant proteins with altered SSB-Ct sequences either stimulate more modestly or inhibit ExoI hydrolysis of ssDNA due to increases in the apparent Michaelis constant, highlighting a role for protein complex formation in ExoI substrate binding. Consistent with a model in which SSB stabilizes ExoI substrate binding and melts secondary structures that could impede ExoI processivity, the specific activity of a fusion protein in which ExoI is tethered to SSB is nearly equivalent to that of SSB-stimulated ExoI. Taken together, these studies delineate stimulatory roles for SSB in which protein interactions and ssDNA binding are both important for maximal activity of its protein partners.
Collapse
Affiliation(s)
- Duo Lu
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706-1532, USA
| | | | | | | |
Collapse
|
7
|
Efcavitch JW, Thompson JF. Single-molecule DNA analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:109-128. [PMID: 20636036 DOI: 10.1146/annurev.anchem.111808.073558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.
Collapse
|
8
|
Lu D, Windsor MA, Gellman SH, Keck JL. Peptide inhibitors identify roles for SSB C-terminal residues in SSB/exonuclease I complex formation. Biochemistry 2009; 48:6764-71. [PMID: 19527069 DOI: 10.1021/bi900361r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial single-stranded (ss) DNA-binding proteins (SSBs) facilitate DNA replication, recombination, and repair processes in part by recruiting diverse genome maintenance enzymes to ssDNA. This function utilizes the C-terminus of SSB (SSB-Ct) as a common binding site for SSB's protein partners. The SSB-Ct is a highly conserved, amphipathic sequence comprising acidic and hydrophobic elements. A crystal structure of Escherichia coli exonuclease I (ExoI) bound to a peptide comprising the E. coli SSB-Ct sequence shows that the C-terminal-most SSB-Ct Phe anchors the peptide to a binding pocket on ExoI and implicates electrostatic binding roles for the acidic SSB-Ct residues. Here, we use SSB-Ct peptide variants in competition experiments to examine the roles of individual SSB-Ct residues in binding ExoI in solution. Altering the C-terminal-most Pro or Phe residues in the SSB-Ct strongly impairs SSB-Ct binding to ExoI, confirming a major role for the hydrophobic SSB-Ct residues in binding ExoI. Alteration of N-terminal SSB-Ct residues leads to changes that reflect cumulative electrostatic binding roles for the Asp residues in SSB-Ct. The SSB-Ct peptides also abrogate SSB stimulation of ExoI activity through a competitive inhibition mechanism, indicating that the peptides can disrupt ExoI/SSB/ssDNA ternary complexes. Differences in the potency of the SSB-Ct peptide variants in the binding and nuclease inhibition studies indicate that the acidic SSB-Ct residues play a more prominent role in the context of the ternary complex than in the minimal ExoI/SSB-Ct interaction. Together, these data identify roles for residues in the SSB-Ct that are important for SSB complex formation with its protein partners.
Collapse
Affiliation(s)
- Duo Lu
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
9
|
Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. NATURE NANOTECHNOLOGY 2009; 4:265-70. [PMID: 19350039 DOI: 10.1038/nnano.2009.12] [Citation(s) in RCA: 1120] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 01/14/2009] [Indexed: 05/02/2023]
Abstract
A single-molecule method for sequencing DNA that does not require fluorescent labelling could reduce costs and increase sequencing speeds. An exonuclease enzyme might be used to cleave individual nucleotide molecules from the DNA, and when coupled to an appropriate detection system, these nucleotides could be identified in the correct order. Here, we show that a protein nanopore with a covalently attached adapter molecule can continuously identify unlabelled nucleoside 5'-monophosphate molecules with accuracies averaging 99.8%. Methylated cytosine can also be distinguished from the four standard DNA bases: guanine, adenine, thymine and cytosine. The operating conditions are compatible with the exonuclease, and the kinetic data show that the nucleotides have a high probability of translocation through the nanopore and, therefore, of not being registered twice. This highly accurate tool is suitable for integration into a system for sequencing nucleic acids and for analysing epigenetic modifications.
Collapse
Affiliation(s)
- James Clarke
- Oxford Nanopore Technologies Ltd, Begbroke Science Park, Sandy Lane, Oxford OX5 1PF, UK
| | | | | | | | | | | |
Collapse
|
10
|
Leuba SH, Wheeler TB, Cheng CM, LeDuc PR, Fernández-Sierra M, Quiñones E. Structure and dynamics of single DNA molecules manipulated by magnetic tweezers and or flow. Methods 2008; 47:214-22. [PMID: 19015032 DOI: 10.1016/j.ymeth.2008.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022] Open
Abstract
Here we describe the use of magnetic tweezers and or microfluidics to manipulate single DNA molecules. We describe experiment which employ magnetic tweezers coupled to an inverted microscope as well as the use of a magnetic tweezers setup with an upright microscope. Using a chamber prepared via soft lithography, we also describe a microfluidic device for the manipulation of individual DNA molecules. Finally, we present some past successful examples of using these approaches to elucidate unique information about protein-nucleic acid interactions.
Collapse
Affiliation(s)
- Sanford H Leuba
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | | | | | | | | |
Collapse
|
11
|
Werner JH, McCarney ER, Keller RA, Plaxco KW, Goodwin PM. Increasing the resolution of single pair fluorescence resonance energy transfer measurements in solution via molecular cytometry. Anal Chem 2007; 79:3509-13. [PMID: 17385843 DOI: 10.1021/ac070142c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a method to increase the resolution of single pair fluorescence resonance energy transfer (spFRET) measurements in aqueous solutions. Solution-based spFRET measurements of fluorescently labeled biological molecules (proteins, RNA, DNA) are often used to obtain histograms of molecular conformation without resorting to sample immobilization. However, for solution-phase spFRET studies, the number of photons detected from a single molecule as it diffuses through an open confocal volume element are quite limited. An "average" transit may yield on the order of 40 photons. Shot noise on the number of detected photons substantially limits the resolution of the measurement. The method reported here uses a hydrodynamically focused sample stream to ensure molecules traverse the full width of an excitation laser beam. This substantially increases the average number of photons detected per molecular transit (approximately 85 photons/molecule), which increases measurement precision. In addition, this method minimizes another source of heterogeneity present in diffusive measures of spFRET: the distribution of paths taken through the excitation laser beam. We demonstrate here using a FRET labeled protein sample (a FynSH3 domain) that superior resolution (a factor of approximately 2) can be obtained via molecular cytometry compared to spFRET measurements based upon diffusion through an open confocal volume element.
Collapse
Affiliation(s)
- James H Werner
- Center for Integrated Nanotechnologies, and Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
| | | | | | | | | |
Collapse
|
12
|
Enderlein J. Nucleotide specificity versus complex heterogeneity in exonuclease activity measurements. Biophys J 2006; 92:1556-8. [PMID: 17142274 PMCID: PMC1796820 DOI: 10.1529/biophysj.106.095851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recent publication reported on measurements of Exonuclease I activity using a real-time fluorescence method that measures the time required by molecules of Exonuclease I to hydrolyze single-stranded DNA that was synthesized to have two fluorescently labeled nucleotides. The observed fluorescence-intensity curves were interpreted as a sign of strong heterogeneity of the activity of Exonuclease I. Here, I propose a different model, which assumes that Exonuclease I activity is nucleotide-dependent, and that a fluorescent label bound to a nucleotide significantly slows its cleavage rate. The presented model fits the observed data equally well, but can be used to make specific predictions upon observable sequence dependence of measured fluorescence-intensity curves.
Collapse
Affiliation(s)
- Jörg Enderlein
- Institut für Neurowissenschaft und Biophysik 1, Forschungszentrum Jülich, Jülich, Germany.
| |
Collapse
|
13
|
Abstract
Single-molecule studies allow the study of subtle activity differences due to local folding in proteins, but are time consuming and difficult because only a few molecules are observed in one experiment. We developed an assay where we can simultaneously measure the activity of hundreds of individual molecules. The assay utilizes a synthetic chymotrypsin substrate that is nonfluorescent before cleavage by chymotrypsin, but is intensely fluorescent afterward. We encapsulated the enzyme and substrate in micron-sized droplets of water surrounded by silicone oil where each microdroplet contains <1 enzyme on average. A microscope and charge-coupled device camera are used to measure the fluorescence intensity of the same individual droplet over time. Based on these measurements, we conclude that enzymatic reactions could occur within this emulsion system, the statistical average activity of individual chymotrypsin molecules is similar to that measured in bulk, and the activity of individual chymotrypsin is heterogeneous.
Collapse
Affiliation(s)
- Alan I Lee
- Department of Biomedical Engineering, Henry Samueli School of Engineering, University of California, Irvine, 92697, USA
| | | |
Collapse
|