1
|
Kk S, Persson F, Fritzsche J, Beech JP, Tegenfeldt JO, Westerlund F. Fluorescence Microscopy of Nanochannel-Confined DNA. Methods Mol Biol 2024; 2694:175-202. [PMID: 37824005 DOI: 10.1007/978-1-0716-3377-9_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: 10/13/2023]
Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
Collapse
Affiliation(s)
- Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jason P Beech
- NanoLund and Department of Physics, Lund University, Lund, Sweden
| | | | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
2
|
Gopinath A, Thachuk C, Mitskovets A, Atwater HA, Kirkpatrick D, Rothemund PWK. Absolute and arbitrary orientation of single-molecule shapes. Science 2021; 371:371/6531/eabd6179. [DOI: 10.1126/science.abd6179] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/14/2020] [Indexed: 11/02/2022]
Abstract
DNA origami is a modular platform for the combination of molecular and
colloidal components to create optical, electronic, and biological devices.
Integration of such nanoscale devices with microfabricated connectors and circuits
is challenging: Large numbers of freely diffusing devices must be fixed at desired
locations with desired alignment. We present a DNA origami molecule whose energy
landscape on lithographic binding sites has a unique maximum. This property
enabled device alignment within 3.2° on silica surfaces. Orientation was absolute
(all degrees of freedom were specified) and arbitrary (the orientation of every
molecule was independently specified). The use of orientation to optimize device
performance was shown by aligning fluorescent emission dipoles within
microfabricated optical cavities. Large-scale integration was demonstrated with an
array of 3456 DNA origami with 12 distinct orientations that indicated the
polarization of excitation light.
Collapse
Affiliation(s)
- Ashwin Gopinath
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chris Thachuk
- Department of Computing and Mathematical Science, California Institute of Technology, Pasadena, CA 91125, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Anya Mitskovets
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry A. Atwater
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - David Kirkpatrick
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul W. K. Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Science, California Institute of Technology, Pasadena, CA 91125, USA
- Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
3
|
DNA surface exploration and operator bypassing during target search. Nature 2020; 583:858-861. [PMID: 32581356 DOI: 10.1038/s41586-020-2413-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/07/2020] [Indexed: 11/08/2022]
Abstract
Many proteins that bind specific DNA sequences search the genome by combining three-dimensional diffusion with one-dimensional sliding on nonspecific DNA1-5. Here we combine resonance energy transfer and fluorescence correlation measurements to characterize how individual lac repressor (LacI) molecules explore the DNA surface during the one-dimensional phase of target search. To track the rotation of sliding LacI molecules on the microsecond timescale, we use real-time single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy (SMCT-FCS). The fluctuations in fluorescence signal are accurately described by rotation-coupled sliding, in which LacI traverses about 40 base pairs (bp) per revolution. This distance substantially exceeds the 10.5-bp helical pitch of DNA; this suggests that the sliding protein frequently hops out of the DNA groove, which would result in the frequent bypassing of target sequences. We directly observe such bypassing using single-molecule fluorescence resonance energy transfer (smFRET). A combined analysis of the smFRET and SMCT-FCS data shows that LacI hops one or two grooves (10-20 bp) every 200-700 μs. Our data suggest a trade-off between speed and accuracy during sliding: the weak nature of nonspecific protein-DNA interactions underlies operator bypassing, but also speeds up sliding. We anticipate that SMCT-FCS, which monitors rotational diffusion on the microsecond timescale while tracking individual molecules with millisecond resolution, will be applicable to the real-time investigation of many other biological interactions and will effectively extend the accessible time regime for observing these interactions by two orders of magnitude.
Collapse
|
4
|
Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.
Collapse
|
5
|
Roushan M, Kaur P, Karpusenko A, Countryman PJ, Ortiz CP, Fang Lim S, Wang H, Riehn R. Probing transient protein-mediated DNA linkages using nanoconfinement. BIOMICROFLUIDICS 2014; 8:034113. [PMID: 25379073 PMCID: PMC4162420 DOI: 10.1063/1.4882775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/30/2014] [Indexed: 05/16/2023]
Abstract
We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
Collapse
Affiliation(s)
- Maedeh Roushan
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Parminder Kaur
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Alena Karpusenko
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | | | - Carlos P Ortiz
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Shuang Fang Lim
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Hong Wang
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Robert Riehn
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| |
Collapse
|
6
|
Frykholm K, Alizadehheidari M, Fritzsche J, Wigenius J, Modesti M, Persson F, Westerlund F. Probing physical properties of a DNA-protein complex using nanofluidic channels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:884-7. [PMID: 24382826 DOI: 10.1002/smll.201302028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/08/2013] [Indexed: 05/28/2023]
Abstract
A method to investigate physical properties of a DNA-protein complex in solution is demonstrated. By using tapered nanochannels and lipid passivation the persistence length of a RecA filament formed on double-stranded DNA is determined to 1.15 μm, in agreement with the literature, without attaching protein or DNA to any handles or surfaces.
Collapse
Affiliation(s)
- Karolin Frykholm
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | | | | | | | | | | | | |
Collapse
|
7
|
Werner E, Westerlund F, Tegenfeldt JO, Mehlig B. Monomer Distributions and Intrachain Collisions of a Polymer Confined to a Channel. Macromolecules 2013. [DOI: 10.1021/ma400464c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- E. Werner
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| | - F. Westerlund
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - J. O. Tegenfeldt
- Department of Physics, Division
of Solid State Physics, Lund University, Lund, Sweden
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Göteborg, Sweden
| |
Collapse
|
8
|
Pitter DRG, Wigenius J, Brown AS, Baker JD, Westerlund F, Wilson JN. Turn-on, fluorescent nuclear stains with live cell compatibility. Org Lett 2013; 15:1330-3. [PMID: 23461418 DOI: 10.1021/ol400268t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-binding, green and yellow fluorescent probes with excellent brightness and high on/off ratios are reported. The probes are membrane permeable, live-cell compatible, and optimally matched to 405 nm and 514 nm laser lines, making them attractive alternatives to UV-excited and blue emissive Hoechst 33342 and DAPI nuclear stains. Their electronic structure was investigated by optical spectroscopy supported by TD-DFT calculations. DNA binding is accompanied by 27- to 75-fold emission enhancements, and linear dichroism demonstrates that one dye is a groove binder while the other intercalates into DNA.
Collapse
Affiliation(s)
- Demar R G Pitter
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, USA
| | | | | | | | | | | |
Collapse
|
9
|
Chen YL. Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels. BIOMICROFLUIDICS 2013; 7:54119. [PMID: 24255695 PMCID: PMC3820673 DOI: 10.1063/1.4826157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 05/14/2023]
Abstract
We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length. In nanochannels smaller than the persistence length, the chain relaxation time is found to have cubic dependence on the channel size. It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement. For thinner chains, looped chain configurations are found in channels with height comparable to the persistence length, with very slow relaxation compared to un-looped chains. Larger effective chain widths inhibit the formation of hairpin loops.
Collapse
Affiliation(s)
- Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan ; Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan ; Department of Physics, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
10
|
Werner E, Persson F, Westerlund F, Tegenfeldt JO, Mehlig B. Orientational correlations in confined DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041802. [PMID: 23214605 DOI: 10.1103/physreve.86.041802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 05/14/2023]
Abstract
We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.
Collapse
Affiliation(s)
- E Werner
- Department of Physics, University of Gothenburg, Sweden
| | | | | | | | | |
Collapse
|
11
|
Marie R, Kristensen A. Nanofluidic devices towards single DNA molecule sequence mapping. JOURNAL OF BIOPHOTONICS 2012; 5:673-686. [PMID: 22815200 DOI: 10.1002/jbio.201200050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/18/2012] [Accepted: 06/18/2012] [Indexed: 06/01/2023]
Abstract
Nanofluidics enables the imaging of stretched single molecules with potential applications for single molecule sequence mapping. Lab-on-a-chip devices for single cell trapping and lyzing, genomic DNA extraction from single cells, and optical mapping of genomic length DNA has been demonstrated separately. Yet the pursuit for applying DNA optical mapping to solve real genomics challenges is still to come. We review lab-on-a-chip devices from literature that could be part of a complete system for the sequence mapping of single DNA molecules.
Collapse
Affiliation(s)
- Rodolphe Marie
- Department of micro- and nanotechnology, Technical University of Denmark, Oersteds plads Building 345east, 2800 Kongens Lyngby, Denmark.
| | | |
Collapse
|
12
|
Persson F, Fritzsche J, Mir KU, Modesti M, Westerlund F, Tegenfeldt JO. Lipid-based passivation in nanofluidics. NANO LETTERS 2012; 12:2260-5. [PMID: 22432814 PMCID: PMC3348678 DOI: 10.1021/nl204535h] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/16/2012] [Indexed: 05/19/2023]
Abstract
Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.
Collapse
Affiliation(s)
- Fredrik Persson
- Department of Physics, University
of Gothenburg, Gothenburg, Sweden
- Department for Cell and Molecular
Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Kalim U. Mir
- The Wellcome
Trust Centre for
Human Genetics, University of Oxford, Oxford,
United Kingdom
| | - Mauro Modesti
- Centre de
Recherche en Cancérologie
de Marseille, CNRS-UMR7258, Inserm-U1068, Institut Paoli-Calmettes, Université Aix-Marseille, France
| | - Fredrik Westerlund
- Department of Chemical and Biological
Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jonas O. Tegenfeldt
- Department of Physics, University
of Gothenburg, Gothenburg, Sweden
- Division
of Solid State Physics, Lund University, Lund, Sweden
| |
Collapse
|
13
|
Electrokinetic DNA transport in 20 nm-high nanoslits: Evidence for movement through a wall-adsorbed. Electrophoresis 2011; 32:2402-9. [DOI: 10.1002/elps.201100278] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 11/07/2022]
|
14
|
Persson F, Bingen P, Staudt T, Engelhardt J, Tegenfeldt JO, Hell SW. Fluorescence nanoscopy of single DNA molecules by using stimulated emission depletion (STED). Angew Chem Int Ed Engl 2011; 50:5581-3. [PMID: 21557413 PMCID: PMC3229986 DOI: 10.1002/anie.201100371] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Indexed: 11/29/2022]
Affiliation(s)
- F Persson
- Department of Physics, University of GothenburgFysikgränd 3, 412 96 Gothenburg (Sweden)
| | - P Bingen
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - T Staudt
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - J Engelhardt
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - J O Tegenfeldt
- Department of Physics, University of GothenburgFysikgränd 3, 412 96 Gothenburg (Sweden)
| | - Stefan W Hell
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| |
Collapse
|
15
|
Persson F, Bingen P, Staudt T, Engelhardt J, Tegenfeldt JO, Hell SW. Fluoreszenznanoskopie einzelner DNA-Moleküle mit Fluoreszenzverhinderung durch stimulierte Emission (STED). Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
16
|
Transition between two regimes describing internal fluctuation of DNA in a nanochannel. PLoS One 2011; 6:e16890. [PMID: 21423606 PMCID: PMC3057976 DOI: 10.1371/journal.pone.0016890] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 01/05/2011] [Indexed: 11/19/2022] Open
Abstract
We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA.
Collapse
|
17
|
Abstract
Stretching of DNA in nanoscale confinement allows for direct visualization of the genetic contents of the DNA on the single DNA molecule level. DNA stretched in nanoscale confinement also allows for studies of DNA-protein interactions and DNA polymer physics in confined environments. This chapter describes the basic steps to fabricate the nanostructures, to perform the experiments, and to analyze the data.
Collapse
Affiliation(s)
- Fredrik Persson
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | | | | |
Collapse
|
18
|
Westerlund F, Persson F, Kristensen A, Tegenfeldt JO. Fluorescence enhancement of single DNA molecules confined in Si/SiO2 nanochannels. LAB ON A CHIP 2010; 10:2049-51. [PMID: 20544105 DOI: 10.1039/c004878j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We demonstrate that the detected emission intensity from YOYO-labeled DNA molecules confined in 180 nm deep Si/SiO2 nanofunnels changes significantly and not monotonically with the width of the funnel. This effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.
Collapse
|
19
|
Persson F, Tegenfeldt JO. DNA in nanochannels--directly visualizing genomic information. Chem Soc Rev 2010; 39:985-99. [PMID: 20179820 DOI: 10.1039/b912918a] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The power of nanofluidic channels to analyze DNA is described along with practical experimental hints. As an introduction, a general overview is given on conventional DNA analysis tools, as well as tools under development towards the $1000 genome. The focus of this tutorial review is the stretching of DNA in nanoscale channels for coarse-grained mapping of DNA. To understand the behavior of the DNA, basic theory is discussed. Experimental details are revealed so that the reader, with the proper equipment, should be able to perform experiments. Basic approaches to the analysis of the data are discussed. Finally, potential future directions are discussed including the application of melting mapping as a simple barcode for the DNA.
Collapse
|
20
|
Gradinaru CC, Marushchak DO, Samim M, Krull UJ. Fluorescence anisotropy: from single molecules to live cells. Analyst 2010; 135:452-9. [PMID: 20174695 DOI: 10.1039/b920242k] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The polarization of light emitted by fluorescent probes is an easily accessible physical quantity that is related to a multitude of molecular parameters including conformation, orientation, size and the nanoscale environment conditions, such as dynamic viscosity and temperature. In analytical biochemistry and analytical chemistry applied to biological problems, fluorescence anisotropy is widely used for measuring the folding state of proteins and nucleic acids, and the affinity constant of ligands through titration experiments. The emphasis of this review is on new multi-parameter single-molecule detection schemes and their bioanalytical applications, and on the use of ensemble polarization assays to study binding and conformational dynamics of proteins and aptamers and for high-throughput discovery of small-molecule drugs.
Collapse
Affiliation(s)
- Claudiu C Gradinaru
- Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto, Canada.
| | | | | | | |
Collapse
|
21
|
Salieb-Beugelaar GB, Dorfman KD, van den Berg A, Eijkel JCT. Electrophoretic separation of DNA in gels and nanostructures. LAB ON A CHIP 2009; 9:2508-2523. [PMID: 19680576 DOI: 10.1039/b905448k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The development of nanostructure devices has opened the door to new DNA separation techniques and fundamental investigations. With advanced nanotechnologies, artificial gels (e.g. nanopillar arrays, nanofilters) can be manufactured with controlled and ordered geometries. This contrast with gels, where the pores are disordered and the range of available pore sizes is limited by the level of cross-linking and the mechanical properties of the gel. In this review, we recall the theories developed for free-solution and gel electrophoresis (extended Ogston model, biased reptation and entropic trapping) and from this perspective, suggestions for future concepts for fast DNA separation using nanostructures will be given.
Collapse
Affiliation(s)
- G B Salieb-Beugelaar
- BIOS/Lab-on-a-Chip Group, Mesa+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands.
| | | | | | | |
Collapse
|