|
1
|
Fang L, Hsieh CC, Larson RG. Molecular Imaging of Shear-Induced Polymer Migration in Dilute Solutions near a Surface. Macromolecules 2007. [DOI: 10.1021/ma062630c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Fang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - Chih-Chen Hsieh
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| | - Ronald G. Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
|
2
|
Zhang CY, Johnson LW. Quantum dot-based fluorescence resonance energy transfer with improved FRET efficiency in capillary flows. Anal Chem 2007; 78:5532-7. [PMID: 16878892 DOI: 10.1021/ac0605389] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence resonance energy transfer (FRET)-based nanosensors with quantum dots (QDs) as donors and organic dyes as acceptors have long been of interest for the detection of biomolecules such as nucleic acids, but their low FRET efficiency in bulk solution has prevented the sensitive detection of nucleic acids due to the large size of the QDs and the long length of nucleic acids. Here we describe a novel approach to improve the detection sensitivity of QD-based nanosensors using single-molecule detection in a capillary flow. In comparison with bulk measurement, single-molecule detection in a capillary flow possesses the unique advantages of improved FRET efficiency, high sensitivity, prevention of photobleaching, and low sample consumption. Greater FRET efficiency was obtained due to the deformation of DNA in the capillary stream. This technique can be easily extended to sensitive bimolecular analysis in microfluidic chips, and it may also offer a promising approach to study the deformation of small nucleic acids in fluid flow.
Collapse
Affiliation(s)
- Chun-Yang Zhang
- Department of Chemistry, York College and The Graduate Center, The City University of New York, Jamaica, New York 11451, USA
| | | |
Collapse
|
|
3
|
Yamashita K, Miyazaki M, Yamaguchi Y, Nakamura H, Maeda H. Microfluidic Thermodynamics of the Shift in Thermal Stability of DNA Duplex in a Microchannel Laminar Flow. J Phys Chem B 2007; 111:6127-33. [PMID: 17500552 DOI: 10.1021/jp0686745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper reports the shift in thermal stability of DNA duplex and its thermodynamics spectroscopically, caused by stretching and orientation of DNA strands in a microchannel laminar flow. For direct spectroscopic measurement of the microchannel, we prepared an in-house temperature-controllable microchannel-type flow cell. The melting curves of DNA oligomers in a microchannel laminar flow were measured. For DNA oligomers with more than 10 base pairs, the melting curve shifted to the high-temperature side with higher flow speed. However, for 8-base-pair DNA oligomers, a change in the melting profile was not observed in batchwise and microchannel flows. We undertook microfluidic thermodynamic analysis to elucidate details of the shift in thermal stability of the DNA duplex in a microchannel laminar flow. Enthalpy-entropy compensation is applicable to the microfluidic thermal stability shift. We studied the relationships between the enthalpy-entropy compensation and DNA strand length or flow speed. Results showed that the enthalpy-entropy compensation was influenced by both DNA strand length and flow speed, and the penalties of enthalpy were 2-12% greater than the benefits of entropy.
Collapse
Affiliation(s)
- Kenichi Yamashita
- Micro-& Nano-space Chemistry Group, Nanotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 807-1, Shuku-machi, Tosu, Saga 841-0052, Japan
| | | | | | | | | |
Collapse
|
|
4
|
Teclemariam NP, Beck VA, Shaqfeh ESG, Muller SJ. Dynamics of DNA Polymers in Post Arrays: Comparison of Single Molecule Experiments and Simulations. Macromolecules 2007. [DOI: 10.1021/ma062892e] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nerayo P. Teclemariam
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Victor A. Beck
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Eric S. G. Shaqfeh
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Susan J. Muller
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California 94720; Department of Chemical Engineering, Stanford University, Stanford, California 94305; and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| |
Collapse
|
|
5
|
Teixeira RE, Dambal AK, Richter DH, Shaqfeh ESG, Chu S. The Individualistic Dynamics of Entangled DNA in Solution. Macromolecules 2007. [DOI: 10.1021/ma062932e] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rodrigo E. Teixeira
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, Department of Mechanical Engineering, Stanford University, Stanford, California 94305, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ajey K. Dambal
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, Department of Mechanical Engineering, Stanford University, Stanford, California 94305, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - David H. Richter
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, Department of Mechanical Engineering, Stanford University, Stanford, California 94305, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Eric S. G. Shaqfeh
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, Department of Mechanical Engineering, Stanford University, Stanford, California 94305, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Steven Chu
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, Department of Mechanical Engineering, Stanford University, Stanford, California 94305, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| |
Collapse
|
|
6
|
Bellan LM, Cross JD, Strychalski EA, Moran-Mirabal J, Craighead HG. Individually resolved DNA molecules stretched and embedded in electrospun polymer nanofibers. NANO LETTERS 2006; 6:2526-30. [PMID: 17090085 DOI: 10.1021/nl061894+] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We have used the flow characteristics of an electrospinning jet to elongate and fix DNA molecules. We embedded and observed fluorescently labeled lambda bacteriophage DNA molecules in polyethylene oxide nanofibers. The embedded DNA molecules were imaged using fluorescence microscopy and found to be stretched to lengths approaching the full dyed contour length.
Collapse
Affiliation(s)
- Leon M Bellan
- School of Applied and Engineering Physics and Department of Physics, Cornell University, Ithaca, New York 14853, USA.
| | | | | | | | | |
Collapse
|
|
7
|
Laib S, Robertson RM, Smith DE. Preparation and Characterization of a Set of Linear DNA Molecules for Polymer Physics and Rheology Studies. Macromolecules 2006. [DOI: 10.1021/ma0601464] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephan Laib
- Department of Physics, Mail Code 0379, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Rae M. Robertson
- Department of Physics, Mail Code 0379, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Douglas E. Smith
- Department of Physics, Mail Code 0379, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| |
Collapse
|
|
8
|
Sunthar P, Nguyen DA, Dubbelboer R, Prakash JR, Sridhar T. Measurement and Prediction of the Elongational Stress Growth in a Dilute Solution of DNA Molecules. Macromolecules 2005. [DOI: 10.1021/ma0511907] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Sunthar
- Department of Chemical Engineering, Monash University, Melbourne VIC 3800, Australia
| | - Duc At Nguyen
- Department of Chemical Engineering, Monash University, Melbourne VIC 3800, Australia
| | - Roelf Dubbelboer
- Department of Chemical Engineering, Monash University, Melbourne VIC 3800, Australia
| | - J. Ravi Prakash
- Department of Chemical Engineering, Monash University, Melbourne VIC 3800, Australia
| | - Tam Sridhar
- Department of Chemical Engineering, Monash University, Melbourne VIC 3800, Australia
| |
Collapse
|
|
9
|
Randall GC, Doyle PS. DNA Deformation in Electric Fields: DNA Driven Past a Cylindrical Obstruction. Macromolecules 2005. [DOI: 10.1021/ma048073g] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Greg C. Randall
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| |
Collapse
|
|
10
|
Teixeira RE, Babcock HP, Shaqfeh ESG, Chu S. Shear Thinning and Tumbling Dynamics of Single Polymers in the Flow-Gradient Plane. Macromolecules 2004. [DOI: 10.1021/ma048077l] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rodrigo E. Teixeira
- Department of Chemical Engineering, Stanford University, Departments of Physics and Applied Physics, Stanford University, and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Hazen P. Babcock
- Department of Chemical Engineering, Stanford University, Departments of Physics and Applied Physics, Stanford University, and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Eric S. G. Shaqfeh
- Department of Chemical Engineering, Stanford University, Departments of Physics and Applied Physics, Stanford University, and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| | - Steven Chu
- Department of Chemical Engineering, Stanford University, Departments of Physics and Applied Physics, Stanford University, and Department of Mechanical Engineering, Stanford University, Stanford, California 94305
| |
Collapse
|
|
11
|
Sunthar P, Prakash JR. Parameter-Free Prediction of DNA Conformations in Elongational Flow by Successive Fine Graining. Macromolecules 2004. [DOI: 10.1021/ma035941l] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Sunthar
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia
| | - J. Ravi Prakash
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia
| |
Collapse
|
|
12
|
Zheng J, Yeung ES. Anomalous radial migration of single DNA molecules in capillary electrophoresis. Anal Chem 2002; 74:4536-47. [PMID: 12236367 DOI: 10.1021/ac0257344] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the unexpected radial migration of DNA molecules in capillary electrophoresis (CE) with applied Poiseuille flow. Such movement can contribute to anomalous migration times, peak dispersion, and size and shape selectivity in CE. When Poiseuille flow is applied from the cathode to the anode, DNA molecules move toward the center of the capillary, forming a narrow, highly concentrated zone. Conversely, when the flow is applied from the anode to the cathode, DNA molecules move toward the walls, leaving a DNA-depleted zone around the axis. We showed that the deformation and orientation of DNA molecules under Poiseuille flow was responsible for the radial migration. By analyzing the forces acting on the deformed and oriented DNA molecules, we derived an expression for the radial lift force, which explained our results very well under different conditions with Poiseuille flow only, electrophoresis only, and the combination of Poiseuille flow and electrophoresis. Factors governing the direction and velocity of radial migration were elucidated. Potential applications of this phenomenon include an alternative to sheath flow in flow cytometry, improving precision and reliability of single-molecule detection, reduction of wall adsorption, and size separation with a mechanism akin to field-flow fractionation. On the negative side, nonuniform electroosmotic flow along the capillary or microfluidic channel is common in CE, and radial migration of certain analytes cannot be neglected.
Collapse
Affiliation(s)
- Jinjian Zheng
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames 50011, USA
| | | |
Collapse
|
|
13
|
Harper JT, Humphrey NF, Pfeffer WT, Huzurbazar SV, Bahr DB, Welch BC. Spatial variability in the flow of a valley glacier: Deformation of a large array of boreholes. ACTA ACUST UNITED AC 2001. [DOI: 10.1029/2000jb900440] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|