1
|
Dahan L, Huang L, Kedmi R, Behlke MA, Peer D. SNP detection in mRNA in living cells using allele specific FRET probes. PLoS One 2013; 8:e72389. [PMID: 24039756 PMCID: PMC3767744 DOI: 10.1371/journal.pone.0072389] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/09/2013] [Indexed: 12/24/2022] Open
Abstract
Live mRNA detection allows real time monitoring of specific transcripts and genetic alterations. The main challenge of live genetic detection is overcoming the high background generated by unbound probes and reaching high level of specificity with minimal off target effects. The use of Fluorescence Resonance Energy Transfer (FRET) probes allows differentiation between bound and unbound probes thus decreasing background. Probe specificity can be optimized by adjusting the length and through use of chemical modifications that alter binding affinity. Herein, we report the use of two oligonucleotide FRET probe system to detect a single nucleotide polymorphism (SNP) in murine Hras mRNA, which is associated with malignant transformations. The FRET oligonucleotides were modified with phosphorothioate (PS) bonds, 2′OMe RNA and LNA residues to enhance nuclease stability and improve SNP discrimination. Our results show that a point mutation in Hras can be detected in endogenous RNA of living cells. As determined by an Acceptor Photobleaching method, FRET levels were higher in cells transfected with perfect match FRET probes whereas a single mismatch showed decreased FRET signal. This approach promotes in vivo molecular imaging methods and could further be applied in cancer diagnosis and theranostic strategies.
Collapse
Affiliation(s)
- Liya Dahan
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lingyan Huang
- Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Ranit Kedmi
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Mark A. Behlke
- Integrated DNA Technologies, Coralville, Iowa, United States of America
- * E-mail: (MAB); (DP)
| | - Dan Peer
- Department of Cell Research and Immunology, Tel Aviv University, Tel Aviv, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (MAB); (DP)
| |
Collapse
|
2
|
Browne KA, Deheyn DD, Brown RC, Weeks I. Spectrally resolved chemiluminescent probes for sensitive multiplex molecular quantification. Anal Chem 2012; 84:9222-9. [PMID: 23088160 DOI: 10.1021/ac3017423] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Luminophores are frequently utilized probe labels for detecting biological analytes. Multiple fluorescent luminophores, or fluorophores, can be readily distinguished from one another based on different energy excitation and emission wavelengths and lifetimes. However, suitable methods and reagents for distinguishing multiples of the much more sensitive chemically initiated luminophores have been limited. Herein we describe a new class of hybrid luminophore probes that emit light of distinct wavelength ranges and intensities upon energy transfer (ET) from an in-common, acridinium ester chemiluminophore to a covalently conjugated fluorophore. This format supports rapid, rational design of spectrally resolvable, chemically initiated probes. Time-resolved spectrographic and luminescence characterizations indicate that ET is not dependent on overlap in the emission spectrum of the luminophore and the absorption spectra of acceptors, suggesting a non-Förster resonance ET mechanism. Analysis of a combination of the chemiluminophore and new chemiluminophore-acceptor conjugate probes demonstrates the benefits of their use in sensitive, multiplex quantification of nucleic acid sequences indicative of environmentally relevant microbes without prior enzymatic amplification.
Collapse
Affiliation(s)
- Kenneth A Browne
- Gen-Probe Incorporated, 10210 Genetic Center Drive, San Diego, California 92121, United States.
| | | | | | | |
Collapse
|
3
|
Ziessel R, Harriman A. Artificial light-harvesting antennae: electronic energy transfer by way of molecular funnels. Chem Commun (Camb) 2011; 47:611-31. [DOI: 10.1039/c0cc02687e] [Citation(s) in RCA: 342] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
4
|
Opanasyuk O, Johansson LBÅ. Extended Förster theory: a quantitative approach to the determination of inter-chromophore distances in biomacromolecules. Phys Chem Chem Phys 2010; 12:7758-67. [DOI: 10.1039/b924113b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
5
|
|
6
|
Yeung SHI, Seo TS, Crouse CA, Greenspoon SA, Chiesl TN, Ban JD, Mathies RA. Fluorescence energy transfer-labeled primers for high-performance forensic DNA profiling. Electrophoresis 2008; 29:2251-9. [DOI: 10.1002/elps.200700772] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
7
|
Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| |
Collapse
|
8
|
Zhao W, Carreira EM. Conformationally restricted aza-BODIPY: highly fluorescent, stable near-infrared absorbing dyes. Chemistry 2007; 12:7254-63. [PMID: 16850516 DOI: 10.1002/chem.200600527] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Novel NIR fluorescent, conformational restricted aza-dipyrromethene boron difluoride (aza-BODIPY) dyes were prepared by an efficient process. Such conformational restricted aza-BODIPY dyes possess intense absorption, strong fluorescence, high chemical and photostability. Additionally, the sharp fluorescence of non-amine containing aza-BODIPY dyes is insensitive to solvent polarity.
Collapse
Affiliation(s)
- Weili Zhao
- Laboratorium für Organische Chemie, ETH Zürich, HCI H335, 8093 Zürich
| | | |
Collapse
|
9
|
Kumar S, Fuller CW. Chapter 4 Advances in Dye-Nucleotide Conjugate Chemistry for DNA Sequencing. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/s1871-0069(06)02004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
|
10
|
Jiao GS, Thoresen LH, Kim TG, Haaland WC, Gao F, Topp MR, Hochstrasser RM, Metzker ML, Burgess K. Syntheses, Photophysical Properties, and Application of Through-Bond Energy-Transfer Cassettes for Biotechnology. Chemistry 2006; 12:7816-26. [PMID: 16888738 DOI: 10.1002/chem.200600197] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.
Collapse
Affiliation(s)
- Guan-Sheng Jiao
- Department of Chemistry, Texas A & M University P.O. Box 30012, College Station, Texas 77842, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Sapsford KE, Berti L, Medintz IL. Materialien für den resonanten Fluoreszenzenergietransfer (FRET): jenseits klassischer Donor-Acceptor-Kombinationen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503873] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
12
|
Sapsford KE, Berti L, Medintz IL. Materials for Fluorescence Resonance Energy Transfer Analysis: Beyond Traditional Donor–Acceptor Combinations. Angew Chem Int Ed Engl 2006; 45:4562-89. [PMID: 16819760 DOI: 10.1002/anie.200503873] [Citation(s) in RCA: 1028] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The use of Förster or fluorescence resonance energy transfer (FRET) as a spectroscopic technique has been in practice for over 50 years. A search of ISI Web of Science with just the acronym "FRET" returns more than 2300 citations from various areas such as structural elucidation of biological molecules and their interactions, in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting and metallic nanomaterials. The advent of new classes of fluorophores including nanocrystals, nanoparticles, polymers, and genetically encoded proteins, in conjunction with ever more sophisticated equipment, has been vital in this development. This review gives a critical overview of the major classes of fluorophore materials that may act as donor, acceptor, or both in a FRET configuration. We focus in particular on the benefits and limitations of these materials and their combinations, as well as the available methods of bioconjugation.
Collapse
Affiliation(s)
- Kim E Sapsford
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC 20375, USA
| | | | | |
Collapse
|
13
|
Zhao W, Carreira EM. Conformationally Restricted Aza-Bodipy: A Highly Fluorescent, Stable, Near-Infrared-Absorbing Dye. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461868] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
14
|
Zhao W, Carreira EM. Conformationally Restricted Aza-Bodipy: A Highly Fluorescent, Stable, Near-Infrared-Absorbing Dye. Angew Chem Int Ed Engl 2005; 44:1677-9. [PMID: 15693049 DOI: 10.1002/anie.200461868] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Weili Zhao
- Laboratorium für Organische Chemie, ETH Hönggerberg, HCI H335, 8093 Zürich, Switzerland
| | | |
Collapse
|
15
|
Kan CW, Fredlake CP, Doherty EAS, Barron AE. DNA sequencing and genotyping in miniaturized electrophoresis systems. Electrophoresis 2004; 25:3564-88. [PMID: 15565709 DOI: 10.1002/elps.200406161] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.
Collapse
Affiliation(s)
- Cheuk-Wai Kan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | | | | | | |
Collapse
|
16
|
Berg ES, Skaug K. Liposome encapsulation of the internal control for whole process quality assurance of nucleic acid amplification-based assays. J Microbiol Methods 2003; 55:303-9. [PMID: 14500022 DOI: 10.1016/s0167-7012(03)00165-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A system intended for whole process quality assurance of nucleic acid amplification assays was developed based on the use of liposomes as cell-mimicking vehicles for the internal control, allowing introduction of the internal control directly into the crude biological specimens. By the proof of principle testing, the Roche Cobas Amplicor CT assay was chosen as model system and the Roche CT/NG Internal Control was thus loaded into the liposomes. The liposome/DNA particles were spiked into a Chlamydia trachomatis-positive urine specimen. A quantitative "in-house" duplex real-time C. trachomatis PCR assay showed that liposomes having Blue Dextran 2000 polysaccharide co-entrapped were the most suited particles as they were efficiently deposited by the centrifugation carried out according to the Roche urine specimen preparation procedure. Furthermore, it was demonstrated that the liposome/DNA particles might be used for whole process quality assurance of Amplicor assay without major modifications of the assay protocol. An additional feature of the use of these liposomes was that the pellet became blue coloured and that might facilitate a thorough removal of the urine supernatant without increasing the risk of disturbance of the pellet. Principally, the liposome/internal control system is versatile and seems to be applicable for whole process quality control of amplification-based assays for detection of various pathogens.
Collapse
Affiliation(s)
- E S Berg
- Division for Infectious Disease Control, National Institute of Public Health, PO Box 4404 Torshov, N-0403, Oslo, Norway.
| | | |
Collapse
|
17
|
Berti L, Xie J, Medintz IL, Glazer AN, Mathies RA. Energy transfer cassettes for facile labeling of sequencing and PCR primers. Anal Biochem 2001; 292:188-97. [PMID: 11355850 DOI: 10.1006/abio.2001.5069] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence energy transfer (ET) primers and terminators are the reagents of choice for multiplex DNA sequencing and analysis. We present here the design, synthesis and evaluation of a four-color set of ET cassettes, fluorescent labeling reagents that can be quantitatively coupled to a thiol-activated target through a disulfide exchange reaction. The ET cassette consists of a sugar-phosphate spacer with a FAM donor at the 3'-end, an acceptor linked to a modified T-base at the 5'-end of the spacer and a mixed disulfide for coupling to a thiol at the 5'-end. The acceptor dye emission intensities of ET labeled primers produced in this manner are comparable to commercial ET primers. The utility of our ET cassette-labeled primers is demonstrated by performing four-color capillary electrophoresis sequencing with the M13(-21)forward primer and by generating and analyzing a set of single-nucleotide-polymorphism-specific PCR amplicons.
Collapse
Affiliation(s)
- L Berti
- Department of Chemistry, University of California, Berkeley 94720, USA
| | | | | | | | | |
Collapse
|
18
|
Xu Y, Karalkar NB, Kool ET. Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations. Nat Biotechnol 2001; 19:148-52. [PMID: 11175729 DOI: 10.1038/84414] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enzymatic ligation methods are useful in diagnostic detection of DNA sequences. Here we describe the investigation of nonenzymatic phosphorothioate-iodide DNA autoligation chemistry as a method for detection and identification of both RNA and DNA sequences. Combining ligation specificity with the hybridization specificity of the ligated product is shown to yield discrimination of a point mutation as high as >10(4)-fold. Unlike enzymatic ligations, this reaction is found to be equally efficient on RNA or DNA templates. The reaction is also shown to exhibit a significant level of self-amplification, with the template acting in catalytic fashion to ligate multiple pairs of probes. A strategy for fluorescence labeling of three autoligating energy transfer (ALET) probes and directly competing them for autoligation on a target sequence is described. The method is tested in several formats, including solution phase, gel, and blot assays. The ALET probe design offers direct RNA detection, combining high sequence specificity with an easily detectable color change by fluorescence resonance energy transfer (FRET).
Collapse
Affiliation(s)
- Y Xu
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | | | | |
Collapse
|
19
|
Abstract
We describe wavelength-shifting molecular beacons, which are nucleic acid hybridization probes that fluoresce in a variety of different colors, yet are excited by a common monochromatic light source. The twin functions of absorption of energy from the excitation light and emission of that energy in the form of fluorescent light are assigned to two separate fluorophores in the same probe. These probes contain a harvester fluorophore that absorbs strongly in the wavelength range of the monochromatic light source, an emitter fluorophore of the desired emission color, and a nonfluorescent quencher. In the absence of complementary nucleic acid targets, the probes are dark, whereas in the presence of targets, they fluoresce-not in the emission range of the harvester fluorophore that absorbs the light, but rather in the emission range of the emitter fluorophore. This shift in emission spectrum is due to the transfer of the absorbed energy from the harvester fluorophore to the emitter fluorophore by fluorescence resonance energy transfer, and it only takes place in probes that are bound to targets. Wavelength-shifting molecular beacons are substantially brighter than conventional molecular beacons that contain a fluorophore that cannot efficiently absorb energy from the available monochromatic light source. We describe the spectral characteristics of wavelength-shifting molecular beacons, and we demonstrate how their use improves and simplifies multiplex genetic analyses.
Collapse
Affiliation(s)
- S Tyagi
- Department of Molecular Genetics, Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.
| | | | | |
Collapse
|
20
|
Hanning A, Westberg J, Roeraade J. A liquid core waveguide fluorescence detector for multicapillary electrophoresis applied to DNA sequencing in a 91-capillary array. Electrophoresis 2000; 21:3290-304. [PMID: 11001228 DOI: 10.1002/1522-2683(20000901)21:15<3290::aid-elps3290>3.0.co;2-j] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new laser-induced fluorescence (LIF) detector for multicapillary electrophoresis is presented. The detection principle is based on waveguiding of the emitted fluorescence from the point of illumination to the capillary ends by total internal reflection (TIR) and imaging of the capillary ends. The capillaries themselves thus act as liquid core waveguides (LCWs). At the illumination point, the capillaries are arranged in a planar array, which allows clean and efficient illumination with a line-focused laser beam. The capillary ends are rearranged into a small, densely packed two-dimensional array, which is imaged end-on with high light collection efficiency and excellent image quality. Wavelength dispersion is obtained with a single prism. Intercapillary optical crosstalk is less than 0.5%, and rejection of stray light is very efficient. The detector is applied to four-color DNA sequencing by gel electrophoresis in a 91-capillary array, with simple fluorescein and rhodamine dyes as fluorophores. Since the imaged two-dimensional array is so compact, the detector has a high potential for very large-scale multiplexing.
Collapse
Affiliation(s)
- A Hanning
- Royal Institute of Technology, Department of Analytical Chemistry, Stockholm, Sweden
| | | | | |
Collapse
|
21
|
Abstract
A poor man's approach to genotyping for research and high-throughput diagnostics.
Collapse
Affiliation(s)
- M Schuelke
- Department of Neuropediatrics, Charité University Hospital, Augustenburger Platz 1, D-13353 Berlin, Germany.
| |
Collapse
|
22
|
Synthesis and fluorescent properties of 5-(1-pyrenylethynyl)-2′-deoxyuridine-containing oligodeoxynucleotides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02758859] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
23
|
Dolník V. DNA sequencing by capillary electrophoresis (review). JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1999; 41:103-19. [PMID: 10626769 DOI: 10.1016/s0165-022x(99)00041-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
DNA sequencing by capillary electrophoresis has been reviewed with an emphasis on progress during the last four years. The effects of sample purification, composition of sieving matrices, electric field strength, temperature, wall coating and DNA labeling on the DNA sequencing performance are discussed. Multicapillary array instrumentation is compared with one-capillary systems. Integrated systems that perform the whole DNA sequencing operation online starting from the DNA amplification through base calling and data processing are discussed.
Collapse
Affiliation(s)
- V Dolník
- Molecular Dynamics, Sunnyvale, CA 94086, USA.
| |
Collapse
|
24
|
Schmalzing D, Koutny L, Salas-Solano O, Adourian A, Matsudaira P, Ehrlich D. Recent developments in DNA sequencing by capillary and microdevice electrophoresis. Electrophoresis 1999; 20:3066-77. [PMID: 10596815 DOI: 10.1002/(sici)1522-2683(19991001)20:15/16<3066::aid-elps3066>3.0.co;2-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The present review covers papers published in the years 1997 and 1998 on DNA sequencing by capillary and microdevice electrophoresis. The article does not include other electrophoretic DNA applications such as analysis of oligonucleotides, genotyping, and mutational analysis. Capillary gel electrophoresis (CGE) is starting to become a viable competitor to slab gel electrophoresis for DNA sequencing. Commercially available multicapillary array sequencers are now entering sequencing facilities which to date have totally relied on traditional slab gel technology. CGE research on DNA sequencing therefore becomes increasingly concerned with the critical task of fine-tuning the operational parameters to create robust sequencing systems. Electrophoretic microdevices are being considered the next technological step in DNA sequencing by electrophoresis.
Collapse
Affiliation(s)
- D Schmalzing
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Scherer JR, Kheterpal I, Radhakrishnan A, Ja WW, Mathies RA. Ultra-high throughput rotary capillary array electrophoresis scanner for fluorescent DNA sequencing and analysis. Electrophoresis 1999; 20:1508-17. [PMID: 10424474 DOI: 10.1002/(sici)1522-2683(19990601)20:7<1508::aid-elps1508>3.0.co;2-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have constructed a rotary confocal fluorescence scanner and capillary array electrophoresis system that is designed to analyze over 1000 DNA sequencing or fragment sizing separations in parallel. Capillaries are arranged around the surface of a cylinder and a rotating objective in the middle of the cylinder excites and collects fluorescence from labeled DNA fragments as they pass the capillary detection window. The capillaries are pressure-filled with a replaceable matrix and the samples are electrokinetically injected in parallel from a stainless steel microtiter plate at the cathode end. We demonstrate that the instrument is capable of producing four-color data from all capillaries at a scan rate of 4 Hz (corresponding to a linear scan velocity of 121 cm/s). M13 sequencing data were obtained using a 128 capillary array mounted in half of the first quadrant of the scanner. In this initial run, read lengths greater than 500 bases were obtained in over 60% of the capillaries.
Collapse
Affiliation(s)
- J R Scherer
- Department of Chemistry, University of California, Berkeley 94720, USA
| | | | | | | | | |
Collapse
|
26
|
Liu S, Shi Y, Ja WW, Mathies RA. Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels. Anal Chem 1999; 71:566-73. [PMID: 9989377 DOI: 10.1021/ac980783v] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA sequencing separations have been performed in microfabricated electrophoresis channels with the goal of determining whether high-quality sequencing is feasible with these microdevices. The separation matrix, separation temperature, channel length and depth, injector size, and injection parameters were optimized. DNA fragment sizing separations demonstrated that 50-micron-deep channels provide the best sensitivity for our detection configuration. One-color sequencing separations of single-stranded M13mp18 DNA on 3% linear polyacrylamide (LPA) were used to optimize the twin-T injector size, injection conditions, and temperature. The best one-color separations were observed with a 250-micron twin-T injector, an injection time of 60 s, and a temperature of 35 degrees C. The first 500 bases appeared in 9.2 min with a resolution of > 0.5, and the separation extended to 700 bases. The best four-color sequencing separations were performed using 4% LPA, a temperature of 40 degrees C, and a 100-micron twin-T injector. These four-color runs were complete in only 20 min, could be automatically base-called using BaseFinder to over 600 bp after the primer, and were 99.4% accurate to 500 bp. These results significantly advance the quality of microchip-based electrophoretic sequencing and indicate the feasibility of performing high-speed genomic sequencing with microfabricated electrophoretic devices.
Collapse
Affiliation(s)
- S Liu
- Department of Chemistry, University of California, Berkeley 94720, USA
| | | | | | | |
Collapse
|
27
|
Hung SC, Mathies RA, Glazer AN. Comparison of fluorescence energy transfer primers with different donor-acceptor dye combinations. Anal Biochem 1998; 255:32-8. [PMID: 9448839 DOI: 10.1006/abio.1997.2451] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fluorescence energy transfer (ET) primers are far superior to single dye-labeled primers as labels for DNA sequencing and polymerase chain reaction amplification. We compare here ET primers with different donor and acceptor dye combinations with respect to the relative acceptor fluorescence emission intensity and the amount of residual donor fluorescence emission. Primers with the following donor/acceptor pairs were synthesized: 6-carboxyfluorescein/6-carboxy-X-rhodamine (FAM-ROX), 3-(epsilon-carboxypentyl)-3'-ethyl-5,5'-dimethyloxacarbocyanine/ 6-carboxy-X-rhodamine (CYA-ROX), and the 4,4-difluoro-4-bora-3 alpha,4 alpha-diaza-s-indacene-3-propionic acid (BODIPY) derivatives, 5,7-dimethyl-BODIPY/5-(4-phenyl-1,3-butadienyl) BODIPY (BODIPY503/512-BODIPY581/591). Variables examined included the length of the 5'-amino linker arm, the number of base pairs between the donor and acceptor, and the excitation wavelength (488 or 514 nm). Of the primers examined, CYA-ROX primers offer the best combination of acceptor fluorescence emission intensity and spectral purity.
Collapse
Affiliation(s)
- S C Hung
- Department of Molecular and Cell Biology, University of California Berkeley 94720, USA
| | | | | |
Collapse
|