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Craig DB, Arriaga E, Wong JCY, Lu H, Dovichi ANJ. Peer Reviewed: Life and Death of a Single Enzyme Molecule. Anal Chem 2011. [DOI: 10.1021/ac9817164] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dombkowski AA, Sultana Z, Craig DB, Jamil H. In silico analysis of combinatorial microRNA activity reveals target genes and pathways associated with breast cancer metastasis. Cancer Inform 2011; 10:13-29. [PMID: 21552493 PMCID: PMC3085424 DOI: 10.4137/cin.s6631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. Aberrant microRNA activity has been reported in many diseases, and studies often find numerous microRNAs concurrently dysregulated. Most target genes have binding sites for multiple microRNAs, and mounting evidence indicates that it is important to consider their combinatorial effect on target gene repression. A recent study associated the coincident loss of expression of six microRNAs with metastatic potential in breast cancer. Here, we used a new computational method, miR-AT!, to investigate combinatorial activity among this group of microRNAs. We found that the set of transcripts having multiple target sites for these microRNAs was significantly enriched with genes involved in cellular processes commonly perturbed in metastatic tumors: cell cycle regulation, cytoskeleton organization, and cell adhesion. Network analysis revealed numerous target genes upstream of cyclin D1 and c-Myc, indicating that the collective loss of the six microRNAs may have a focal effect on these two key regulatory nodes. A number of genes previously implicated in cancer metastasis are among the predicted combinatorial targets, including TGFB1, ARPC3, and RANKL. In summary, our analysis reveals extensive combinatorial interactions that have notable implications for their potential role in breast cancer metastasis and in therapeutic development.
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Craig DB, Haslam AM, Coombs JM, Nichols ER. Kinetic studies of unmodified individual Escherichia coli β-galactosidase molecules in free solution. Biochem Cell Biol 2010; 88:451-8. [DOI: 10.1139/o09-120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Assays were performed on individual Escherichia coli β-galactosidase molecules at 2 different concentrations of the substrate DDAO-β-d-galactoside using a free zone capillary electrophoresis–based protocol with an in-laboratory–constructed instrument utilizing laser-induced fluorescence detection. In a typical run, 2 enzyme molecules were injected into the capillary. They were separated from each other by a brief period of electrophoresis and incubated on the capillary in the presence of the substrate. They were then mobilized on the capillary into a zone of substrate at a different concentration, re-incubated, and the product peaks mobilized past the detector . The relative change in activity as the concentration was increased differed between molecules, suggesting differences in Km. In a different experiment, the capillary was filled with on average 13 enzyme molecules per run, incubated, and the activities of the individual molecules determined. The shapes of the distribution curves of single molecule activities obtained at different concentrations of the substrate resorufin-β-d-galactoside were indistinguishable, suggesting a homogeneous Km. To explain why individual enzyme molecules behaved as if they were heterogeneous with respect to Km but the population behaved as if it were homogeneous, theoretical Michaelis–Menten curves were constructed. The curves for populations with heterogeneous Km values were found to be indistinguishable from that of a homogeneous population.
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Nichols ER, Shadabi E, Craig DB. Effect of alteration of translation error rate on enzyme microheterogeneity as assessed by variation in single molecule electrophoretic mobility and catalytic activity. Biochem Cell Biol 2009; 87:517-29. [DOI: 10.1139/o09-010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The role of translation error for Escherichia coli individual β-galactosidase molecule catalytic and electrophoretic heterogeneity was investigated using CE-LIF. An E. coli rpsL mutant with a hyperaccurate translation phenotype produced enzyme molecules that exhibited significantly less catalytic heterogeneity but no reduction of electrophoretic heterogeneity. Enzyme expressed with streptomycin-induced translation error had increased thermolability, lower activity, and no significant change to catalytic or electrophoretic heterogeneity. Modeling of the electrophoretic behaviour of β-galactosidase suggested that variation of the hydrodynamic radius may be the most significant contributor to electrophoretic heterogeneity.
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Craig DB, Nichols ER. Continuous flow assay for the simultaneous measurement of the electrophoretic mobility, catalytic activity and its variation over time of individual molecules of Escherichia coli beta-galactosidase. Electrophoresis 2009; 29:4298-303. [PMID: 19016504 DOI: 10.1002/elps.200800482] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A CE-LIF detection-based assay was developed for the study of individual molecules of Escherichia coli beta-galactosidase. The assay allows for the simultaneous measurement of the electrophoretic mobility, catalytic activity and the variation in activity over time of individual enzyme molecules. In addition to showing the microheterogeneity of the enzyme molecules with respect to mobility and activity, it was demonstrated that at elevated temperatures the enzyme activity fluctuates over time. Incubation at varying temperatures showed that individual beta-galactosidase molecules exhibit differences in their change in activity upon a change in incubation temperature. Incubation at one temperature, followed by an incubation at an elevated temperature and subsequent incubation back at the initial lower temperature caused the molecules to have a different activity than they had initially. Additionally, thermal denaturation was found to cause a rapid and complete loss of activity.
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Nichols ER, Craig DB. Measurement of the differences in electrophoretic mobilities of individual molecules ofE. coliβ-galactosidase provides insight into structural differences which underlie enzyme microheterogeneity. Electrophoresis 2008; 29:4257-69. [DOI: 10.1002/elps.200800060] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Nichols ER, Craig DB. Single Molecule Assays Reveal Differences Between In Vitro and In Vivo Synthesized β-Galactosidase. Protein J 2008; 27:376-83. [DOI: 10.1007/s10930-008-9147-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nichols ER, Gavina JMA, McLeod RG, Craig DB. Single Molecule Assays of β-Galactosidase from Two Wild-type Strains of E. coli: Effects of Protease Inhibitors on Microheterogeneity and Different Relative Activities with Differing Substrates. Protein J 2007; 26:95-105. [PMID: 17253128 DOI: 10.1007/s10930-006-9050-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Beta-galactosidase was induced in E. coli wild type strains ATCC 8677 and 35321 in the presence of various protease inhibitors. Single enzyme molecule assays were performed using a capillary electrophoresis based protocol. The presence of the protease inhibitors had a minimal effect on the average and distribution of single molecule activities. Two novel capillary electrophoresis based single enzyme molecule assays for beta-galactosidase were developed using DDAO-beta-D-galactopyranoside and fluorescein-beta-D-digalactopyranoside as substrates. Double incubations were performed on individual enzyme molecules to demonstrate the reproducibility of the assays. Assays performed on beta-galactosidase from strains 8677 and 35321 demonstrated that the relative activities of the enzyme for the different substrates differed between the strains. Sequencing showed that these two strains differ in their primary sequence by a single amino acid substitution in position 280, which is in the region of the active site.
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Craig DB, Wetzl BK, Duerkop A, Wolfbeis OS. Determination of picomolar concentrations of proteins using novel amino reactive chameleon labels and capillary electrophoresis laser-induced fluorescence detection. Electrophoresis 2005; 26:2208-13. [PMID: 15880625 DOI: 10.1002/elps.200410332] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Py-1 and Py-6 are novel amino-reactive fluorescent reagents. The names given to them reflect that they consist of a pyrylium group attached to small aromatic moieties. Upon reaction with a primary amine there is a large spectral shift in the reagent, rendering them effectively fluorogenic. In this study, these reagents were used to label a test protein, (human serum albumin), and the sample was analyzed by capillary electrophoresis and laser-induced fluorescence detection. Detection limits after a 60 min labeling reaction at 22 degrees C (Py-1) and 50 degrees C (Py-6) were 6.5 ng/mL (98 pM) for Py-1 and 1.2 ng/mL (18 pM) for Py-6. Separation of immunoglobulin G (IgG), human serum albumin, lipase, and myoglobin after labeling with Py-6 were performed. The method was further modified to make it amenable to automation. Unlike many other amino reactive reagents used to label protein amino groups, reaction with Py-1 and Py-6 do not alter the charge of the protein and the advantage of this with respect to electrophoretic separations is discussed.
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Wetzl BK, Yarmoluk SM, Craig DB, Wolfbeis OS. Chameleon Labels for Staining and Quantifying Proteins. Angew Chem Int Ed Engl 2004; 43:5400-2. [PMID: 15468079 DOI: 10.1002/anie.200460508] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wetzl BK, Yarmoluk SM, Craig DB, Wolfbeis OS. Ein Chamäleon-Marker zur Anfärbung und quantitativen Bestimmung von Proteinen. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460508] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Craig DB, Nachtigall JT, Ash HL, Shoemaker GK, Dyck AC, Wawrykow TMJ, Gudbjartson HL. Differences in the average single molecule activities of E. coli beta-galactosidase: effect of source, enzyme molecule age and temperature of induction. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:555-61. [PMID: 14703989 DOI: 10.1023/b:jopc.0000005505.73032.16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using a capillary electrophoresis-based method, single enzyme molecule assays were performed on E. coli beta-galactosidase from three different sets of samples. The first set consisted of lysates of induced cells from five different strains of the bacteria, as well as two different commercial preparations of the enzyme. These samples were found to have substantially different distributions of single molecule activities. For the second set of samples, beta-galactosidase expression was induced for 1.5 hr, followed by further incubation where expression was repressed. Assays were performed on the lysates of the preinduction and on the lysates from aliquots taken set times postinduction. The recently induced enzyme had a 25% higher average single molecule activity than the basally expressed enzyme. This average activity returned to the basal value 3.5 hr postinduction and remained unchanged thereafter. Finally, beta-galactosidase was induced at 26 and 42 degrees C. The enzyme was assayed before and after partial thermal denaturation. The samples were found to be indistinguishable with respect to their average single molecule activities.
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Shoemaker GK, Juers DH, Coombs JML, Matthews BW, Craig DB. Crystallization of beta-galactosidase does not reduce the range of activity of individual molecules. Biochemistry 2003; 42:1707-10. [PMID: 12578385 DOI: 10.1021/bi0204138] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By use of a capillary electrophoresis-based procedure, it is possible to measure the activity of individual molecules of beta-galactosidase. Molecules from the crystallized enzyme as well as the original enzyme preparation used to grow the crystals both displayed a range of activity of 20-fold or greater. beta-Galactosidase molecules obtained from two different crystals had indistinguishable activity distributions of 31,600 +/- 1100 and 31,800 +/- 1100 reactions min(-1) (enzyme molecule)(-1). This activity was found to be significantly different from that of the enzyme used to grow the crystals, which showed an activity distribution of 38,500 +/- 900 reactions min(-1) (enzyme molecule)(-1).
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Dyck AC, Craig DB. Individual molecules of thermostable alkaline phosphatase support different catalytic rates at room temperature. LUMINESCENCE 2002; 17:15-8. [PMID: 11816058 DOI: 10.1002/bio.672] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermus thermophilus cells were grown at 70 degrees C, lysed and the lysate subjected to single molecule alkaline phosphatase assays, using a capillary electrophoresis laser-induced fluorescence detection-based method. The enzyme was found to be heterogeneous with respect to catalytic rate when assayed at room temperature. Turnover numbers ranged 12-fold, with an average of 400 +/- 200 reactions/min for the 80 molecules assayed.
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Tuominen EK, Zhu K, Wallace CJ, Clark-Lewis I, Craig DB, Rytomaa M, Kinnunen PK. ATP induces a conformational change in lipid-bound cytochrome c. J Biol Chem 2001; 276:19356-62. [PMID: 11279142 DOI: 10.1074/jbc.m100853200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Resonance energy transfer studies using a pyrene-labeled phospholipid derivative 1-palmitoyl-2-[10-(pyren-1-yl)decanoyl]-sn-glycero-3-phosphoglycerol (donor) and the heme (acceptor) of cytochrome c (cyt c) have indicated that ATP causes changes in the conformation of the lipid-bound protein (Rytömaa, M., Mustonen, P., and Kinnunen, P. K. J. (1992) J. Biol. Chem. 267, 22243-22248). Accordingly, after binding cyt c via its so called C-site to neat phosphatidylglycerol liposomes (mole fraction of PG = 1.0) has commenced, further quenching of donor fluorescence is caused by ATP, saturating at 2 mm nucleotide. ATP-induced conformational changes in liposome-associated cyt c could be directly demonstrated by CD in the Soret band region (380-460 nm). The latter data were further supported by time-resolved spectroscopy using the fluorescent cyt c analog with a Zn(2+)-substituted heme moiety. A high affinity ATP-binding site has been demonstrated in cyt c (Craig, D. B., and Wallace, C. J. A. (1993) Protein Sci. 2, 966-976) that is compromised by replacing the invariant Arg(91) to norleucine. Although no major effects on conformation and function of cyt c were concluded due to the modification, a significantly reduced effect by ATP on the lipid-bound [Nle(91)]cyt c was evident, implying that this modulation is mediated via the Arg(91)-containing binding site.
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Craig DB, Hall T, Goltz DM. Escherichia coli beta-galactosidase is heterogeneous with respect to a requirement for magnesium. Biometals 2000; 13:223-9. [PMID: 11127894 DOI: 10.1023/a:1009218512190] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Commercially obtained E. coli beta-galactosidase was stored at 25 degrees C in buffer containing 1 mM MgCl2 and in buffer containing no added MgCl2. Samples were removed at set times and the activity of individual enzyme molecules assayed. When stored in the presence of 1 mM magnesium, the number of active molecules did not change over a 2.5-h period. When stored in the absence of added MgCl2, over half the enzyme molecules became inactive within the first hour. However, those molecules which retained activity remained active for the duration of the experiment. This indicates that there may exist two populations of E. coli beta-galactosidase, one which requires storage in the presence of the higher concentration of Mg2+ in order to remain active. There was no observed correlation between this requirement for magnesium and reaction rate. Additionally, the presence of the 1 mM MgCl2 was found to decrease the average activity of the beta-galactosidase molecules under the conditions employed.
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Craig DB, Hall T. Newly induced beta-galactosidase molecules have a higher activity than the basally expressed enzyme. JOURNAL OF CLINICAL LASER MEDICINE & SURGERY 2000; 18:209-13. [PMID: 11573513 DOI: 10.1089/10445470050144065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The objective of this study was to compare the activities of individual molecules of induced and basally expressed Escherichia coli beta-galactosidase. BACKGROUND DATA Single-molecule assays of enzymes have determined that individual molecules are not identical. They differ with respect to catalytic rate. The structural cause and cellular role of this microheterogeneity is as yet unknown. METHODS E. coli were grown and induced to produce beta-galactosidase by treatment with isopropyl-beta-D-thiogalactopyranoside. Cells were lysed and the beta-galactosidase assayed with capillary electrophoresis instrumentation utilizing post-column, laser-induced fluorescence detection. The enzyme obtained from treated cells were compared to that from untreated cells. RESULTS The activity of newly induced beta-galactosidase was found to be approximately 20% greater than that of the basally expressed enzyme. This measured difference is statistically significant. CONCLUSIONS Production of beta-galactosidase in E. coli under differing conditions results in differences in the activities of the individual enzyme molecules.
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Abstract
A laser-induced fluorescence detector for liquid chromatography was developed. This detector was assessed by utilizing it in conjunction with gel filtration chromatography. Using the 488 nm line of an argon ion laser for excitation and monitoring the emitted fluorescence centering at 535 nm, the limit of detection of fluorescein was 580 fM. Bovine serum albumin labeled with fluorescein was detected at a concentration of 500 fM.
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Eggertson MJ, Craig DB. beta-galactosidase assay using capillary electrophoresis laser-induced fluorescence detection and resorufin-beta-D-galactopyranoside as substrate. Biomed Chromatogr 1999; 13:516-9. [PMID: 10611604 DOI: 10.1002/(sici)1099-0801(199912)13:8<516::aid-bmc918>3.0.co;2-u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
beta-Galactosidase was incubated for 60 min with the fluorogenic substrate resorufin-beta-D-galactopyranoside, which is converted by the action of the enzyme into resorufin and galactose. A 160 pL aliquot of reaction mixture was analyzed by capillary electrophoresis utilizing laser-induced fluorescence detection. Based on the detection of the resorufin formed, the limit of detection of beta-galactosidase was 1.5 x 10(-15) M or 900 molecules of enzyme in a 1 microL sample.
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Eggertson MJ, Craig DB. β-Galactosidase assay using capillary electrophoresis laser-induced fluorescence detection and resorufin-β-D-galactopyranoside as substrate. Biomed Chromatogr 1999. [DOI: 10.1002/(sici)1099-0801(199912)13:8%3c516::aid-bmc918%3e3.0.co;2-u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Byrick RJ, Craig DB. Consequences of inadequate Canadian physician resource planning. Can J Anaesth 1999; 46:913-8. [PMID: 10522575 DOI: 10.1007/bf03013123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Craig DB, Wong JC, Polakowski R, Dovichi NJ. General protease assay method coupling solid-phase substrate extraction and capillary electrophoresis. Anal Chem 1998; 70:3824-7. [PMID: 9751024 DOI: 10.1021/ac9801061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Capillary electrophoresis with laser-induced fluorescence detection was used to develop a universal, highly specific protease assay. In this method, a peptide, biotinylated at the N-terminus, is labeled with fluorescein at a lysine residue near the C-terminus. Impurities are removed from the fluorescence labeling mixture by solid-phase extraction of the substrate on immobilized streptavidin, followed by extensive washing. The purified fluorescent substrate is dissociated from the streptavidin and incubated with the protease. The peptide sequence between the biotin and fluorescent label contains the cleavage sequence of the protease of interest. After cleavage, the fluorescent product does not contain a biotin group. A second solid-phase extraction is used to remove unreacted substrate to dramatically lower the background signal. The product is detected by capillary electrophoresis, which provides powerful discrimination against products generated by nonspecific proteases. With chymotrypsin as a test protease, product was detected with as little as 10 pg/mL (4.6 x 10(-13) M) chymotrypsin, or 5 amol of enzyme in the 10-microL sample volume.
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Craig DB, Polakowski RM, Arriaga E, Wong JC, Ahmadzadeh H, Stathakis C, Dovichi NJ. Sodium dodecyl sulfate-capillary electrophoresis of proteins in a sieving matrix utilizing two-spectral channel laser-induced fluorescence detection. Electrophoresis 1998; 19:2175-8. [PMID: 9761200 DOI: 10.1002/elps.1150191222] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report a method for protein labeling, separation by capillary electrophoresis in a polymer sieving matrix, and detection by laser-induced fluorescence. Different dyes are used to label standard and sample proteins. A two-spectral channel detector resolves fluorescence from the sample and standards. Comparison of the migration time of the sample and standards permits the precise determination of molecular weight, irrespective of variations in run-to-run migration times.
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Craig DB, Martens DJ, Embil JM. Single dose medication vial packaging deficiencies. Can J Anaesth 1998; 45:501-8. [PMID: 9669001 DOI: 10.1007/bf03012698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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