Name: dna electrophoresis using thiazole orange instead of ethidium bromide or alternative dyes
Uploaded: 2019-03-31T13:00:00
Description: Watch this Scientific Journal Video about DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes at JoVE.com

This work was supported by startup funds to TDG from Christopher Newport University.&#160;

1. Preparing the gel
NOTE: For general gel electrophoresis protocols, see also P.Y. Lee, et al.14.&#160;
<ol>
	<li>Mix agarose (~1% w/v, percentage can be varied for particular size separations) in buffer (approximately 70 mL for a mini-gel (8 x&#160;7 cm)). Buffers are commonly TAE (tris-acetate-EDTA, 40 mM Tris, 20 mM acetate, 1 mM EDTA, pH approximately 8.6) or TBE (tris-borate-EDTA, 90 mM Tris, 90 mM borate, 2 mM EDTA, pH approximately 8.3)).</li>
	<li>Ad...

<ol>
	<li>O'Neil, C. S., Beach, J. L., Gruber, T. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thiazole+orange+as+an+everyday+replacement+for+ethidium+bromide+and+costly+DNA+dyes+for+electrophoresis.">Thiazole orange as an everyday replacement for ethidium bromide and costly DNA dyes for electrophoresis.</a> Electrophoresis. 39 (12), 1474-1477 (2018).</li><li>McCann, J., Choi, E., Yamasaki, E., Ames, B. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+carcinogens+as+mutagens+in+the+Salmonella/microsome+test:+assay+of+300+chemicals.">Detection of carcinogens as mutagens in the Salmonella/microsome test: assay of 300 chemicals.</a> Proceedings of the National Academy of Sciences of the United States of America. 72 (12), 5135-5139 (1975).</li><li>Evenson, W. E., Boden, L. M., Muzikar, K. A., O&#8217;Leary, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=1H+and+13C+NMR+Assignments+for+the+Cyanine+Dyes+SYBR+Safe+and+Thiazole+Orange.">1H and 13C NMR Assignments for the Cyanine Dyes SYBR Safe and Thiazole Orange.</a> The Journal of Organic Chemistry. 77 (23), 10967-10971 (2012).</li><li>Beaudet, M., Cox, G., Yue, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Molecular Probes, Inc. , (2005).</li><li>Pfeifer, G. P., You, Y. H., Besaratinia, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+induced+by+ultraviolet+light.">Mutations induced by ultraviolet light.</a> Mutation Research. 571 (1-2), 19-31 (2005).</li><li>Cariello, N. F., Keohavong, P., Sanderson, B. J., Thilly, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+damage+produced+by+ethidium+bromide+staining+and+exposure+to+ultraviolet+light.">DNA damage produced by ethidium bromide staining and exposure to ultraviolet light.</a> Nucleic Acids Research. 16 (9), 4157 (1988).</li><li>Hartman, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transillumination+can+profoundly+reduce+transformation+frequencies.">Transillumination can profoundly reduce transformation frequencies.</a> BioTechniques. 11 (6), 747-748 (1991).</li><li>Lee, L. G., Chen, C. H., Chiu, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thiazole+orange:+a+new+dye+for+reticulocyte+analysis.">Thiazole orange: a new dye for reticulocyte analysis.</a> Cytometry. 7 (6), 508-517 (1986).</li><li>Nygren, J., Svanvik, N., Kubista, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Interactions+Between+the+Fluorescent+Dye+Thiazole+Orange+and+DNA.">The Interactions Between the Fluorescent Dye Thiazole Orange and DNA.</a> Biopolymers. , 1-13 (1998).</li><li>Svanvik, N., Westman, G., Wang, D., Kubista, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Light-Up+Probes:+Thiazole+Orange-Conjugated+Peptide+Nucleic+Acid+for+Detection+of+Target+Nucleic+Acid+in+Homogeneous+Solution.">Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution.</a> Analytical Biochemistry. 281 (1), 26-35 (2000).</li><li>Yang, P., De Cian, A., Teulade-Fichou, M. P., Mergny, J. L., Monchaud, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+Bisquinolinium/Thiazole+Orange+Conjugates+for+Fluorescent+Sensing+of+G-Quadruplex+DNA.">Engineering Bisquinolinium/Thiazole Orange Conjugates for Fluorescent Sensing of G-Quadruplex DNA.</a> Angewandte Chemie International Edition. 48 (12), 2188-2191 (2009).</li><li>Fang, G. M., Chamiolo, J., Kankowski, S., Hovelmann, F., Friedrich, D., Lower, A., Meier, J. C., Seitz, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+bright+FIT-PNA+hybridization+probe+for+the+hybridization+state+specific+analysis+of+a+C+&#8594;+U+RNA+edit+via+FRET+in+a+binary+system.">A bright FIT-PNA hybridization probe for the hybridization state specific analysis of a C &#8594; U RNA edit via FRET in a binary system.</a> Chemical Science. 9 (21), 4794-4800 (2018).</li><li>Pei, R., Rothman, J., Xie, Y., Stojanovic, M. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Light-up+properties+of+complexes+between+thiazole+orange-small+molecule+conjugates+and+aptamers.">Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers.</a> Nucleic Acids Research. 37 (8), e59-e59 (2009).</li><li>Lee, P. Y., Costumbrado, J., Hsu, C. Y., Kim, Y. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agarose+Gel+Electrophoresis+for+the+Separation+of+DNA+Fragments.">Agarose Gel Electrophoresis for the Separation of DNA Fragments.</a> Journal of Visualized Experiments. (62), 1-5 (2012).</li><li>Vogelstein, B., Gillespie, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparative+and+analytical+purification+of+DNA+from+agarose.">Preparative and analytical purification of DNA from agarose.</a> Proceedings of the National Academy of Sciences of the United States of America. 76 (2), 615-619 (1979).</li></ol>

Ethidium bromide has long been a standard tool in the molecular biology lab, despite known toxicity. It also suffers from requiring UV light, which damages the DNA as it is being detected. Thiazole orange offers an inexpensive alternative to ethidium bromide, as well as useful but expensive commercial dyes.&#160;
The benefits of thiazole orange are thus two-fold. First, thiazole orange can simply be used as a replacement to ethidium bromide. Gels can be prepared identically to EtBr, with TO su...

The purpose of this method is to identify DNA in agarose gels using thiazole orange (TO) for fluorescence detection. Due to its low cost and favorable safety profile, thiazole orange may see particular benefit in undergraduate teaching labs and research labs performing molecular biology, especially ligations and cloning.
Ethidium bromide remains the most common dye for detection of DNA in agarose gels. This is primarily because it can be obtained very inexpensively and only requires excitation with UV light for detection. Both ethidium bromide and thiazole orange are inexpensive, with low detection limits (1-2 ng/lane)1. There are two main drawbacks to ethidium bromide, however, that thiazole orange improves upon.&#160;
First, ethidium bromide is a mutagen2 with special handling, shipping, and disposal requirements, whereas thiazole orange is less mutagenic (3&#8211;4x less mutagenic in Ames test)3,4 and can be generally disposed of with common chemical waste.
Second, ethidium bromide requires UV light for detection. Thiazole orange can similarly use UV light if desired, but can also be detected with blue light. UV light, while commonly used, has a few salient disadvantages. First, it is damaging to human skin and eyes. While UV light can be used safely by trained professionals, accidental skin or eye damage (functionally similar to sunburns) from laboratory UV light are not uncommon particularly with inexperienced scientists. Second, UV light is extremely damaging to DNA samples5, which reduces the success of downstream experiments (such as ligation and transformation)1,6,7. TO allows detection with blue light (&#955;ex,max = 510 nm (488 nm and 470 nm also show strong excitation)), which does not cause skin damage or DNA damage (although any intense light may still be harmful to eyes), greatly decreasing the risks to both the scientist and the sample.&#160;
TO is not the only fluorescent dye alternative to ethidium bromide; its advantage is cost. TO was discovered in the 1980s as a reticulocyte stain8, and has found utility in a number of DNA-based fluorescence experiments9,10,11,12,13. It is currently sold by multiple suppliers. TO is the parent compound of additional, more expensive, blue-light&#8211;detectable commercial dyes, and behaves similarly during electrophoresis, using UV or blue light for detection1. Furthermore, while other dyes are more sensitive to very low DNA concentrations than either EtBr or TO, for generic electrophoresis experiments, such dyes are prohibitively expensive in many contexts.&#160;

<table border="0" cellpadding="0" cellspacing="0" style="width:572px;" width="573">
	<tbody>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">2-log DNA ladder</td>
			<td style="width:71px;">New England Biolabs</td>
			<td style="width:119px;">N0469S</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Agarose (Genetic Analysis Grade)</td>
			<td style="width:71px;">Fisher</td>
			<td style="width:119px;">BP1356-100</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Blue-light flashlight</td>
			<td style="width:71px;">WAYLLSHINE (Amazon)</td>
			<td style="width:119px;">WAYLLSHINE Scalable Blue LED</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ChemiDoc MP</td>
			<td style="width:71px;">Biorad</td>
			<td style="width:119px;">1708280</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">DMSO</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">D8418</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ethidium bromide</td>
			<td style="width:71px;">Fisher</td>
			<td style="width:119px;">BP1302-10</td>
			<td>For comparison, not necessary for protocol</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Gel apparatus (Owl Easy Cast)</td>
			<td style="width:71px;">Thermo Scientific</td>
			<td style="width:119px;">B1A</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Qiagen Qiaquick Gel extraction kit</td>
			<td style="width:71px;">Qiagen</td>
			<td style="width:119px;">28704</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Safe Imager Viewing Glasses</td>
			<td style="width:71px;">Invitrogen</td>
			<td style="width:119px;">S37103</td>
			<td>Necessary for using blue light flashlight.*</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">SafeImager 2.0 (Blue light transilluminator)</td>
			<td style="width:71px;">Invitrogen</td>
			<td style="width:119px;">G6600</td>
			<td>Blue light flashlight may be used as alternative</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">SYBR Safe</td>
			<td style="width:71px;">Invitrogen</td>
			<td style="width:119px;">S33102</td>
			<td>For comparison, not necessary for protocol</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">TAE (Tris-Acetate-EDTA)</td>
			<td style="width:71px;">Corning</td>
			<td style="width:119px;">46-010-CM</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Thiazole orange</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">390062</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;"></td>
			<td style="width:71px;"></td>
			<td style="width:119px;"></td>
			<td>*Glasses are also included with Invitrogen G6600</td>
		</tr>
	</tbody>
</table>

dna electrophoresis using thiazole orange instead of ethidium bromide or alternative dyes

DNA gel electrophoresis using agarose is a common tool in molecular biology laboratories, allowing separation of DNA fragments by size. After separation, DNA is visualized by staining. This article demonstrates how to use thiazole orange to stain DNA. Thiazole orange compares favorably to common staining methods, in that it is sensitive, inexpensive, excitable with UV or blue light (to prevent sample damage), and safer than ethidium bromide. Labs already equipped to run DNA electrophoresis experiments using ethidium bromide can generally switch dyes with no additional changes to existing protocols, using UV light for detection. Blue-light detection to avoid sample damage can additionally be achieved with a blue-light source and emission filter. Labs already equipped for blue-light detection can simply switch dyes with no additional changes to existing protocols.

Thiazole orange enables detection of DNA, without using ethidium bromide and without using DNA-damaging UV light. Ethidium bromide is well-known to be mutagenic, so eliminating it from the lab may be advantageous. UV light damages DNA and lowers transformation efficiency significantly, whereas blue light does not damage DNA. Detection limits are similar between ethidium bromide, thiazole orange, and a common, blue-light&#8211;detectable commercial DNA dye (Figure 1, see Table of Mate...

Watch this Scientific Journal Video about DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes at JoVE.com

DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes

Here, we present a protocol to use thiazole orange for the detection of DNA in gel electrophoresis experiments. The use of thiazole orange allows elimination of ethidium bromide, and fluorescence detection can be achieved with either UV or blue light.

DNA gel electrophoresis using agarose is a common tool in molecular biology laboratories, allowing separation of DNA fragments by size. After separation, ...

This protocol is an easy and inexpensive alternative to using ethidium bromide for DNA detection during electrophoresis. By removing ethidium bromide, either UV light or blue light can be used for detection. Blue light is not damaging to DNA, which improves the chance of success for downstream experiments.It's really easy to try this out. You just have to replace the ethidium bromide in your gels with thiazole orange. To begin, prepare 1%mini-gels by mixing approximately 0.7 grams of agarose in 70 milliliters of tris-acetate-EDTA or tris-borate buffers.Next, dissolve thiazole orange in DMSO to make a 10, 000X stock solution. While not particularly light sensitive, store thiazole orange in the dark when not in use. For long-term storage, make aliquots of the thiazole orange-DMSO mixture and freeze them.Then, add thiazole orange to a final concentration of 1.3 micrograms per milliliter, and microwave the mixture of agarose buffer and thiazole orange to dissolve agarose for approximately 60 seconds. Pour the agarose mixture into a gel casting apparatus containing an appropriate comb, and allow the agarose solution to solidify into a gel. To load the gel, first place the gel in the electrophoresis apparatus, if not already present.Then add TAE or TBE running buffer to cover the surface of the gel. Next, using a loading dye, load 10 microliters of a DNA sample. Include a DNA sizing ladder for reference.Attach the cover and electrodes, and run the mini-gel at 100 volts until the loading dye travels approximately four to seven centimeters for a mini-gel. If thiazole orange was not applied prior to gel casting, stain the gel by immersing it in the buffer containing thiazole orange with gentle agitation for about 20 minutes or until the bands are fully detected. To visualize the gel using a UV transilluminator, remove the gel from the electrophoresis apparatus and place it on the UV transilluminator.To visualize the gel using a blue light transilluminator or a flashlight, place the gel on the blue light transilluminator or direct the blue LED flashlight at the gel from above or below. Use an amber emission filter to filter out the blue light, enabling visualization of fluorescence from DNA thiazole orange complexes and to protect dyes. For further digestion or ligation, cut out desired DNA bands from the gel and proceed to extracting DNA using a readily available kit or protocol.Select appropriate excitation and emission settings in the gel-imaging apparatus. In the absence of an imaging system with appropriate filters, place an amber filter between the camera and the gel blue-light excitation source. Detection limits are similar between ethidium bromide, thiazole orange, and a common blue-light-detectable commercial DNA dye, with the detection limit for all three dyes being one to two nanograms per lane in a mini-gel.Thiazole orange-stained agarose gel of a restriction digest is detectable when it is excited with a UV or a blue light transilluminator or with a blue light flashlight. While thiazole orange appears to be less hazardous than ethidium bromide, standard personal protective equipment such as gloves and goggles should still be worn.

dna-electrophoresis-using-thiazole-orange-instead-ethidium-bromide-or

Research

JoVE Journal

Biochemistry

Sheathless Capillary Electrophoresis&#8211;Mass Spectrometry for Metabolic Profiling of Biological Samples

In metabolomics, a wide range of analytical techniques is used for the global profiling of (endogenous) metabolites in complex samples. In this paper, a protocol is presented for the analysis of anionic and cationic metabolites in biological samples by capillary electrophoresis&#8211;mass spectrometry (CE-MS). CE is well-suited for the analysis of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. A recently developed sheathless interfacing design, i.e., a porous tip interface, is used for coupling CE to electrospray ionization (ESI) MS. This interfacing approach allows the effective use of the intrinsically low-flow property of CE in combination with MS, resulting in nanomolar detection limits for a broad range of polar metabolite classes. The protocol presented here is based on employing a bare fused-silica capillary with a porous tip emitter at low-pH separation conditions for the analysis of a broad array of metabolite classes in biological samples. It is demonstrated that the same sheathless CE-MS method can be used for the profiling of cationic metabolites, including amino acids, nucleosides and small peptides, or anionic metabolites, including sugar phosphates, nucleotides and organic acids, by only switching the MS detection and separation voltage polarity. Highly information-rich metabolic profiles in various biological samples, such as urine, cerebrospinal fluid and extracts of the glioblastoma cell line, can be obtained by this protocol in less than 1 hr of CE-MS analysis.

Sheathless Capillary Electrophoresis&amp;#8211;Mass Spectrometry for Metabolic Profiling of Biological Samples

A protocol for metabolic profiling of biological samples by capillary electrophoresis&#8211;mass spectrometry using a sheathless porous tip interface design is presented.

In metabolomics, a wide range of analytical techniques is used for the global profiling of (endogenous) metabolites in complex samples. In this paper, a ...

Characterization of Multi-subunit Protein Complexes of Human MxA Using Non-denaturing Polyacrylamide Gel-electrophoresis

The formation of oligomeric complexes is a crucial prerequisite for the proper structure and function of many proteins. The interferon-induced antiviral effector protein MxA exerts a broad antiviral activity against many viruses. MxA is a dynamin-like GTPase and has the capacity to form oligomeric structures of higher order. However, whether oligomerization of MxA is required for its antiviral activity is an issue of debate. We describe here a simple protocol to assess the oligomeric state of endogenously or ectopically expressed MxA in the cytoplasmic fraction of human cell lines by non-denaturing polyacrylamide gel electrophoresis (PAGE) in combination with Western blot analysis. A critical step of the protocol is the choice of detergents to prevent aggregation and/or precipitation of proteins particularly associated with cellular membranes such as MxA, without interfering with its enzymatic activity. Another crucial aspect of the protocol is the irreversible protection of the free thiol groups of cysteine residues by iodoacetamide to prevent artificial interactions of the protein. This protocol is suitable for a simple assessment of the oligomeric state of MxA and furthermore allows a direct correlation of the antiviral activity of MxA interface mutants with their respective oligomeric states.

This article describes a simple and rapid protocol to evaluate the oligomeric state of the dynamin-like GTPase MxA protein from lysates of human cells using a combination of non-denaturing PAGE with western blot analysis.

The formation of oligomeric complexes is a crucial prerequisite for the proper structure and function of many proteins. The interferon-induced antiviral ...

Capillary Electrophoresis Separation of Monoclonal Antibody Isoforms Using a Neutral Capillary

Biotherapeutic proteins, such as monoclonal antibodies (mAbs), are feasible alternatives for the treatment of chronic-degenerative diseases. The biological activity of these proteins depends on their physicochemical properties. The use of high-performance techniques like chromatography and capillary electrophoresis has been described for the analysis of physicochemical heterogeneity of mAbs. Nowadays, capillary zone electrophoresis (CZE) technique constitutes one of the most resolutive and sensitive assays for the analysis of biomolecules. Besides, the electro-driven separation in CZE is governed by extensive properties of matter and offers the advantage of analyzing proteins close to their native state. However, the successful implementation of this technique for routine analysis depends on the skills of the analyst at the critical steps during sample and system preparation. The purpose of this tutorial is to detail the steps to succeed in the CZE analysis of mAbs. Further, this protocol can be used for the development and improvement of skills of the personnel involved in protein analytical chemistry laboratories.

Here, we present a comprehensive capillary zone electrophoresis protocol for the assessment of intrinsic physicochemical heterogeneity of monoclonal antibodies as a quality attribute.

Biotherapeutic proteins, such as monoclonal antibodies (mAbs), are feasible alternatives for the treatment of chronic-degenerative diseases. The ...

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes

Native polyacrylamide gel electrophoresis is a fundamental tool of molecular biology that has been used extensively for the biochemical analysis of RNA-protein interactions. These interactions have been traditionally analyzed with polyacrylamide gels generated between two glass plates and samples electrophoresed vertically. However, polyacrylamide gels cast in trays and electrophoresed horizontally offers several advantages. For example, horizontal gels used to analyze complexes between fluorescent RNA substrates and specific proteins can be imaged multiple times as electrophoresis progresses. This provides the unique opportunity to monitor RNA-protein complexes at several points during the experiment. In addition, horizontal gel electrophoresis makes it possible to analyze many samples in parallel. This can greatly facilitate time course experiments as well as analyzing multiple reactions simultaneously to compare different components and conditions. Here we provide a detailed protocol for generating and using horizontal native gel electrophoresis for analyzing RNA-Protein interactions.

Native polyacrylamide gel electrophoresis is a fundamental tool for analyzing RNA-protein interactions. Traditionally most experiments have used vertical gels. However, horizontal gels provide several advantages, such as the opportunity to monitor complexes during electrophoresis. We provide a detailed protocol for generating and using horizontal native gel electrophoresis.

Native polyacrylamide gel electrophoresis is a fundamental tool of molecular biology that has been used extensively for the biochemical analysis of ...

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis can be characterized using an in vitro DNA synthesis assay followed by polyacrylamide gel electrophoresis. The goal of this assay is to quantify synthesis of both natural DNA and modified DNA (M-DNA). These approaches are particularly useful for resolving oligonucleotides with single nucleotide resolution, enabling observation of individual steps during enzymatic oligonucleotide synthesis. These methods have been applied to the evaluation of an array of biochemical and biophysical properties such as the measurement of steady-state rate constants of individual steps of DNA synthesis, the error rate of DNA synthesis, and DNA binding affinity. By using modified components including, but not limited to, modified nucleoside triphosphates (NTP), M-DNA, and/or mutant DNA polymerases, the relative utility of substrate-DNA polymerase pairs can be effectively evaluated. Here, we detail the assay itself, including the changes that must be made to accommodate nontraditional primer DNA labeling strategies such as near-infrared fluorescently labeled DNA. Additionally, we have detailed crucial technical steps for acrylamide gel pouring and running, which can often be technically challenging.

This protocol describes the characterization of DNA polymerase synthesis of modified DNA through observation of changes to near-infrared fluorescently labeled DNA using gel electrophoresis and gel imaging. Acrylamide gels are used for high resolution imaging of the separation of short nucleic acids, which migrate at different rates depending on size.

For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis ...

An Alternative Culture Method to Maintain Genomic Hypomethylation of Mouse Embryonic Stem Cells Using MEK Inhibitor PD0325901 and Vitamin C

Embryonic stem (ES) cells have the potential to differentiate into any of the three germ layers (endoderm, mesoderm, or ectoderm), and can generate many lineages for regenerative medicine. ES cell culture in vitro has long been the subject of widespread concerns. Classically, mouse ES cells are maintained in serum and leukemia inhibitory factor (LIF)-containing medium. However, under serum/LIF conditions, cells show heterogeneity in morphology and the expression profile of pluripotency-related genes, and are mostly in a metastable state. Moreover, cultured ES cells exhibit global hypermethylation, but na&#239;ve ES cells of the inner cell mass (ICM) and primordial germ cells (PGCs) are in a state of global hypomethylation. The hypomethylated state of ICM and PGCs is closely associated with their pluripotency. To improve mouse ES cell culture methods, we have recently developed a new method based on the selectively combined utilization of two small-molecule compounds to maintain the DNA hypomethylated and pluripotent state. Here, we present that the co-treatment of vitamin C (Vc) and PD0325901 can erase about 90% of 5-methylcytosine (5mC) at 5 days in mouse ES cells. The generated 5mC content is comparable to that in PGCs. The mechanistic investigation shows that PD0325901 up-regulates Prdm14 expression to suppress Dnmt3b (de novo DNA methyltransferase) and Dnmt3l (the cofactor of Dnmt3b), by reducing de novo 5mC synthesis. Vc facilitates the conversion of 5mC to 5-hydroxymethylcytosine (5hmC) catalyzed mainly by Tet1 and Tet2, indicating the involvement of both passive and active DNA demethylations. Moreover, under Vc/PD0325901 conditions, mouse ES cells show homogeneous morphology and pluripotent state. Collectively, we propose a novel and chemical-synergy culture method for achieving DNA hypomethylation and maintenance of pluripotency in mouse ES cells. The small-molecule chemical-dependent method overcomes the major shortcomings of serum culture, and holds promise to generate homogeneous ES cells for further clinical applications and researches.

We described in detail two chemical-based protocols for culturing mouse embryonic stem cells. This new method utilizes synergistic mechanisms of promoting Tet-mediated oxidation (by vitamin C) and repressing de novo synthesis of 5-methylcytosine (by PD0325901) to maintain DNA hypomethylation and pluripotency of mouse embryonic stem cells.

Embryonic stem (ES) cells have the potential to differentiate into any of the three germ layers (endoderm, mesoderm, or ectoderm), and can generate many ...

Use of Two Dimensional Semi-denaturing Detergent Agarose Gel Electrophoresis to Confirm Size Heterogeneity of Amyloid or Amyloid-like Fibers

Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. The ability to readily detect the formation of these fibers under various experimental conditions is essential for understanding their potential function. Many methods have been used to detect the fibers, but not without some drawbacks. For example, electron microscopy (EM), or staining with Congo Red or Thioflavin T often requires purification of the fibers. On the other hand, semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) allows detection of the SDS-resistant amyloid-like fibers in the cell extracts without purification. In addition, it allows the comparison of the size difference of the fibers. More importantly, it can be used to identify specific proteins within the fibers by Western blotting. It is less time consuming and more easily accessible to a wider number of labs. SDD-AGE results often show variable degree of heterogeneity. It raises the question whether part of the heterogeneity results from the dissociation of the protein complex during the electrophoresis in the presence of SDS. For this reason, we have employed a second dimension of SDD-AGE to determine if the size heterogeneity seen in SDD-AGE is truly a result of fiber heterogeneity in vivo and not a result of either degradation or dissociation of some of the proteins during electrophoresis. This method allows fast, qualitative confirmation that the amyloid or amyloid-like fibers are not partially dissociating during the SDD-AGE process.

Here we use two-dimensional semi-denaturing agarose gel electrophoresis to confirm the presence of amyloid-like fibers of heterogeneous size and exclude the possibility that the size heterogeneity is due to dissociation of the amyloid fibers during the gel running process.

Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. ...

Analysis of AtHIRD11 Intrinsic Disorder and Binding Towards Metal Ions by Capillary Gel Electrophoresis and Affinity Capillary Electrophoresis

Plants are strongly dependent on their environment. In order to adjust to stressful changes (e.g., drought and high salinity), higher plants evolve classes of intrinsically disordered proteins (IDPs) to reduce oxidative and osmotic stress. This article uses a combination of capillary gel electrophoresis (CGE) and mobility shift affinity electrophoresis (ACE) in order to describe the binding behavior of different conformers of the IDP AtHIRD11 from Arabidopsis thaliana. CGE is used to confirm the purity of AtHIRD11 and to exclude fragments, posttranslational modifications, and other impurities as reasons for complex peak patterns. In this part of the experiment, the different sample components are separated by a viscous gel inside a capillary by their different masses and detected with a diode array detector. Afterward, the binding behavior of the sample towards various metal ions is investigated by ACE. In this case, the ligand is added to the buffer solution and the shift in migration time is measured in order to determine whether a binding event has occurred or not. One of the advantages of using the combination of CGE and ACE to determine the binding behavior of an IDP is the possibility to automate the gel electrophoresis and the binding assay. Furthermore, CGE shows a lower limit of detection than the classical gel electrophoresis and ACE is able to determine the manner of binding a ligand in a fast manner. In addition, ACE can also be applied to other charged species than metal ions. However, the use of this method for binding experiments is limited in its ability to determine the number of binding sites. Nevertheless, the combination of CGE and ACE can be adapted for characterizing the binding behavior of any protein sample towards numerous charged ligands.

This protocol combines the characterization of a protein sample by capillary gel electrophoresis and a fast-binding screening for charged ligands by affinity capillary electrophoresis. It is recommended for proteins with a flexible structure, such as intrinsically disordered proteins, to determine any differences in binding for different conformers.

Plants are strongly dependent on their environment. In order to adjust to stressful changes (e.g., drought and high salinity), higher plants evolve ...

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. The binding of prokaryotic DnaG-like primases to DNA occurs at a specific trinucleotide recognition sequence. It is a pivotal step in the formation of Okazaki fragments. Conventional biochemical tools that are used to determine the DNA recognition sequence of DNA primase provide only limited information. Using a high-throughput microarray-based binding assay and consecutive biochemical analyses, it has been shown that 1) the specific binding context (flanking sequences of the recognition site) influences the binding strength of the DNA primase to its template DNA, and 2) stronger binding of primase to the DNA yields longer RNA primers, indicating higher processivity of the enzyme. This method combines PBM and primase activity assay and is designated as high-throughput primase profiling (HTPP), and it allows characterization of specific sequence recognition by DNA primase in unprecedented time and scalability.&#160;

Protein binding microarray (PBM) experiments combined with biochemical assays link the binding and catalytic properties of DNA primase, an enzyme that synthesizes RNA primers on template DNA. This method, designated as high-throughput primase profiling (HTPP), can be used to reveal DNA-binding patterns of a variety of enzymes.

DNA primase synthesizes short RNA primers that initiate DNA synthesis of Okazaki fragments on the lagging strand by DNA polymerase during DNA replication. ...

Absolute Quantitation of Inositol Pyrophosphates by Capillary Electrophoresis Electrospray Ionization Mass Spectrometry

Inositol pyrophosphates (PP-InsPs) are an important group of intracellular signaling molecules. Derived from inositol phosphates (InsPs), these molecules feature the presence of at least one energetic pyrophosphate moiety on the myo-inositol ring. They exist ubiquitously in eukaryotes and operate as metabolic messengers surveying phosphate homeostasis, insulin sensitivity, and cellular energy charge. Owing to the absence of a chromophore in these metabolites, a very high charge density, and low abundance, their analysis requires radioactive tracer, and thus it is convoluted and expensive. Here, the study presents a detailed protocol to perform absolute and high throughput quantitation of inositol pyrophosphates from mammalian cells by capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS). This method enables the sensitive profiling of all biologically relevant PP-InsPs species in mammalian cells, enabling baseline separation of regioisomers. Absolute cellular concentrations of PP-InsPs, including minor isomers, and monitoring of their temporal changes in HCT116 cells under several experimental conditions are presented.

A procedure for capillary electrophoresis electrospray ionization mass spectrometry for the absolute quantitation of inositol pyrophosphates from mammalian cell extracts is described.

Inositol pyrophosphates (PP-InsPs) are an important group of intracellular signaling molecules. Derived from inositol phosphates (InsPs), these molecules ...