We gratefully thank T. Ragucci, B. Watkins, S. Wong, and B. Wallek at Lynntech, Inc. for technical assistance and many helpful discussions. This work was supported by the US National Science Foundation (NSF) under grant CBET-0933688.

1. Basic Design of the Convective Thermocycler
<ol>
<li>We have constructed a simple convective thermocycling device consisting of interchangeable plastic reaction chamber "cartridges" that are sandwiched between two aluminum plates whose temperatures are independently controlled7 (Figure 2).</li>
<li>Cylindrical reactor wells are embedded by machining arrays of holes in polycarbonate blocks, with different combinations of hole diameter and plastic sheet thickness employed to achieve the desired aspect ratios (height/diameter = h/d). Two different reactor geometries are considered in the results presented here: h/d = 9: h = 15.9 mm, d = 1.75 mm, 38.2 &mu;L volume; h/d = 3: h = 6.02 mm, d = 1.98 mm, 18.5 &mu;L volume.</li>
<li>The bottom surface of the reactor is heated using an aluminum block containing cartridge heaters interfaced with a microprocesser driven temperature controller.</li>
<li>The temperature at the reactor's upper surface is regulated using an aluminum block connected to a recirculating water bath.</li>
<li>The entire assembly is clamped together using nylon screws to limit thermal conduction between the opposing aluminum blocks.</li>
</ol>
2. Preparation and Loading of the PCR Reaction Mixture
<ol>
<li>A typical 100 &mu;L reaction mixture contains 10 &mu;L of 10x buffer solution, 6 &mu;L of 25 mM MgCl2, 10 &mu;L of dNTPs (2 mM each), 41.2 &mu;L of DI water, 10 &mu;L of &beta;-actin probe, 10 &mu;L of &beta;-actin forward primer, 10 &mu;L of &beta;-actin reverse primer, 2 &mu;L of human genomic template DNA (10 ng/&mu;L) and 0.8 &mu;L of KOD DNA polymerase (2.5 units/ &mu;L).</li>
<li>Before loading reagents, seal the bottom surface of the PCR chamber using a thin sheet of aluminum tape.</li>
<li>Rinse the reactor wells with a 10 mg/mL aqueous solution of bovine serum albumin followed by Rain-X Anti-Fog.</li>
<li>Pipette reagents into the reactor wells using long gel-loading pipette tips and seal the upper surface with FEP Teflon tape.</li>
</ol>
3. Running the Reaction in the Convective Thermocycler
<ol>
<li>Before beginning the reaction, preheat both aluminum blocks to the desired upper and lower surface temperatures.</li>
<li>Sandwich the plastic reactor loaded with PCR reagents between the aluminum heating blocks, and quickly clamp the assembly together using nylon screws.</li>
<li>After the reaction has proceeded for the desired time, switch off the heaters and place the lower (hot) surface of the device on top of a chilled metal block to rapidly cool it and stop the convective flow.</li>
<li>Remove the plastic reactor and pipette the products out of the wells (using the long gel loading tips) for subsequent analysis.</li>
</ol>
4. Performing Gel Electrophoresis Analysis
<ol>
<li>Prepare a 2 wt% agarose gel by heating 10 g of agarose with 500 mL of 1x buffer on a stirring hot plate until the solution becomes clear.</li>
<li>Load the agarose gel into the casting tray and insert the comb. Let the gel set for ~ 30 min.</li>
<li>Remove the comb and add 1x TAE buffer until the gel is submerged.</li>
<li>Fluorescently stained DNA samples contain 2 &mu;L 100x SYBR Green I solution, 2 &mu;L DNA sample, 2 &mu;L 6x Orange Loading Dye, and 4 &mu;L TAE buffer.</li>
<li>Add the DNA samples into the wells and run the separation at 60 V for 1 h with a 100 bp DNA ladder sizing marker.</li>
<li>Remove the gel and photograph it under UV light to obtain the result.</li>
</ol>
5. Representative Results:
Optimal design of convective thermocyclers involves choosing the correct reactor geometry that will generate a circulatory flow capable of transporting reagents through the key temperatures involved in the PCR process. The geometric parameters that can be varied in the cylindrical reactors considered here are the height (h) and diameter (d), or equivalently the aspect ratio (h/d). We have explored the 3-D flow fields inside convective PCR reactors over a range of different aspect ratios using computational fluid dynamics (CFD), and found that unexpectedly complex patterns can arise. More importantly, our analysis has uncovered a subset of these complex flow fields that significantly accelerate the reaction12.
These geometric effects can be clearly seen by comparing the flow fields in reactors at high and low aspect ratios. In the high aspect ratio case (h/d = 9; a tall, skinny cylinder), fluid elements are advected along trajectories tracing out paths that are essentially closed loops, and they are locked-in to follow the same paths for long periods of time (Figure 3a). Consequently, there is little opportunity for exchange between flow trajectories that expose reagents to the optimal sequence of thermal conditions for PCR (oscillating between the annealing and denaturing extremes at the reactor's top and bottom surfaces) and the much larger ensemble of remaining trajectories that do not contribute to amplification (localized closer to the center of the reactor). 
The flow field is much different at a smaller aspect ratio (h/d = 3; a shorter, wider cylinder), becoming more chaotic in the sense that the fluid element trajectories no longer follow closed paths (Figure 3b). Thus, even though reagents are subjected to a more complex temperature profile, fluid elements are able to explore a much wider range of trajectories so that more of the reagent volume has an opportunity to experience optimal thermal profiles. These results counterintuitively suggest that while individual flow trajectories at h/d = 9 may appear to be more favorable for PCR by producing temperature profiles that "look" similar to those employed in a conventional thermocycler, the chaotic nature of the flow field at h/d = 3 ultimately dominates on a global scale by promoting enhanced exchange so that reagents do not become trapped in unfavorable trajectories for very long.
To test this hypothesis and determine which reactor geometry was more favorable for PCR, we used both of them to perform PCR replication of a 295 bp target associated with the &beta;-actin gene from a human genomic DNA template. Remarkably, we routinely achieved amplification of the correct target product in only 10 min at h/d = 3 (Figure 4a), while the same reaction required at least 20 min before detectable products were observed at h/d = 9 (Figure 4b). The reaction specificity is also much greater at h/d = 3 where a single PCR product is obtained, while multiple nonspecific products are generated at h/d = 9 where the flow field traps fluid elements in unfavorable thermal trajectories for extended periods of time.

 <img src="/files/ftp_upload/2366/2366fig1.jpg" alt="Figure 1" /> 
Figure 1. Thermal convection in a cylindrical chamber whose top and bottom surfaces are maintained at different fixed temperatures. If the temperature at the bottom surface is higher than at the top, a vertical density gradient is established within the enclosed fluid that is capable of generating a circulatory flow pattern. With the right choice of geometric parameters (height h and diameter d), the convective flow field can be harnessed to actuate PCR thermocycling when the top and bottom surfaces are manintained near annealing and denaturing temperatures, respectively (gravity acts vertically downward).
 <img src="/files/ftp_upload/2366/2366fig2.jpg" alt="Figure 2" /> 
Figure 2. (a) Key components of a convective flow PCR thermocyler. A reactor cartridge consists of a polycarbonate block containing an array of cylindrical chambers. The block is sandwiched between a top plate designed to be connected to a circulating water bath and a bottom plate incorporating embedded heaters. (b) The PCR reagents are loaded and sealed inside the reactor cartridge, after which the device is assembled to perform the reaction. Upon completion, the procucts can be easily pipetted out for subsequent analysis.
 <img src="/files/ftp_upload/2366/2366fig3.jpg" alt="Figure 3" /> 
Figure 3. Computational simulations of 3-D convective flow fields generated inside cylindrical reactors with temperatures of 53 and 96 &deg;C imposed at the top and bottom surfaces, respectively. Results are shown at aspect ratios of (a) h/d = 9 (38.2 &mu;L reactor volume) and (b) h/d = 3 (18.5 &mu;L reactor volume). A representative trajectory followed by a fluid element traveling through the 3D flow field is shown at the left along with top- and side view projections of the path; the corresponding plot of temperature versus time following a fluid element is shown at the right. The thermal profile at h/d = 9 appears close to that of a conventional thermocycler, but the chaotic flow field at h/d = 3 is counterintuitively more favorable for PCR.
 <img src="/files/ftp_upload/2366/2366fig4.jpg" alt="Figure 4" /> 
Figure 4. DNA replication results obtained in the reactor geometries shown in Figure 3 (upper and lower surfaces were maintained at 53 and 96 &deg;C, respectively). (a) PCR is greatly accelerated at h/d = 3, as evident by strong products visible after only 10 min of reaction time (M: 100 bp ladder, lanes 1-4: products from parallel reactions in 4 different cylindrical chambers). (b) The same reaction performed at h/d = 9 requires at least 20 min before visible products are observed, and multiple bands are evident indicating replication of non-specific target DNA in addition to the desired product (M: 100 bp ladder, lanes 1-2: products from parallel reactions in 2 different cylindrical chambers).

<ol>
	<li>Spitzack, K. D., Ugaz, V. M., Minteer, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidic+Techniques:+Reviews+and+Protocols.">Microfluidic Techniques: Reviews and Protocols.</a> Methods in Molecular Biology. , (2005).</li><li>Krishnan, M., Ugaz, V. M., Burns, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PCR+in+a+Rayleigh-B&#233;nard+convection+cell.">PCR in a Rayleigh-B&#233;nard convection cell.</a> Science. 298, 793-793 (2002).</li><li>Braun, D., Goddard, N. L., Libchaber, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exponential+DNA+replication+by+laminar+convection.">Exponential DNA replication by laminar convection.</a> Physical Review Letters. 91, 158103-158103 (2003).</li><li>Chen, Z., Qian, S., Abrams, W. R., Malamud, D., Bau, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermosiphon-based+PCR+reactor:+experiment+and+modeling.">Thermosiphon-based PCR reactor: experiment and modeling.</a> Analytical Chemistry. 76, 3707-3715 (2004).</li><li>Wheeler, E. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Convectively+driven+polymerase+chain+reaction+thermal+cycler.">Convectively driven polymerase chain reaction thermal cycler.</a> Analytical Chemistry. 76, 4011-4016 (2004).</li><li>Krishnan, M., Agrawal, N., Burns, M. A., Ugaz, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactions+and+fluidics+in+miniaturized+natural+convection+systems.">Reactions and fluidics in miniaturized natural convection systems.</a> Analytical Chemistry. 76, 6254-6265 (2004).</li><li>Ugaz, V. M., Krishnan, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+convective+flow+based+approaches+for+high-throughput+PCR+thermocycling.">Novel convective flow based approaches for high-throughput PCR thermocycling.</a> Journal of the Association for Laboratory Automation (JALA). 9, 318-323 (2004).</li><li>Yao, D. J., Chen, J. R., Ju, W. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micro-Rayleigh-Benard+convection+polymerase+chain+reaction+system.">Micro-Rayleigh-Benard convection polymerase chain reaction system.</a> Journal of Micro-Nanolithography MEMS and MOEMS. 6, 043007-043007 (2007).</li><li>Agrawal, N., Hassan, Y. A., Ugaz, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Pocket-sized+Convective+PCR+Thermocycler.">A Pocket-sized Convective PCR Thermocycler.</a> Angewandte Chemie International Edition. 46, 4316-4319 (2007).</li><li>Yariv, E., Ben-Dov, G., Dorfman, K. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polymerase+chain+reaction+in+natural+convection+systems:+A+convection-diffusion-reaction+model.">Polymerase chain reaction in natural convection systems: A convection-diffusion-reaction model.</a> Europhysics Letters. 71, 1008-1014 (2005).</li><li>Allen, J. W., Kenward, M., Dorfman, K. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coupled+flow+and+reaction+during+natural+convection+PCR.">Coupled flow and reaction during natural convection PCR.</a> Microfluidics and Nanofluidics. 6, 121-130 (2009).</li><li>Muddu, R., Hassan, Y. A., Ugaz, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accelerated+Biochemistry+by+Chaotic+Stirring.">Accelerated Biochemistry by Chaotic Stirring.</a> , (2010).</li></ol>

No conflicts of interest declared.

The interplay between flow and chemical reaction can change dramatically under the influence of chaotic advection. But these complex flow states are challenging to study, particularly in realistic geometries where 3D effects become important. Rayleigh-B&eacute;nard convection at h/d &gt; 1 not only provides a convenient platform to explore these phenomena, their application to perform PCR also enables the coupling between flow and chemical reactions to be probed. This unique capability makes it possible to select optimal flow states where chaotic effects act (counterintuitively) to accelerate the rate of DNA replication.

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>KOD DNA Polymerase kit</td>
<td>&nbsp;</td>
<td>Novagen</td>
<td>71085-3</td>
<td>&nbsp;</td>
<tr>
<td>TaqMan &beta;-actin Control Reagents kit</td>
<td>&nbsp;</td>
<td>Applied Biosystems</td>
<td>401846</td>
<td>&nbsp;</td>
<tr>
<td>Aluminum tape</td>
<td>&nbsp;</td>
<td>Axygen, Inc.</td>
<td>PCR-AS-200</td>
<td>&nbsp;</td>
<tr>
<td>Bovine serum albumin</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>A2153</td>
<td>&nbsp;</td>
<tr>
<td>Rain-X Anti-Fog</td>
<td>&nbsp;</td>
<td>SOPUS Products</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Long Gel-loading Pipette Tips</td>
<td>&nbsp;</td>
<td>Fisher Scientific</td>
<td>05-408-151</td>
<td>&nbsp;</td>
<tr>
<td>FEP Teflon tape</td>
<td>&nbsp;</td>
<td>McMaster-Carr</td>
<td>7562A17</td>
<td>&nbsp;</td>
<tr>
<td>Agarose gel</td>
<td>&nbsp;</td>
<td>Bio-Rad</td>
<td>161-3107</td>
<td>&nbsp;</td>
<tr>
<td>TAE running buffer</td>
<td>&nbsp;</td>
<td>Bio-Rad</td>
<td>141-0743</td>
<td>&nbsp;</td>
<tr>
<td>SYBR Green I</td>
<td>&nbsp;</td>
<td>Invitrogen/Molecular Probes</td>
<td>S7563</td>
<td>&nbsp;</td>
<tr>
<td>6x Orange Loading Dye</td>
<td>&nbsp;</td>
<td>Fermentas</td>
<td>R0631</td>
<td>&nbsp;</td>
<tr>
<td>100 bp DNA ladder sizing marker</td>
<td>&nbsp;</td>
<td>Bio-Rad</td>
<td>170-8202</td>
<td>&nbsp;</td>		</tbody>
		</table>
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rapid pcr thermocycling using microscale thermal convection

Many molecular biology assays depend in some way on the polymerase chain reaction (PCR) to amplify an initially dilute target DNA sample to a detectable concentration level. But the design of conventional PCR thermocycling hardware, predominantly based on massive metal heating blocks whose temperature is regulated by thermoelectric heaters, severely limits the achievable reaction speed1. Considerable electrical power is also required to repeatedly heat and cool the reagent mixture, limiting the ability to deploy these instruments in a portable format.
Thermal convection has emerged as a promising alternative thermocycling approach that has the potential to overcome these limitations2-9. Convective flows are an everyday occurrence in a diverse array of settings ranging from the Earth's atmosphere, oceans, and interior, to decorative and colorful lava lamps. Fluid motion is initiated in the same way in each case: a buoyancy driven instability arises when a confined volume of fluid is subjected to a spatial temperature gradient. These same phenomena offer an attractive way to perform PCR thermocycling. By applying a static temperature gradient across an appropriately designed reactor geometry, a continuous circulatory flow can be established that will repeatedly transport PCR reagents through temperature zones associated with the denaturing, annealing, and extension stages of the reaction (Figure 1). Thermocycling can therefore be actuated in a pseudo-isothermal manner by simply holding two opposing surfaces at fixed temperatures, completely eliminating the need to repeatedly heat and cool the instrument.
One of the main challenges facing design of convective thermocyclers is the need to precisely control the spatial velocity and temperature distributions within the reactor to ensure that the reagents sequentially occupy the correct temperature zones for a sufficient period of time10,11. Here we describe results of our efforts to probe the full 3-D velocity and temperature distributions in microscale convective thermocyclers12. Unexpectedly, we have discovered a subset of complex flow trajectories that are highly favorable for PCR due to a synergistic combination of (1) continuous exchange among flow paths that provides an enhanced opportunity for reagents to sample the full range of optimal temperature profiles, and (2) increased time spent within the extension temperature zone the rate limiting step of PCR. Extremely rapid DNA amplification times (under 10 min) are achievable in reactors designed to generate these flows.

Watch this Scientific Journal Video about Rapid PCR Thermocycling using Microscale Thermal Convection at JoVE.com

Rapid PCR Thermocycling using Microscale Thermal Convection

We describe a novel method to perform DNA replication via the polymerase chain reaction (PCR). Thermal convection is harnessed to continuously shuttle reagents between denaturing, annealing, and extension conditions by maintaining opposing surfaces of the reactor at constant temperature. This inherently simple design promises to make rapid PCR more accessible.

Many molecular biology assays depend in some way on the polymerase chain reaction (PCR) to amplify an initially dilute target DNA sample to a detectable ...

rapid-pcr-thermocycling-using-microscale-thermal-convection

Research

JoVE Journal

Biology

22.6K Views.  Texas A&M University. אנו מתארים שיטה חדשה לבצע שכפול הדנ"א באמצעות תגובת שרשרת פולימרז (PCR). הסעה תרמית היא רתומה ריאגנטים מעבורת ברציפות בין denaturing, חישול, ותנאי הרחבה על ידי שמירה על משטחים מנוגדים של הכור בטמפרטורה קבועה. זהו עיצוב פשוט מטבעו מבטיח לעשות PCR מהיר יותר נגיש.

Video: Rapid PCR Thermocycling using Microscale Thermal Convection

Rapid Genotyping of Mouse Tissue Using Sigma's Extract-N-Amp Tissue PCR Kit

Genomic detection of DNA via PCR amplification and detection on an electrophoretic gel is a standard way that the genotype of a tissue sample is determined. Conventional preparation of tissues for PCR-ready DNA often take several hours to days, depending on the tissue sample. The genotype of the sample may thus be delayed for several days, which is not an option for many different types of experiments. Here we demonstrate the complete genotyping of a mouse tail sample, including tissue digestion and PCR readout, in one and a half hours using Sigma's SYBR Green Extract-N-Amp Tissue PCR Kit. First, we demonstrate the fifteen-minute extraction of DNA from the tissue sample. Then, we demonstrate the real time read-out of the PCR amplification of the sample, which allows for the identification of a positive sample as it is being amplified. Together, the rapid extraction and real-time readout allow for a prompt identification of genotype of a variety different types of tissues through the reliable method of PCR.

Rapid Genotyping of Mouse Tissue Using Sigma&#039;s Extract-N-Amp Tissue PCR Kit

The complete genotyping of a mouse tail sample, including tissue digestion and PCR readout, is done in one and a half hours using Sigma's SYBR Green Extract-N-Amp Tissue PCR kit.

Genomic detection of DNA via PCR amplification and detection on an electrophoretic gel is a standard way that the genotype of a tissue sample is ...

Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to &gt;98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts.
Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process.
Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method.

The Solaris qPCR Gene Expression Assays are novel pre-designed qPCR primer/probe combinations designed to simplify the qPCR process without sacrificing the specificity and robustness of the assay.

The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and ...

Rapid Homogeneous Detection of Biological Assays Using Magnetic Modulation Biosensing System

A magnetic modulation biosensing system (MMB) [1,2] rapidly and homogeneously detected biological targets at low concentrations without any washing or separation step. When the IL-8 target was present, a 'sandwich'-based assay attached magnetic beads with IL-8 capture antibody to streptavidin coupled fluorescent protein via the IL-8 target and a biotinylated IL-8 antibody. The magnetic beads are maneuvered into oscillatory motion by applying an alternating magnetic field gradient through two electromagnetic poles. The fluorescent proteins, which are attached to the magnetic beads are condensed into the detection area and their movement in and out of an orthogonal laser beam produces a periodic fluorescent signal that is demodulated using synchronous detection. The magnetic modulation biosensing system was previously used to detect the coding sequences of the non-structural Ibaraki virus protein 3 (NS3) complementary DNA (cDNA) [2]. The techniques that are demonstrated in this work for external manipulation and condensation of particles may be used for other applications, e.g. delivery of magnetically-coupled drugs in-vivo or enhancing the contrast for in-vivo imaging applications.

Magnetic modulation biosensing system is utilized to rapidly, sensitively and simply detect biological assays, such as DNA molecules and proteins.

A magnetic modulation biosensing system (MMB) [1,2] rapidly and homogeneously detected biological targets at low concentrations without any washing or ...

Profiling of Pre-micro RNAs and microRNAs using Quantitative Real-time PCR (qPCR) Arrays

Quantitative real-time PCR (QPCR) has emerged as an accurate and valuable tool in profiling gene expression levels.  One of its many advantages is a lower detection limit compared to other methods of gene expression profiling while using smaller amounts of input for each assay.  Automated qPCR setup has improved this field by allowing for greater reproducibility.  Its convenient and rapid setup allows for high-throughput experiments, enabling the profiling of many different genes simultaneously in each experiment.  This method along with internal plate controls also reduces experimental variables common to other techniques.  
We recently developed a qPCR assay for profiling of pre-microRNAs  (pre-miRNAs) using a set of 186 primer pairs.  MicroRNAs have emerged as a novel class of small, non-coding RNAs with the ability to regulate many mRNA targets at the post-transcriptional level.  These small RNAs are first transcribed by RNA polymerase II as a primary miRNA (pri-miRNA) transcript, which is then cleaved into the precursor miRNA (pre-miRNA).  Pre-miRNAs are exported to the cytoplasm where Dicer cleaves the hairpin loop to yield mature miRNAs.  Increases in miRNA levels can be observed at both the precursor and mature miRNA levels and profiling of both of these forms can be useful.  There are several commercially available assays for mature miRNAs; however, their high cost may deter researchers from this profiling technique.  Here, we discuss a cost-effective, reliable, SYBR-based qPCR method of profiling pre-miRNAs.  Changes in pre-miRNA levels often reflect mature miRNA changes and can be a useful indicator of mature miRNA expression.  However, simultaneous profiling of both pre-miRNAs and mature miRNAs may be optimal as they can contribute nonredundant information and provide insight into microRNA processing.  Furthermore, the technique described here can be expanded to encompass the profiling of other library sets for specific pathways or pathogens.

Profiling of Pre-micro RNAs and microRNAs using Quantitative Real-time PCR qPCR Arrays

We will demonstrate the setup and analysis of pre-microRNA 96-well arrays for QPCR using a robot as well as by hand with a Thermo Scientific Matrix multichannel pipette.

Quantitative real-time PCR (QPCR) has emerged as an accurate and valuable tool in profiling gene expression levels.  One of its many advantages is a lower ...

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, messages are carried by neurotransmitters released from presynaptic terminals and received by receptors on postsynaptic cells. Our previous research in Caenorhabditis elegans has shown that VSM-1 negatively regulates exocytosis. Additionally, analysis of synapses in vsm-1 mutants showed that animals lacking a fully functional VSM-1 have increased synaptic connectivity. Based on these preliminary findings, we hypothesized that C. elegans VSM-1 may play a crucial role in synaptogenesis. To test this hypothesis, double-labeled microarray analysis was performed, and gene expression profiles were determined. First, total RNA was isolated, reversely transcribed to cDNA, and hybridized to the DNA microarrays. Then, in-silico analysis of fluorescent probe hybridization revealed significant induction of many genes coding for members of the major sperm protein family (MSP) in mutants with enhanced synaptogenesis. MSPs are the major component of sperm in C. elegans and appear to signal nematode oocyte maturation and ovulation . In fruit flies, Chai and colleagues 1 demonstrated that MSP-like molecules regulate presynaptic bouton number and size at the neuromuscular junction. Moreover, analysis performed by Tsuda and coworkers 2 suggested that MSPs may act as ligands for Eph receptors and trigger receptor tyrosine kinase signaling cascades. Lastly, real time PCR analysis corroborated that the gene coding for MSP-32 is induced in vsm-1(ok1468) mutants. Taken together, research performed by our laboratory has shown that vsm-1 mutants have a significant increase in synaptic density, which could be mediated by MSP-32 signaling.

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Microarray analysis was conducted to determine genetic expression profiles in C. elegans, and real-time PCR was used to validate and quantify microarray data.

Synapses are composed of a presynaptic active zone in the signaling cell and a postsynaptic terminal in the target cell. In the case of chemical synapses, ...

Optimized PCR-based Detection of Mycoplasma

The maintenance of contamination-free cell lines is essential to cell-based research. Among the biggest contaminant concerns are mycoplasma contamination. Although mycoplasma do not usually kill contaminated cells, they are difficult to detect and can cause a variety of effects on cultured cells, including altered metabolism, slowed proliferation and chromosomal aberrations. In short, mycoplasma contamination compromises the value of those cell lines in providing accurate data for life science research.
The sources of mycoplasma contamination in the laboratory are very challenging to completely control. As certain mycoplasma species are found on human skin, they can be introduced through poor aseptic technique. Additionally, they can come from contaminated supplements such as fetal bovine serum, and most importantly from other contaminated cell cultures. Once mycoplasma contaminates a culture, it can quickly spread to contaminate other areas of the lab. Strict adherence to good laboratory practices such as good aseptic technique are key, and routine testing for mycoplasma is highly recommended for successful control of mycoplasma contamination.
PCR-based detection of mycoplasma has become a very popular method for routine cell line maintenance. PCR-based detection methods are highly sensitive and can provide rapid results, which allows researchers to respond quickly to isolate and eliminate contamination once it is detected in comparison to the time required using microbiological techniques. The LookOut Mycoplasma PCR Detection Kit is highly sensitive, with a detection limit of only 2 genomes per &mu;l. Taking advantage of the highly specific JumpStart Taq DNA Polymerase and a proprietary primer design, false positives are greatly reduced. The convenient 8-tube format, strips pre-coated with dNTPs, and associated primers helps increase the throughput to meet the needs of customers with larger collections of cell lines.
Given the extreme sensitivity of the kit, great care must be taken to prevent inadvertent contamination of samples and reagents. The step-by-step protocol we demonstrate highlights the precautions and practices required for reliable mycoplasma detection. We also show and discuss typical results and their interpretation. Our goal is to ensure the success of researchers using the LookOut Mycoplasma PCR Detection Kit.

The LookOut Mycoplasma PCR Detection Kit utilizes the polymerase chain reaction (PCR), which is established as the method of choice for highest sensitivity in the detection of Mycoplasma, Acholeplasma, and Ureaplasma contamination in cell cultures and other cell culture derived biologicals.

The maintenance of contamination-free cell lines is essential to cell-based research. Among the biggest contaminant concerns are mycoplasma contamination. ...

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Quantitative characterization of protein interactions is essential in practically any field of life sciences, particularly drug discovery. Most of currently available methods of KD determination require access to purified protein of interest, generation of which can be time-consuming and expensive. We have developed a protocol that allows for determination of binding affinity by microscale thermophoresis (MST) without purification of the target protein from cell lysates. The method involves overexpression of the GFP-fused protein and cell lysis in non-denaturing conditions. Application of the method to STAT3-GFP transiently expressed in HEK293 cells allowed to determine for the first time the affinity of the well-studied transcription factor to oligonucleotides with different sequences. The protocol is straightforward and can have a variety of application for studying interactions of proteins with small molecules, peptides, DNA, RNA, and proteins.

Microscale thermophoresis (MST) can be widely used for determination of binding affinity without purification of the target protein from cell lysates. The protocol involves overexpression of the GFP-fused protein, cell lysis in non-denaturing conditions, and detection of MST signal in the presence of varying concentrations of the ligand.

Quantitative characterization of protein  interactions is essential in practically any field of life sciences,  particularly drug discovery. Most of ...

Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

Zebrafish is a powerful vertebrate model system for studying development, modeling disease, and performing drug screening. Recently a variety of genetic tools have been introduced, including multiple strategies for inducing mutations and generating transgenic lines. However, large-scale screening is limited by traditional genotyping methods, which are time-consuming and labor-intensive. Here we describe a technique to analyze zebrafish genotypes by PCR combined with high-resolution melting analysis (HRMA).&#160;This approach is rapid, sensitive, and inexpensive, with lower risk of contamination artifacts.&#160;Genotyping by PCR with HRMA can be used for embryos or adult fish, including in high-throughput screening protocols.

PCR combined with high-resolution melt analysis (HRMA) is demonstrated as a rapid and efficient method to genotype zebrafish.

Zebrafish is a powerful vertebrate model system for studying development, modeling disease, and performing drug screening. Recently a variety of genetic ...

Detecting the Lyme Disease Spirochete, Borrelia Burgdorferi, in Ticks Using Nested PCR

Lyme disease is a serious vector-borne infection that is caused by the Borrelia burgdorferi sensu lato family of spirochetes, which are transmitted to humans through the bite of infected Ixodes ticks. The primary etiological agent in North America is Borrelia burgdorferi sensu stricto. As geographic risk regions expand, it is prudent to support robust surveillance programs that can measure tick infection rates, and communicate findings to clinicians, veterinarians, and the general public. The molecular technique of nested polymerase chain reaction (nPCR) has long been used for this purpose, and it remains a central, inexpensive, and robust approach in the detection of Borrelia in both ticks and wildlife. 
This article demonstrates the application of nPCR to tick DNA extracts to identify infected specimens. Two independent B. burgdorferi targets, genes encoding Flagellin B (FlaB) and Outer surface protein A (OspA), have been used extensively with this technique. The protocol involves tick collection, DNA extraction, and then an initial round of PCR to detect each of the two Borrelia-specific loci. Subsequent polymerase chain reaction (PCR) uses the product of the first reaction as a new template to generate smaller, internal amplification fragments. The nested approach improves upon both the specificity and sensitivity of conventional PCR. A tick is considered positive for the pathogen when inner amplicons from both Borrelia genes can be detected by agarose gel electrophoresis.

Detecting the Lyme Disease Spirochete, Borrelia Burgdorferi, in Ticks Using Nested PCR

Nested PCR is a sensitive, specific, and straightforward technique that can be applied to tick DNA extracts to probe for Borrelia burgdorferi, the causative agent of Lyme disease. The initial PCR experiment uses gene-specific primers to generate long amplicons, which then become templates for a subsequent reaction using internal primers.

Lyme disease is a serious vector-borne infection that is caused by the Borrelia burgdorferi sensu lato family of spirochetes, which are transmitted to ...

Rapid Lipid Droplet Isolation Protocol Using a Well-established Organelle Isolation Kit

Lipid droplets (LDs) are bioactive organelles found within the cytosol of the most eukaryotic and some prokaryotic cells. LDs are composed of neutral lipids encased by a monolayer of phospholipids and proteins. Hepatic LD lipids, such as ceramides, and proteins are implicated in several diseases that cause hepatic steatosis. Although previous methods have been established for LD isolation, they require a time-consuming preparation of reagents and are not designed for the isolation of multiple subcellular compartments. We sought to establish a new protocol to enable the isolation of LDs, endoplasmic reticulum (ER), and lysosomes from a single mouse liver.
Further, all reagents used in the protocol presented here are commercially available and require minimal reagent preparation without sacrificing LD purity. Here we present data comparing this new protocol to a standard sucrose gradient protocol, demonstrating comparable purity, morphology, and yield. Additionally, we can isolate ER and lysosomes using the same sample, providing detailed insight into the formation and intracellular flux of lipids and their associated proteins.

This protocol establishes a novel method of lipid droplet isolation and purification from mouse livers, using a well-established endoplasmic reticulum isolation kit.

Lipid droplets (LDs) are bioactive organelles found within the cytosol of the most eukaryotic and some prokaryotic cells. LDs are composed of neutral ...