Name: visual detection of multiple nucleic acids in a capillary array
Uploaded: 2017-11-15T14:00:00
Description: Watch this Scientific Journal Video about Visual Detection of Multiple Nucleic Acids in a Capillary Array at JoVE.com

This study was funded in part by National Natural Science Foundation of China Grants (31370813, 3147670, 31670831 and 31600672,), the National Transgenic Plant Special Fund (2016ZX08012-003, 2016ZX08012-005), Program for New Century Excellent Talents in University, the National Key Research and Development Project of China (2016YFA0500601) and China Postdoctoral Science Foundation (2016M591667).

NOTE: This protocol assumes that the stainless steel mold bearing the shape for the desired micro-channels and the loading adaptor have already been made (3D files are provided as Supplemental Files 1 and 2). This protocol also assumes that plant DNA isolation has already been carried out.
1. Fabrication of the Capillary Array-based Ready-to-use Cassette
<ol>
	<li>Clean the stainless-steel mold.
	<ol>
		<li>Wash the stainless-steel mold by d...

<ol>
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The CALM platform demonstrated here, which combines the LAMP technology with a capillary array, enables the simultaneous detection of multiple GMO-related gene targets in a single, highly effective and easy to operate test.
To successfully perform the multiplex LAMP reactions in the cassette, three critical points need to be noticed. Firstly, achieving the same height for the upper side of the capillaries and the hydrophilic and hydrophobic pattern of the capillary array are critical for simul...

Low-cost, quick, and easy to use systems for the simultaneous detection of multiple nucleic acids are urgently needed in a wide range of fields, such as clinical diagnostics1,2,3, GMO detection4,5,6, microbial monitoring7,8,9, forensic analysis10,11, and especially point-of-care tests (POCTs), where resources are usually limited12,13,14.
Polymerase chain reaction (PCR), including its derivative methods real-time PCR and multiplex PCR, is the most widely applied technique for detection in these fields. However, these methods typically only detect one target in one test15 and they require electricity and sophisticated professional equipment.
Another promising technology for detecting nucleic acids is Loop-mediated isothermal amplification (LAMP), which was first described in 200016. LAMP is a high efficiency DNA detection method. Theoretically, it can amplify from 1 copy to 109 copies of amplicons within one hour, all performed at a constant temperature, (i.e., between 60 - 65 &#176;C). Successful amplification will produce a large amount of the insoluble byproduct pyrophosphate and cause a change in turbidity17, which could be directly observed by the naked eye. A color change can also be observed by the addition of metal ions or fluorescent dyes such as Calcein18, Nucleic acid dye19, and hydroxyl naphthol blue20. Because of the advantages of high sensitivity and convenience of operation, LAMP is being widely applied in nucleic acid detection.
Currently, there are mainly two strategies for multiplex LAMP assays. One is to perform multiple LAMP assays by having multiple LAMP primer sets in one tube21,22,23. However, the multiplicity and the amplification efficiency would be limited by the intrinsic interference and competition among different primer sets. Furthermore, it can be difficult to identify different LAMP products in the same reaction. Another strategy is based on physical isolation. Different primer sets were isolated into individual miniaturized compartments, and multiple LAMP reactions are then performed simultaneously24,25. These approaches, which are generally based on microfluidic chips, provide a potential solution for high-throughput LAMP reactions. However, the manufacture of the chips and the multiplex pre-coating of primer sets is complicated, which may increase costs and decrease reproducibility.
Recently, a few studies have described performing LAMP reactions in capillaries to bypass the complicated fabrication of microfluidic chips and have achieved low-cost detection26,27. However, with regards to high-throughput analysis, these capillaries are similar to miniature versions of PCR strip tubes, because the samples and reaction reagents (including the different primer sets) must be individually prepared and delivered to different reaction units within capillaries. To achieve parallel and multiplex analysis, additional equipment, for example a multichannel syringe pump, is required for parallel loading of samples or reagents.
To overcome the limitations associated with the current methods for multiplex detection of nucleic acids, we have developed a miniaturized platform which combines visual LAMP technology with a capillary array. This platform is multi-target, compact in size, low cost, and easy to operate28. Herein, we describe the details of how to fabricate the capillary array and perform the LAMP reactions in the array. The protocol described here has been standardized using genetically modified organism (GMO) detection as a model. Importantly, this protocol can also be used in high-throughput detection of other nucleic acid targets.

<table>
	<tbody>
		<tr>
			<td>UltraEverDry(super-hydrophobic coat)</td>
			<td>UltraTech</td>
			<td>4001</td>
			<td>supplier:Exiron chemistry(CHINA) CO.,LTD.</td>
		</tr>
		<tr>
			<td>PDMS</td>
			<td>Dow Corning</td>
			<td>8332557</td>
			<td></td>
		</tr>
		<tr>
			<td>Bst polymerase</td>
			<td>New England BioLabs</td>
			<td>M0275L</td>
			<td></td>
		</tr>
		<tr>
			<td>betain</td>
			<td>Sigma-Aldrich</td>
			<td>B0300-1VL</td>
			<td></td>
		</tr>
		<tr>
			<td>calcein</td>
			<td>Sigma-Aldrich</td>
			<td>C0875-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>MnCl2</td>
			<td>Sigma-Aldrich</td>
			<td>MKBP0495V</td>
			<td></td>
		</tr>
		<tr>
			<td>MgSO4</td>
			<td>New England BioLabs</td>
			<td>B1003S</td>
			<td></td>
		</tr>
		<tr>
			<td>dNTPs</td>
			<td>Shanghai Sangon</td>
			<td>B804BA0022</td>
			<td></td>
		</tr>
		<tr>
			<td>chitosan</td>
			<td>Shanghai Sangon</td>
			<td>LJ0805S309J</td>
			<td></td>
		</tr>
		<tr>
			<td>Photoshop 7.0 software</td>
			<td>Adobe Systems Inc., CA, USA</td>
			<td></td>
			<td>Image analysis</td>
		</tr>
		<tr>
			<td>GenePix Pro 6.1</td>
			<td>Molecular Devices, CA, USA</td>
			<td></td>
			<td>microarray analysis software</td>
		</tr>
		<tr>
			<td>AutoCAD</td>
			<td>Adobe Systems Inc.</td>
			<td></td>
			<td>3D construction software</td>
		</tr>
		<tr>
			<td>UV filter (ZWB2)</td>
			<td>YXSensing</td>
			<td></td>
			<td>supplier : taobao</td>
		</tr>
	</tbody>
</table>

visual detection of multiple nucleic acids in a capillary array

Multi-target, short time, and resource-affordable methodologies for the detection of multiple nucleic acids in a single, easy to operate test are urgently needed in disease diagnosis, microbial monitoring, genetically modified organism (GMO) detection, and forensic analysis. We have previously described the platform called CALM (Capillary Array-based Loop-mediated isothermal amplification for Multiplex visual detection of nucleic acids). Herein, we describe improved fabrication and performance processes for this platform. Here, we apply a small, ready-to-use cassette assembled by capillary array for multiplex visual detection of nucleic acids. The capillary array is pre-treated into a hydrophobic and hydrophilic pattern before fixing loop-mediated isothermal amplification (LAMP) primer sets in capillaries. After assembly of the loading adaptor, LAMP reaction mixture is loaded and isolated into each capillary, due to capillary force by a single pipetting step. The LAMP reactions are performed in parallel in the capillaries. The results are visually read out by illumination with a hand-held UV flashlight. Using this platform, we demonstrate monitoring of 8 frequently appearing elements and genes in GMO samples with high specificity and sensitivity. In summary, the platform described herein is intended to facilitate the detection of multiple nucleic acids. We believe it will be widely applicable in fields where high-throughput nucleic acid analysis is required.

In this method, it is important to prevent cross-contamination among different capillaries during the sample loading. For this purpose, chitosan was introduced, which could retain the primers in individual capillaries. To test whether it worked or not, we pre-fixed the ADH1 (endogenous reference gene of maize) primer set in the capillary cassette with the pattern of &#34;T&#34; and &#34;U&#34;, as illustrated in Figure 3a. As...

Watch this Scientific Journal Video about Visual Detection of Multiple Nucleic Acids in a Capillary Array at JoVE.com

Visual Detection of Multiple Nucleic Acids in a Capillary Array

This protocol describes the fabrication of a small, ready-to-use cassette that can be applied for visual detection of multiple nucleic acids in a single, test that is easy to operate. In this approach, a capillary array was used for multiplex and highly efficient detection of GMO targets.

Multi-target, short time, and resource-affordable methodologies for the detection of multiple nucleic acids in a single, easy to operate test are urgently ...

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