Real-time Tracking of DNA Fragment Separation by Smartphone

Summary

Traditional slab gel electrophoresis (SGE) experiments require a complicated apparatus and high chemical consumption. This work presents a protocol that describes a low-cost method to separate DNA fragments within a short timeframe.

Abstract

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

Introduction

Slab gel electrophoresis (SGE) is the most effective method for DNA fragment separation^1,2,3,4,5 and thus it is deemed a versatile tool in biochemical and biological analyses^6,7,8. However, many experiments indicate that SGE is restricted by the following four problems: (1) the separations take many hours, and even days; (2) the chemical consumption is very high; (3) it requires a complicated apparatus (e.g.,

Protocol

1. Basic Design of the SGE Chip

1. Use any transparent plastic, such as polymethylmethacrylate (PMMA) or polycarbonate.
   Note: The SGE chip is demonstrated in Figure 1B. The SGE chip consists of cylindrical holes for the TBE buffer, channels for DNA separation, and two lanes embedded along the holes for the electrode.
2. Fabricate arrays of SGE channels in the PMMA block using a laser engraving machine.
   Note: The geometric parameters of the chip are dependent upon the size of the DNA to be separated. For example, the optimal channel parameters for the SGE chip are 2.5 mm x 4.0 mm x 90 mm (width x depth x lengt....

Results

Figure 4, Figure 5, and Figure 6 represent a typical result after the gel electrophoresis of 50, 100, and 1,000 bp DNA ladders. After the experiment, the DNA fragments were well-separated. Furthermore, the same samples were separated in the 4 channels of the SGE chip, showing that DNA fragments of the same size move the same distance in each experiment.

The separation performance of the DNA ladder can be .......

Discussion

Agarose gel electrophoresis is widely employed for the separation of DNA, RNA, and protein. This work proposes a new method to replace the traditional gel electrophoresis protocol. Results demonstrate that 50, 100, and 1,000 bp DNA ladders can be separated well in such a small assembled device. The great advantage of this method is that not only can it separate the nucleic acids with little chemical consumption, but it can also record the separation process. Although the DNA fragments looks wide in F.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
10×TBE	Beijing Solarbio Science & Technology Co., Ltd.	T1051
50 bp DNA ladder	Takara Bio Inc.	3421A
100 bp DNA ladder	Takara Bio Inc.	3422A
1 kbp DNA ladder	Takara Bio Inc.	3426A
SYBR GREEN	Takara Bio Inc.	5760A
Agarose	Sigma-Aldrich Corporate	V900510