Related Experiment Video
Updated: Jul 18, 2025

Phthalic Acid Ester-Binding DNA Aptamer Selection, Characterization, and Application to an Electrochemical Aptasensor
Published on: March 21, 2018
An efficient extraction method for short single-stranded DNA from agarose gels in aptamer screening.
Chunmin Pu1, Xiaoyan Liao1, Xianming Shi2
1Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
A new method using amino-modified silica-coated magnetic particles efficiently extracts short single-stranded DNA (ssDNA) from agarose gel. This technique shows superior performance compared to existing commercial kits for aptamer screening applications.
Area of Science:
- Biotechnology
- Molecular Biology
- Biochemistry
Background:
- Efficient extraction of short single-stranded DNA (ssDNA) from agarose gel is crucial for aptamer screening.
- Existing DNA extraction kits are often optimized for double-stranded DNA (dsDNA) and show limited efficacy for short ssDNA.
Purpose of the Study:
- To develop a novel and efficient method for extracting short ssDNA from agarose gel.
- To evaluate the performance of the new method against commercially available DNA gel extraction kits.
Main Methods:
- Development of a method utilizing amino-modified silica-coated magnetic particles (ASMPs).
- Incorporation of centrifugation with silica wool and ASMP adsorption for ssDNA capture.
- Optimization of desorption using reagents with phosphate groups.
Main Results:
- The novel ASMP-based method demonstrated high efficiency in short ssDNA extraction.
- Comparative analysis showed superior performance over three commercial kits (Q-kit, S-kit, V-kit).
- Relative recovery rates: M-dNTP (100.00%) > M-BB (63.38%) > Q-kit (46.64%) > S-kit (15.98%) > V-kit (0.38%).
Conclusions:
- The developed ASMP method provides a promising solution for short ssDNA extraction from agarose gel.
- This method significantly improves efficiency and recovery rates for aptamer screening applications.
Related Concept Videos
DNA Agarose Gel Electrophoresis
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
In cloning experiments, both the insert and vector DNA...
DNA Isolation
Southern Blot
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

