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Updated: May 27, 2026
11:35
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
Published on: August 21, 2016
Mapping DNA quantity into electrophoretic mobility through quantum dot nanotethers for high-resolution genetic and
Yi Zhang1, Kelvin J Liu, Tian-Li Wang
1Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
ACS Nano
|December 6, 2011
Summary
We developed a quantum dot electrophoretic mobility shift assay (QEMSA) to precisely quantify DNA. This novel nanoassembly method detects subtle genetic and epigenetic changes in cancer, outperforming qPCR.
Area of Science:
- Nanotechnology
- Molecular Biology
- Biochemistry
Background:
- Nanoparticle properties drive new applications.
- Electrophoretic mobility of nanoassemblies is sensitive to surface modifications.
- Current DNA quantification methods have limitations in detecting small changes.
Purpose of the Study:
- To report a new method for precisely modulating nanoassembly electrophoretic mobility.
- To develop a novel quantum dot-enabled nanoassay (QEMSA) for DNA quantification.
- To apply QEMSA for genetic and epigenetic analysis in cancer.
Main Methods:
- Utilizing streptavidin-coated quantum dots (QDs) and biotin-labeled DNA to form nanoassemblies.
- Modulating QD surface charge via DNA conjugation to alter electrophoretic mobility.
- Employing standard agarose gel electrophoresis to detect mobility shifts.
- Developing an analytical model to explain the observed behavior.
Main Results:
- Precise modulation of nanoassembly electrophoretic mobility by DNA conjugation degree.
- QEMSA accurately quantifies DNA targets, detecting 1.1-fold (9%) changes, exceeding qPCR sensitivity.
- QEMSA successfully analyzed cancer gene copy number variation (CNV) and DNA methylation with superior accuracy.
Conclusions:
- QEMSA offers a novel, highly sensitive method for DNA quantification.
- The assay accurately maps DNA quantity to electrophoretic band shifts.
- QEMSA demonstrates significant potential for genetic and epigenetic cancer analysis, surpassing conventional techniques.
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