Mapping DNA quantity into electrophoretic mobility through quantum dot nanotethers for high-resolution genetic and epigenetic analysis

Yi Zhang, Kelvin J. Liu, Tian-Li Wang, Ie Ming Shih, Tza Huei Wang

Research output: Contribution to journalArticle

Abstract

Figure Persented: Newly discovered nanoparticle properties have driven the development of novel applications and uses. We report a new observation where the electrophoretic mobility of a quantum dot/DNA nanoassembly can be precisely modulated by the degree of surface DNA conjugation. By using streptavidin-coated quantum dots (QDs) as nanotethers to gather biotin-labeled DNA into electrophoretic nanoassemblies, the QD surface charge is modulated and transformed into electrophoretic mobility shifts using standard agarose gel electrophoresis. Typical fluorescent assays quantify based on relative intensity. However, this phenomenon uses a novel approach that accurately maps DNA quantity into shifts in relative band position. This property was applied in a QD-enabled nanoassay called quantum dot electrophoretic mobility shift assay (QEMSA) that enables accurate quantification of DNA targets down to 1.1-fold (9%) changes in quantity, beyond what is achievable in qPCR. In addition to these experimental findings, an analytical model is presented to explain this behavior. Finally, QEMSA was applied to both genetic and epigenetic analysis of cancer. First, it was used to analyze copy number variation (CNV) of the RSF1/HBXAP gene, where conventional approaches for CNV analysis based on comparative genomic hybridization (CGH), microarrays, and qPCR are unable to reliably differentiate less than 2-fold changes in copy number. Then, QEMSA was used for DNA methylation analysis of the p16/CDK2A tumor suppressor gene, where its ability to detect subtle changes in methylation was shown to be superior to that of qPCR.

Original languageEnglish (US)
Pages (from-to)858-864
Number of pages7
JournalACS Nano
Volume6
Issue number1
DOIs
StatePublished - Jan 24 2012

Fingerprint

Electrophoretic mobility
Semiconductor quantum dots
DNA
deoxyribonucleic acid
quantum dots
high resolution
Assays
shift
methylation
Genes
tumor suppressor genes
biotin
Methylation
Streptavidin
Surface charge
Microarrays
electrophoresis
Biotin
Electrophoresis
conjugation

Keywords

  • copy number variation
  • DNA
  • DNA methylation
  • electrophoretic mobility
  • nanotether
  • quantum dot

ASJC Scopus subject areas

  • Engineering(all)
  • Materials Science(all)
  • Physics and Astronomy(all)

Cite this

Mapping DNA quantity into electrophoretic mobility through quantum dot nanotethers for high-resolution genetic and epigenetic analysis. / Zhang, Yi; Liu, Kelvin J.; Wang, Tian-Li; Shih, Ie Ming; Wang, Tza Huei.

In: ACS Nano, Vol. 6, No. 1, 24.01.2012, p. 858-864.

Research output: Contribution to journalArticle

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