Real-time analysis and selection of methylated DNA by fluorescence- activated single molecule sorting in a nanofluidic channel

Benjamin R. Cipriany, Patrick J. Murphy, James A. Hagarman, Aline Cerf, David Latulippe, Stephen L. Levy, Jaime J. Benítez, Christine P. Tan, Juraj Topolancik, Paul D. Soloway, Harold G. Craighead

Research output: Contribution to journalArticle

44 Scopus citations

Abstract

Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state. This device evaluates the fluorescence from labeled epigenetic modifications to actuate sorting. This technology has demonstrated up to 98% accuracy in molecule sorting and has achieved postsorting sample recovery on femtogram quantities of genetic material. We have applied it to sort methylated DNA molecules using simultaneous, multicolor fluorescence to identify methyl binding domain protein-1 (MBD1) bound to full-duplex DNA. The functionality enabled by this nanofluidic platform now provides a workflow for color-multiplexed detection, sorting, and recovery of single molecules toward subsequent DNA sequencing.

Original languageEnglish (US)
Pages (from-to)8477-8482
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number22
DOIs
StatePublished - May 29 2012

ASJC Scopus subject areas

  • General

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