Lighting up individual DNA binding proteins with quantum dots

Yuval Ebenstein, Natalie Gassman, Soohong Kim, Josh Antelman, Younggyu Kim, Sam Ho, Robin Samuel, Xavier Michalet, Shimon Weiss

Research output: Contribution to journalArticlepeer-review


The ability to determine the precise loci and occupancy of DNA-binding proteins is instrumental to our understanding of cellular processes like gene expression and regulation. We propose a single-molecule approach for the direct visualization of proteins bound to their template DNA. Fluorescent quantum dots (QD) are used to label proteins bound to DNA, allowing multicolor, nanometer-resolution localization. Protein-DNA complexes are linearly extended and imaged to determine the precise location of the protein binding sites. The method is demonstrated by detecting individual QD-labeled T7-RNA polymerases on the T7 bacteriophage genome. This work demonstrates the potential of this approach to precisely read protein binding position or, alternatively, "write" such information on extended DNA with QDs via sequence-specific molecular recognition.

Original languageEnglish
Pages (from-to)1598-1603
Number of pages6
JournalNano Letters
Issue number4
StatePublished - 8 Apr 2009
Externally publishedYes


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