Optical Labeling and Detection of Hydroxymethylcytosine – a BioMarker for Cancer
Epigenetic profiling: single-molecule, quantitative optical detection by fluorescent labeling of 5hmC residues. A simple yet highly sensitive 5hmC quantification assay that is compatible with bulk DNA analysis as well as with 5hmC detection on individual DNA molecules.
The Need – and DNA Optical Mapping
Hydroxymethylcytosine is an epigenetic DNA mark discovered only in 2009 and is already considered the 6th base of DNA (after metylcytosine, the 5th base). Due to 5hmC's non-random and tissue specific distribution it is believed to have a functional role in transcription regulation. Moreover, genomic hmC patterns have been shown recently to be more robust than methylation patterns as indictors for some disease states and may potentially serve as powerful biomarkers. In order to capture these patterns, it is necessary to investigate long genomic regions over individual chromosomes. New detection and characterization methods are needed in order to accomplish this goal and drive the field forward.
An emerging technology that utilizes DNA barcoding is Optical Mapping. These techniques use fluorescence imaging of linearly extended DNA molecules to probe information patterns along the molecules. Coupling our hmC specific labeling chemistry with optical mapping provides the ability to simultaneously record epigenetic information such as the DNA modification 5hmC as well as the underlying genetic layout. This will provide long-range epigenetic patterns along individual chromosomes and highlight genomic variation hidden or inaccessible by traditional techniques.
1. A simple UV-vis absorbance measurement is used to simultaneously record the absorbance peaks of DNA and of the spectrally distinct reporter molecule thus enabling ratiometric quantification of the total 5hmC content in a given DNA sample. The simplicity and sensitivity of this absorbance-based assay and its compatibility with automated, multi-well format analysis makes it attractive for high-throughput 5hmC quantification.
2. Single-molecule imaging may be used to map individual 5hmC sites along the genome. This approach promises the most sensitive detection of genomic hmC, opening research into numerous human cell types (including human blood cells) not accessible due to low levels of epigenetic modification.
Provisional patent filed and available for licensing.
Optical detection of epigenetic marks: sensitive quantification and direct imaging of individual hydroxymethylcytosine bases, Chem. Commun., 2013, 49 (77), 8599 - 8601