ac502214z_si_002.avi (9.6 MB)
Methylsorb: A Simple Method for Quantifying DNA Methylation Using DNA–Gold Affinity Interactions
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posted on 2014-10-21, 00:00 authored by Abu Ali
Ibn Sina, Laura G. Carrascosa, Ramkumar Palanisamy, Sakandar Rauf, Muhammad J. A. Shiddiky, Matt TrauThe analysis of DNA methylation is
becoming increasingly important
both in the clinic and also as a research tool to unravel key epigenetic
molecular mechanisms in biology. Current methodologies for the quantification
of regional DNA methylation (i.e., the average methylation over a
region of DNA in the genome) are largely affected by comprehensive
DNA sequencing methodologies which tend to be expensive, tedious,
and time-consuming for many applications. Herein, we report an alternative
DNA methylation detection method referred to as “Methylsorb”,
which is based on the inherent affinity of DNA bases to the gold surface
(i.e., the trend of the affinity interactions is adenine > cytosine
≥ guanine > thymine). Since
the
degree of gold–DNA affinity interaction is highly sequence
dependent, it provides a new capability to detect DNA methylation
by simply monitoring the relative adsorption of bisulfite treated
DNA sequences onto a gold chip. Because the selective physical adsorption
of DNA fragments to gold enable a direct read-out of regional DNA
methylation, the current requirement for DNA sequencing is obviated.
To demonstrate the utility of this method, we present data on the
regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231
cells. The methylation status of these regions was obtained from the
change in relative mass on gold surface with respect to relative adsorption
of an unmethylated DNA source and this was detected using surface
plasmon resonance (SPR) in a label-free and real-time manner. We anticipate
that the simplicity of this method, combined with the high level of
accuracy for identifying the methylation status of cytosines in DNA,
could find broad application in biology and diagnostics.