Center for Molecular Spectroscopy and Dynamics

2019.07 Single-molecule biophysics conference 

DNA methylation is one of the most frequent and critical epigenetic modifications. Abnormal DNA methylation has been implicated in various health issues such as metabolic syndromes and a variety of cancers(1). It is therefore not only of fundamental interest but also of practical significance to probe the degree of DNA methylation by DNA methyltransferases (DNMT) and to characterize DNA methylation profile(2). To this end, several methods have been developed(3).

Here, we propose a new single-molecule-based approach to measure the degree of DNA methylation. It is known that the B-to-Z-DNA transition is sensitive to the extent of DNA methylation: GC repeat sequences with methylated cytosines are easier to convert to Z-DNA than unmethylated, otherwise, identical sequences(4). Thus, we monitored the B-Z transition occurring to individual DNA molecules in various methylation states by single-molecule FRET and could quantitate DNA methylation in a facile manner and establish the relationship between Z-DNA forming capability and the degree of DNA methylation. Besides, we also tested the effects of various DNMT inhibitors, some of which are clinically tested as anti-cancer drugs, discovering that our technique provides a convenient way to evaluate the efficacy of such drugs. Our work clearly demonstrates that the new method is a sensitive, selective, versatile, and viable sensor platform to detect DNMT activity and screen DNMT inhibitors.

Reference

[1]    El-Osta, A. & Wolffe, A. P. DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease. Gene Expr. 9, 63–75 (2000).

[2]    Varinder Singh, P. S. & Capalash, N. DNA Methyltransferase-1 Inhibitors as Epigenetic Therapy for Cancer. Current Cancer Drug Targets 13, 379–399 (2013).

[3]    Nazmul Islam, M. et al. Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 92, 668–678 (2017).

[4]    Lee, M. et al. Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension. Proc. Natl. Acad. Sci. U.S.A. 107, 4985–4990 (2010).