Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

详细信息    查看全文

• 作者：Meni Wanunu ; Devora Cohen-Karni ; Robert R. Johnson ; Lauren Fields ; Jack Benner ; Neil Peterman ; Yu Zheng ; Michael L. Klein ; Marija Drndic
• 刊名：Journal of the American Chemical Society
• 出版年：2011
• 出版时间：January 26, 2011
• 年：2011
• 卷：133
• 期：3
• 页码：486-492
• 全文大小：338K
• 年卷期：v.133,no.3(January 26, 2011)
• ISSN：1520-5126

文摘

Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosine鈥檚 polarity, DNA flexibility, and duplex stability. On the basis of these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.