Title: Dynamic 31P NMR of Backbone Dynamics in DNA

PI:  Mary Hatcher-Skeers

Funding Agency:  NIH

Amount: $ 170,218

Dates: 1/1/05-12/31/07

Abstract

Epigenetics is the inheritance of information based on gene expression.  It determines when and where genetic information will be used.  The most common human epigenetic modification is the methylation of cytosines in CpG steps of DNA sequences (Jones and Baylin 2002).  The methylation state of these steps is known to play a crucial role in imprinting and gene silencing.  This is tremendously important as methyaltion induced gene silencing is considered a precursor in many human cancers (Jones and Laird 1999).  While much work has been done to understand the role of CpG methylation in tumorgenesis, the structural and dynamical effects of methylation are not well understood. 
Our research focuses on how proteins recognize specific DNA sequences and the effects of cytosine methylation on this recognition.  In particular, we study the role of DNA dynamics in this recognition process.  Our previous solid-state deuterium NMR studies of methylated and unmethylated DNA binding sites have shown that cytosine methylation quenches DNA backbone dynamics (Geahigan, Meints et al. 2000; Meints and Drobny 2001).  However, these experiments required extensive sample preparation and allowed the study of only one nucleotide step at a time.  We propose to use phosphorus NMR to investigate the backbone dynamics of each step in methylated and unmethylated DNA samples.  This will allow us to rapidly probe a myriad of DNA binding sites for dynamical effects of cytosine methylation.  The ability to quickly study a large number of binding sites will uncover any trends in methylation effects, which we hope can then be used to design tools for early detection of cancers.