Spectroscopic Study of Cytosine Methylation Effect on Thermodynamics of DNA Duplex Containing CpG Motif

Václav Římal,Ondřej Socha,Josef Štěpánek,Helena Štěpánková

doi:10.1155/2015/842810

Abstract

Effect of cytosine methylation on DNA duplexes was studied by using a model system of three self-complementary DNA octamers containing central CpG motif surrounded by a couple of AT base pairs, CAACGTTG, CATCGATG, and CTTCGAAG, and their analogues with the central cytosine methylated at C5 position. Temperature dependences of1H NMR, UV absorption, and Raman scattering spectra measured for aqueous solutions at concentrations of different orders of magnitude were subjected to a joint analysis that allowed an accurate determination of the enthalpy and entropy of duplex formation. It was revealed that the changes of the enthalpy and entropy contributions are strongly dependent on the base composition in the vicinity of the CpG motif.

Highlights

Methylation of cytosine at carbon position C5 is a highly abundant epigenetic chemical modification of DNA in mammals, occurring mainly in CpG dinucleotide sequences [1]
Effect of cytosine methylation on DNA duplexes was studied by using a model system of three self-complementary DNA octamers containing central CpG motif surrounded by a couple of AT base pairs, CAACGTTG, CATCGATG, and CTTCGAAG, and their analogues with the central cytosine methylated at C5 position
The initial recognition feature is naturally sought in the effect of the cytosine methylation on geometry, dynamics, and/or thermal stability of DNA duplex

Summary

Introduction

Methylation of cytosine at carbon position C5 is a highly abundant epigenetic chemical modification of DNA in mammals, occurring mainly in CpG dinucleotide sequences [1]. Similar results were obtained on a few other CpG motifs containing oligonucleotide sequences: no significant structural modification but indication of the dynamics reduction in [14] and only weak increase of the thermal stability after the methylation (melting temperature increase of 1.4∘C) in [15]. Certain changes in the CpG local geometry by the cytosine methylation were found in the nineties by NMR studies performed on oligonucleotides where the CpG motif was surrounded by two AT nucleotide pairs from both sides These works revealed that in this case the CpG site conformation was not sufficiently locked in a standard B-form geometry even without the cytosine methylation [16,17,18]. Special attention was paid to a precise determination of concentrations and temperatures and to a rigorous determination of melting temperatures from experimental data

Experiment

Results and Discussion

Conclusions