Mesoscopic models applied to the study of the thermodynamic stability of methylated cytosine

MESOSCOPIC MODELS APPLIED TO THE STUDY OF THE THERMODYNAMIC STABILITY OF METHYLATED CYTOSINE

Daniel Batista de Jesus and Gerald Weber

Department of Physics, Federal University of Minas Gerais, Minas Gerais, MG (email: [email protected] , [email protected])

The addition of chemical marks to the canonical structures of DNA is a natural process that impacts the functioning of molecular machinery. Methylation of cytosine at its fifth position (5mC) is the main alteration with known effects on gene silencing and related anomalies like cancer. The silencing process promoted by the 5mC alteration is associated with changes in DNA flexibility, affecting chromatin compaction, and changes in its grooves, affecting recognition processes. High cytosine methylation has been observed in almost all types of cancer, making the detection of methylation pattern alterations a promising diagnostic mechanism. It is known that methylation increases the thermal stability of cytosine, however the intramolecular interactions that lead to this are not understood. Mesoscopic models, with the use of experimental melting temperatures, can be used to understand the origin of the 5mC thermal stability. In this study, we apply mesoscopic models to understand the thermodynamic changes introduced by 5mC which would allow to work out correlations with chemical and biological effects at molecular level.
The effects of cytosine methylation in DNA oligonucleotides was studied with the Peyrard-Bishop model. In this analysis, the UV-Melting data, denaturation temperature, is used to obtain hydrogen bonding parameters for 5mC base pairs and stacking interactions between their nearest-neighbors. It is known that 5mC increases the DNA denaturation temperature and context-dependent effects are observed.
The results obtained show that the stacking parameters exhibit similar behavior for different values of hydrogen bonding. The stacking parameters, comparing CG-GC to 5mCG-GC and 5mCG-GC to 5mCG-G5mC, indicate that the presence of a second methylation is energetically more favorable. The methylation of CpA and CpT is more stabilizing than the first methylation in CpG islands. Furthermore, CpA is more stable than CpT.
The model is sensible to methylation state of the oligonucleotides, with predicted denaturation temperatures close to experimental values. The behavior of the stacking and Morse parameters suggests an application to further understand the intramolecular processes at the chemical and biological levels.

This work was supported by CNPq, CAPES and Fapemig.

Keywords: UV Melting, Nucleotides, Methylated DNA, Cytosine Methylation (5mC), Peyrard-Bishop (PB)