Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA

Abstract

Methyl methanesulfonate (MMS) is a highly toxic DNA-alkylating agent that has a potential to damage the structural integrity of DNA. This work employed multiple biophysical and computational methods to report the MMS mediated structural alterations in the DNA (MMS-DNA). Spectroscopic techniques and gel electrophoresis studies revealed MMS induced exposure of chromophoric groups of DNA; methylation mediated anti→syn conformational change, DNA fragmentation and reduced nucleic acid stability. MMS induced single-stranded regions in the DNA were observed in nuclease S1 assay. FT-IR results indicated MMS mediated loss of the assigned peaks for DNA, partial loss of C-O ribose, loss of deoxyribose region, C-O stretching and bending of the C-OH groups of hexose sugar, a progressive shift in the assigned guanine and adenine peaks, loss of thymine peak, base stacking and presence of C-O-H vibrations of glucose and fructose, indicating direct strand breaks in DNA due to backbone loss. Isothermal titration calorimetry showed MMS-DNA interaction as exothermic with moderate affinity. Dynamic light scattering studies pointed towards methylation followed by the generation of single-stranded regions. Electron microscopy pictured the loss of alignment in parallel base pairs and showed the formation of fibrous aggregates in MMS-DNA. Molecular docking found MMS in close contact with the ribose sugar of DNA backbone having non-bonded interactions. Molecular dynamic simulations confirmed that MMS is capable of interacting with DNA at two levels, one at the level of nitrogenous bases and another at the DNA backbone. The study offers insights into the molecular interaction of MMS and DNA.

Communicated by Ramaswamy H. Sarma

Keywords:

• Cancer
• DNA
• DNA fragmentation
• DNA-alkylation
• methylmethane sulfonate

Acknowledgements

Infrastructure facilities provided by the Department of Science & Technology under DST (FIST & PURSE) program are gratefully acknowledged. USIF, AMU is acknowledged for providing SEM and TEM facilities. NPSF-PARAM YUVA-II and BRAF at C-DAC, Pune is acknowledged for providing supercomputer facility for molecular dynamic simulations studies.

Disclosure statement

No potential competing interest is reported by the authors.

Funding details

This work was funded by UGC-BSR Research Start-up-Grant No-F-30-377/2017 (BSR) to Dr Safia Habib. University Grants Commission.