Abstract
Atomic force microscopy1 (AFM) is a powerful tool for analysing the shapes of individual molecules and the forces acting on them. AFM-based force spectroscopy provides insights into the structural and energetic dynamics2,3,4 of biomolecules by probing the interactions within individual molecules5,6, or between a surface-bound molecule and a cantilever that carries a complementary binding partner7,8,9. Here, we show that an AFM cantilever with an antibody tether can measure the distances between 5-methylcytidine bases in individual DNA strands with a resolution of 4 Å, thereby revealing the DNA methylation pattern, which has an important role in the epigenetic control of gene expression. The antibody is able to bind two 5-methylcytidine bases of a surface-immobilized DNA strand, and retracting the cantilever results in a unique rupture signature reflecting the spacing between two tagged bases. This nanomechanical approach might also allow related chemical patterns to be retrieved from biopolymers at the single-molecule level.
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Acknowledgements
The authors thank L. Wildling, R. Schlapak, C. Riese, C. Hesch, J. Jacak and C. Rankl for expert technical assistance, and G. Kada, G. Schütz, D. Blaas, A. Frischauf and C. Aberger for enlightening discussions. This work was supported by the Gen-Au project ‘Ultra sensitive Proteomics and Genomics’ from the Austrian federal ministry for education, science and culture (R.Z., S.H., J.Pröll, P.H.), the Austrian science fund project P15295 (H.J.G.), the Austria Nano-Initiative/NABIOS (R.Z., S.H., H.J.G., P.H.), the European Commission grant ‘Single Molecule Workstation (SMW)’ no. NMP4-SE-2008-213717 (R.Z., F.K., P.H.), and the Austrian Science Fund project L422-N20 (J.H.).
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R.Z. performed the experiments and data evaluation. S.H. developed the surface chemistry and co-wrote the paper. J.Pröll performed the surface chemistry and selected the DNA sequences. F.K., J.Preiner and A.E. discussed the results. J.H. contributed to the surface chemistry. V.Ph.P. programmed the data evaluation. H.J.G. developed the tip chemistry. P.H. led the experimental design and wrote the paper.
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Zhu, R., Howorka, S., Pröll, J. et al. Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns. Nature Nanotech 5, 788–791 (2010). https://doi.org/10.1038/nnano.2010.212
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DOI: https://doi.org/10.1038/nnano.2010.212
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