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Dependence of nucleosome mechanical stability on DNA mismatches (2024)
Journal Article
Ngo, T. T., Liu, B., Wang, F., Basu, A., Wu, C., & Ha, T. (in press). Dependence of nucleosome mechanical stability on DNA mismatches. eLife, 13, Article RP95514. https://doi.org/10.7554/elife.95514

The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of D... Read More about Dependence of nucleosome mechanical stability on DNA mismatches.

Dependence of Nucleosome Mechanical Stability on DNA Mismatches (2024)
Journal Article
Ngo, T. T. M., Liu, B., Wang, F., Basu, A., Wu, C., & Ha, T. (2024). Dependence of Nucleosome Mechanical Stability on DNA Mismatches. eLife, 13, Article RP95514. https://doi.org/10.7554/elife.95514.1

The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of D... Read More about Dependence of Nucleosome Mechanical Stability on DNA Mismatches.

Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae (2024)
Journal Article
Silva, E. C., Quinde, C. A., Cieza, B., Basu, A., Vila, M. M. D. C., & Balcão, V. M. (2024). Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes, 15(1), Article 113. https://doi.org/10.3390/genes15010113

Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease invol... Read More about Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae.

A method for assaying DNA flexibility (2023)
Journal Article
Cirakli, E., & Basu, A. (2023). A method for assaying DNA flexibility. Methods, 219, 68-72. https://doi.org/10.1016/j.ymeth.2023.09.007

The transcription, replication, packaging, and repair of genetic information ubiquitously involves DNA:protein interactions and other biological processes that require local mechanical distortions of DNA. The energetics of such DNA-deforming processe... Read More about A method for assaying DNA flexibility.

The impact of the sequence-dependent physical properties of DNA on chromain dynamics (2023)
Journal Article
Biswas, A., & Basu, A. (2023). The impact of the sequence-dependent physical properties of DNA on chromain dynamics. Current Opinion in Structural Biology, 83, Article 102698. https://doi.org/10.1016/j.sbi.2023.102698

The local mechanical properties of DNA depend on local sequence. Here we review recent genomic, structural, and computational efforts at deciphering the “mechanical code”, i.e., the mapping between sequence and mechanics. We then discuss works that s... Read More about The impact of the sequence-dependent physical properties of DNA on chromain dynamics.

Deciphering the Mechanical code of the genome and epigenome (2022)
Journal Article
Basu, A., Bobrovnikov, D. G., Cieza, B., Arcon, J. P., Orozco, M., & Ha, T. (2022). Deciphering the Mechanical code of the genome and epigenome. Nature Structural and Molecular Biology, 29, 1178-1187. https://doi.org/10.1101/2020.08.22.262352

Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challengi... Read More about Deciphering the Mechanical code of the genome and epigenome.