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Mondal S, Banerjee S, Dey D, Lahiri H, Mana T, Jana SS, Mukhopadhyay R. Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule. Biochimie 2023; 213:168-175. [PMID: 37211256 DOI: 10.1016/j.biochi.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
High mobility group B1 (HMGB1) is an architectural protein that recognizes the DNA damage sites formed by the platinum anticancer drugs. However, the impact of HMGB1 binding on the structural alterations of the platinum drug-treated single dsDNA molecules has remained largely unknown. Herein, the structural alterations induced by the platinum drugs, the mononuclear cisplatin and it's analog the trinuclear BBR3464, have been probed in presence of HMGB1, by atomic force microscopy (AFM) and AFM-based force spectroscopy. It is observed that the drug-induced DNA loop formation enhanced upon HMGB1 binding, most likely as a result of HMGB1-induced increase in DNA conformational flexibility that allowed the drug-binding sites to come close and form double adducts, thereby resulting in enhanced loop formation via inter-helix cross-linking. Since HMGB1 enhances DNA flexibility, the near-reversible structural transitions as observed in the force-extension curves (for 1 h drug treatment), generally occurred at lower forces in presence of HMGB1. The DNA structural integrity was largely lost after 24 h drug treatment as no reversible transition could be observed. The Young's modulus of the dsDNA molecules, as estimated from the force-extension analysis, increased upon drug treatment, due to formation of the drug-induced covalent cross-links and consequent reduction in DNA flexibility. The Young's modulus increased further in presence of HMGB1 due to HMGB1-induced enhancement in DNA flexibility that could ease formation of the drug-induced covalent cross-links. To our knowledge, this is the first report that shows an increase in the stiffness of the platinum drug-treated DNA molecules in presence of HMGB1.
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Affiliation(s)
- Sourav Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Debapriya Dey
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. Sensors (Basel) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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Kaczorowska A, Lamperska W, Frączkowska K, Masajada J, Drobczyński S, Sobas M, Wróbel T, Chybicka K, Tarkowski R, Kraszewski S, Podbielska H, Kałas W, Kopaczyńska M. Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs. Int J Mol Sci 2020; 21:ijms21114142. [PMID: 32531996 PMCID: PMC7312087 DOI: 10.3390/ijms21114142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022] Open
Abstract
In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.
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Affiliation(s)
- Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Weronika Lamperska
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Kaja Frączkowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Jan Masajada
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Sławomir Drobczyński
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Marta Sobas
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Pasteura 4, 50-367 Wroclaw, Poland; (M.S.); (T.W.)
| | - Tomasz Wróbel
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Pasteura 4, 50-367 Wroclaw, Poland; (M.S.); (T.W.)
| | - Kinga Chybicka
- Department of Experimental Oncology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (K.C.); (W.K.)
| | - Radosław Tarkowski
- Department of Surgical Oncology, Provincial Specialist Hospital, Iwaszkiewicza 5, 59-220 Legnica, Poland;
| | - Sebastian Kraszewski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Halina Podbielska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Wojciech Kałas
- Department of Experimental Oncology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (K.C.); (W.K.)
| | - Marta Kopaczyńska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
- Correspondence: ; Tel.: +48-71-320-46-17
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