Direct Observation of Dynamic Mechanical Regulation of DNA Condensation by Environmental Stimuli

Lee, Amy; Karcz, Adam Paul; Akman, Ryan; Zheng, Tai; Kwon, Sara; Chou, Szu-Ting; Sucayan, Sarah; Tricoli, Lucas; Hustedt, Jason M.; Leng, Qixin; Kahn, Jason D.; Mixson, A. James; Seog, Joonil

doi:10.1002/anie.201403499

Cited by 9 publications

(5 citation statements)

References 36 publications

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“…Dynamic mechanical properties have been investigated in materials with biomolecules . Seog and co‐workers applied optical tweezers method to conduct direct single‐molecular measurement on mechanical properties of DNA complex with 19‐mer poly l ‐lysine and branched histidine‐lysine peptides . Profiles with force plateaus during stretching and relaxation cycles were observed in their force–extension relations.…”

Section: Bridging To Macroscale Motion: How To Relate Events With Twomentioning

confidence: 99%

Nanoarchitectonics for Dynamic Functional Materials from Atomic‐/Molecular‐Level Manipulation to Macroscopic Action

et al. 2015

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mechanisms operate with excellent fl exibility/adaptability originating from cooperation of multiple dynamic systems. [ 1 ] In most cases, the functional components of these systems are assembled through non-covalent dynamic interactions. Although their assembled structures are often ambiguous, or "fuzzy," functions of biological systems are signifi cantly superior to any of the so far precisely constructed artifi cial machines and devices. Thus, fabrication of bio-like systems might be one of the ultimate goals of the science and technology of functional materials. There has already been some success in the synthesis of excellent new materials, [ 2 ] but these are still far inferior to biological materials systems from the point-of-view of specifi city, effi ciency, and adaptability, although incremental progress involving existing technological concepts may not change this situation. A certain paradigm shift in construction concepts of functional materials is necessary to establish an advanced approach towards truly dynamic functions.Fabrication of functional materials requires control of organization of their components with nanometer precision. The novel technological concept of nanotechnology has been established over the past few decades with a view to exploit nanometer-sized phenomena and to fabricate functional materials by precisely controlling the materials' structures at the nanoscale. [ 3 ] Several strategies of nanotechnology are simple extensions of the corresponding successful microtechnologies to nanofabrication. However, the control of nanoscale events and structures requires different approaches to those commonly applied in microtechnology. This is because physical phenomena at the nanoscale are quite different from microscopic phenomena. Effects occurring at the microscopic level are often similar to those occurring in the macroscopic regime. In contrast, nanoscale phenomena involving nanometer-sized objects are strongly infl uenced by thermal/statistical fl uctuations, mutual interactions, and possibly quantum effects between components. In many cases, such mutual actions are dynamically integrated, often resulting in unexpected properties and effects so that components of nanoscale systems cannot be controlled by intuitive means. To understand and therefore control nanoscale phenomena and to Objects in all dimensions are subject to translational dynamism and dynamic mutual interactions, and the ability to exert control over these events is one of the keys to the synthesis of functional materials. For the development of materials with truly dynamic functionalities, a paradigm shift from "nanotechnology" to "nanoarchitectonics" is proposed, with the aim of design and preparation of functional materials through dynamic harmonization of atomic-/molecular-level manipulation and control, chemical nanofabrication, self-organization, and fi eld-controlled organization. Here, various examples of dynamic functional materials are presented from the atom/molecularlevel to macroscopic dimensions. Thes...

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Section: Bridging To Macroscale Motion: How To Relate Events With Twomentioning

confidence: 99%

Nanoarchitectonics for Dynamic Functional Materials from Atomic‐/Molecular‐Level Manipulation to Macroscopic Action

et al. 2015

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“…In contrast to its regioisomer 1, ligand 3 induced a strong increase in CD intensity of AT-rich sequences (ctDNA at 275 nm, AT-DNA at 260 and 282 nm, and ATT at 282 nm) and strong positive ICD bands around 350 nm (Supplementary Materials). Similar condensationlike changes of the nucleic acid structure could be utilized in pharmaceutics for DNA delivery by viral or non-viral vectors in gene therapy [79][80][81]. Furthermore, DNA condensation can be applied in the construction of biosensors based on the liquid-crystalline properties of condensed DNA [82].…”

Section: Discussionmentioning

confidence: 99%

Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands

et al. 2022

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Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences.

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“…Such macromolecules can directly or indirectly interfere in the natural intracellular DNA‐related processes and in the DNA–drug interactions, by changing water activity on the double‐helix, or even by directly interacting with the biopolymer and/or with the drug used . Despite the relevance of such topic, few works have used force spectroscopy to investigate the DNA condensation process at a single molecule level and the interactions of condensed DNA with drugs. …”

Section: Introductionmentioning

confidence: 99%

Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA)

et al. 2017

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In this work, we have studied the interaction between the anticancer drug doxorubicin (doxo) and condensed DNA, using optical tweezers. To perform this task, we use the protein bovine serum albumin (BSA) in the working buffer to mimic two key conditions present in the real intracellular environment: the condensed state of the DNA and the abundant presence of charged macromolecules in the surrounding medium. In particular, we have found that, when doxo is previously intercalated in disperse DNA, the drug hinders the DNA condensation process upon the addition of BSA in the buffer. On the other hand, when bare DNA is firstly condensed by BSA, doxo is capable to intercalate and to unfold the DNA condensates at relatively high concentrations. In addition, a specific interaction between BSA and doxo was verified, which significantly changes the chemical equilibrium of the DNA-doxo interaction. Finally, the presence of BSA in the buffer stabilizes the double-helix structure of the DNA-doxo complexes, preventing partial DNA denaturation induced by the stretching forces.

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Direct Observation of Dynamic Mechanical Regulation of DNA Condensation by Environmental Stimuli

Cited by 9 publications

References 36 publications

Nanoarchitectonics for Dynamic Functional Materials from Atomic‐/Molecular‐Level Manipulation to Macroscopic Action

Nanoarchitectonics for Dynamic Functional Materials from Atomic‐/Molecular‐Level Manipulation to Macroscopic Action

Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands

Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA)

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