Cerium chloride stimulated controlled conversion of B-to-Z DNA in self-assembled nanostructures

Bhanjadeo, Madhabi M.; Nayak, A.; Subudhi, Umakanta

doi:10.1016/j.bbrc.2016.11.133

Cited by 29 publications

(13 citation statements)

References 41 publications

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“…To drive B-DNA into Z-DNA, we utilized the ability of cerium (III) chloride (CeCl 3 ) to form self-assembled Z-DNA aggregate structures at low concentrations (<1 mM). CeCl 3 binds to the phosphate backbone of DNA, which thus neutralizes the electrostatic repulsion, allowing the Z-DNA form to be energetically favored (Bhanjadeo et al, 2017). We first confirmed that CeCl 3 induced conversion of gDNA to Z-form (Bhanjadeo et al, 2017) in a dose-dependent manner by spectroscopic A260/295 absorbance ratio assay (Thomas and Messner, 1988) (Figure S5C).…”

Section: Resultssupporting

confidence: 53%

“…CeCl 3 binds to the phosphate backbone of DNA, which thus neutralizes the electrostatic repulsion, allowing the Z-DNA form to be energetically favored (Bhanjadeo et al, 2017). We first confirmed that CeCl 3 induced conversion of gDNA to Z-form (Bhanjadeo et al, 2017) in a dose-dependent manner by spectroscopic A260/295 absorbance ratio assay (Thomas and Messner, 1988) (Figure S5C). To now determine whether CeCl 3 altered the Z-DNA content of biofilms, mature NTHI biofilms were incubated with increasing concentrations of CeCl 3, then probed for the presence of Z-DNA by IF IgG2a, and IgG purified from unimmunized rabbit serum (5 mg/mL).…”

Section: Resultssupporting

confidence: 53%

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Z-form extracellular DNA is a structural component of the bacterial biofilm matrix

Buzzo

Devaraj

Gloag

et al. 2021

Cell

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Section: Resultssupporting

confidence: 53%

Section: Resultssupporting

confidence: 53%

Z-form extracellular DNA is a structural component of the bacterial biofilm matrix

Buzzo

Devaraj

Gloag

et al. 2021

Cell

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“…Most artificial DNA nanostructures, from the immobile Holliday junction to GDa-sized DNA origami multimers and DNA bricks, are based on the association of DNA oligonucleotides into double helical segments and loops intertwined with one another in various ways. The use of alternative double helical forms (such as Z-DNA) has been limited to few examples, most likely due to the requirement of non-physiological conditions such as reduced water activity or the presence of metal-ion complexes [11,12]. Other DNA secondary structures, such as G-quadruplexes, i-motifs, hairpin dumbbells or loops, have been instead typically used as chemical sensors or topological markers.…”

Section: The Double Helixmentioning

confidence: 99%

Insights into the Structure and Energy of DNA Nanoassemblies

et al. 2020

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Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.

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“…Addition of thiazole orange caused a quick return from the Z‐form to the B‐form DNA. A similar methodology was then utilized by the Subudhi group to report on Ce +3 and La +3 levels based on their interaction with DNA, down to 7.5 × 10 −3 m concentrations with clear shifts in the CD spectra from 280 to 260 nm . The ability to induce and observe such conformational transitions in DNA suggests this as an excellent optical reporter probe of how drugs interact with DNA, especially given that many chemotherapeutics and several other drug classes including some antibiotics target and interact with DNA .…”

Section: Intrinsically Active Dna Materialsmentioning

confidence: 99%

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

Bui

Dı́az

Fontana

et al. 2019

Advanced Optical Materials

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Rapid development of DNA technology has provided a feasible route to creating nanoscale materials. DNA acts as a self‐assembled nanoscaffold capable of assuming any three‐dimensional shape. The ability to integrate dyes and new optical materials such as quantum dots and plasmonic nanoparticles precisely onto these architectures provides new ways to exploit their near‐ and far‐field interactions. A fundamental understanding of these optical processes will help drive development of next‐generation photonic nanomaterials. This review is focused on latest progress in DNA‐based photonic materials and highlights DNA scaffolds for rapidly assembling and prototyping nanoscale optical devices. Three areas are discussed including intrinsically active DNA structures displaying chiral properties, DNA scaffolds hosting plasmonic nanomaterials, and fluorophore‐labeled DNAs that engage in Förster resonance energy transfer and give rise to complex molecular photonic wires. An explanation of what is desired from these optical processes when harnessed sets the tone for what DNA scaffolds are providing toward each focus. Examples from the literature illustrate current progress along with a discussion of challenges to overcome for further improvements. Opportunities to integrate diverse classes of optically active molecules including light‐generating enzymes, fluorescent proteins, nanoclusters, and metal–chelates in new structural combinations on DNA scaffolds are also highlighted.

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Cerium chloride stimulated controlled conversion of B-to-Z DNA in self-assembled nanostructures

Cited by 29 publications

References 41 publications

Z-form extracellular DNA is a structural component of the bacterial biofilm matrix

Z-form extracellular DNA is a structural component of the bacterial biofilm matrix

Insights into the Structure and Energy of DNA Nanoassemblies

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

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