The porphyrin chromophore incorporated at the 5'-position of an oligonucleotide allows the simultaneous detection of the B- to Z-DNA transition via the porphyrin Soret band circular dichroism exciton couplet signal around 420 nm and the oligonucleotide CD region below 300 nm, at micromolar concentrations.
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http://dx.doi.org/10.1039/b603409h | DOI Listing |
J Chem Inf Model
January 2025
Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea.
The amber-OL21 force field (ff) was developed to better describe noncanonical DNA, including Z-DNA. Despite its improvements for DNA simulations, this study found that OL21's scope of application was limited by embedded ff artifacts. In a benchmark set of seven DNA molecules, including two double-stranded DNAs transitioning between B- and Z-DNA and five single-stranded DNAs folding into mini-dumbbell or G-quadruplex structures, the free energy landscapes obtained using OL21 revealed several issues: Z-DNA was overly stabilized; misfolded states in mini-dumbbell DNAs were most stable; DNA GQ folding was consistently biased toward an antiparallel topology.
View Article and Find Full Text PDFACS Omega
November 2024
DNA Nanomaterials & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India.
Rare earth elements have been shown to trigger the B-to-Z DNA transition in diverse self-assembled branched DNA architectures. Herein, we investigated the influence of cerium chloride on the conformational changes of DNA sequences containing repeated cytosine-guanine (CG) or guanine-cytosine (GC) sequences. The CD results show that (CG) repeats were susceptible to the formation of Z-DNA at low concentrations of CeCl.
View Article and Find Full Text PDFNucleic Acids Res
July 2024
Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada.
Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2'F-araC and 2'F-riboG, induce the formation of the Z-form under low ionic strength. We show that oligomers entirely made of these two nucleosides exclusively produce left-handed duplexes that bind to the Zα domain of ADAR1.
View Article and Find Full Text PDFAdv Mater
July 2024
CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.
DNA double-strand breaks (DSBs) yield highly determines radiotherapy efficacy. However, improving the inherent radiosensitivity of tumor DNA to promote radiation-induced DSBs remains a challenge. Using theoretical and experimental models, the underexplored impact of Z-DNA conformations on radiosensitivity, yielding higher DSBs than other DNA conformations, is discovered.
View Article and Find Full Text PDFInt J Biol Macromol
May 2024
DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address:
Zeta potential is commonly referred as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acids. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, for the first time we discover the zeta potential difference between B-DNA and lanthanum chloride-induced Z-DNA.
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