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Landscaping DNA binding potential of piperine derivatives by computational and biophysical methods.
Int J Biol Macromol
November 2024
Department of Molecular Biology, Kannur University, Kannur, Kerala 670661, India. Electronic address:
Piperine, the alkaloid from Black pepper, is known for its wide range of pharmacological effects. The DNA binding activity of piperine was reported earlier. In this work, we explore the DNA duplex binding properties of four piperine derivatives, piperonal, piperonyl alcohol, piperonylic acid, and piperic acid using biophysical and computational techniques.
View Article and Find Full Text PDFDark times: iminothioindoxyl--nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA.
Chem Sci
September 2024
Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Max-von-Laue-Str. 7 60438 Frankfurt Germany
Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, long linkers. In this study, we present two new iminothioindoxyl--nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA regular solid-phase synthesis. Especially with d as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities.
View Article and Find Full Text PDFBiophysics of Chromatin Remodeling.
Annu Rev Biophys
May 2021
T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA; email:
As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-like ATPase motor domains that can translocate along DNA, and a long-standing question in the field is how this activity is used to reposition or slide nucleosomes.
View Article and Find Full Text PDFProtein-induced B-Z transition of DNA duplex containing a 2'-OMe guanosine.
Biochem Biophys Res Commun
December 2020
Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam, 52828, South Korea. Electronic address:
Structural transformation of the canonical right-handed helix, B-DNA, to the non-canonical left-handed helix, Z-DNA, can be induced by the Zα domain of the human RNA editing enzyme ADAR1 (hZα). To characterize the site-specific preferences of binding and structural changes in DNA containing the 2'-O-methyl guanosine derivative (G), titration of the imino proton spectra and chemical shift perturbations were performed on hZα upon binding to Z-DNA. The structural transition between B-Z conformation as the changing ratio between DNA and protein showed a binding affinity of the modified DNA onto the Z-DNA binding protein similar to wild-type DNA or RNA.
View Article and Find Full Text PDFCrystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites.
Nucleic Acids Res
April 2020
Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.
Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts.
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