A novel DNA base-pairing beta-hairpin peptide involving intramolecular hydrogen bonds for induction of beta-hairpin secondary structure and intermolecular complementary hydrogen bonds between thymine and diaminopyridine for molecular recognition has been synthesized.
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http://dx.doi.org/10.1039/b924239b | DOI Listing |
Mikrochim Acta
January 2025
School of Science, Xihua University, Chengdu, 610039, People's Republic of China.
A dual-mode detection platform utilizing colorimetric and Raman was developed based on the exponential amplification reaction (EXPAR) strategy and a "core-satellite" structure constructed by bimetallic nanozymes to detect chloramphenicol (CAP). Initially, DNA-gated metal-organic frameworks (MOFs) incorporating cascaded amplification were used to be nanocarriers for the colorimetric and Raman reporter molecules (3,3',5,5'-tetramethylbiphenyl; TMB). Subsequently, assembled DNA served as gatekeepers to create a stimulus-responsive DNA-gated MOF (TMB@DNA/MOF).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.
From RNA interference to chromatin silencing, diverse genome defense pathways silence selfish genetic elements to safeguard genome integrity. Despite their diversity, different defense pathways share a modular organization, where numerous specificity factors identify diverse targets and common effectors silence them. In the PIWI-interacting RNA (piRNA) pathway, target RNAs are first identified by complementary base pairing with piRNAs and then silenced by PIWI-clade nucleases.
View Article and Find Full Text PDFACS Nano
January 2025
Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California 94720, United States.
DNA nanotechnology has emerged as a powerful approach to engineering biophysical tools, therapeutics, and diagnostics because it enables the construction of designer nanoscale structures with high programmability. Based on DNA base pairing rules, nanostructure size, shape, surface functionality, and structural reconfiguration can be programmed with a degree of spatial, temporal, and energetic precision that is difficult to achieve with other methods. However, the properties and structure of DNA constructs are greatly altered due to spontaneous protein adsorption from biofluids.
View Article and Find Full Text PDFAcc Chem Res
January 2025
Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
ConspectusStructural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures.
View Article and Find Full Text PDFIn duplex DNA, A-T and G-C form Watson-Crick base pairs, and Hoogsteen pairing only dominates upon protein binding or DNA damage. Using NMR, we show that an A-T Hoogsteen base pair previously observed in crystal structures of transposon DNA hairpins bound to TnpA protein forms in solution even in the absence of TnpA. This Hoogsteen base pair, located adjacent to a dinucleotide apical loop, exists in dynamic equilibrium with a minor Watson-Crick conformation (population ∼11% and lifetime ∼55 µs).
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