5282-87-1Relevant academic research and scientific papers
To D or not to D?: On estimating the microenvironment polarity of biomolecular cavities
Sinkeldam, Renatus W.,Tor, Yitzhak
, p. 2523 - 2528 (2008/03/12)
Knowledge of the local polarity of specific cavities in biopolymers can facilitate the design of selective low MW ligands that impact the structure and function of macromolecules. The most common tools for interrogating local polarity are fluorescent probes that are sensitive to their microenvironment. Researchers often evaluate and express this local polarity using dielectric constants, a parameter that reflects an inherent bulk property. A more appropriate expression should take into account solvent-solute interactions at the molecular level. Reevaluation of commonly used fluorophores illustrates the improved correlation between observed Stokes shift changes and ET(30) values as compared to the corresponding dielectric constants. The Royal Society of Chemistry.
A selective, noncovalent assay for base flipping in DNA
O'Neil, Lauren L.,Wiest, Olaf
, p. 16800 - 16801 (2007/10/03)
Base flipping, the conformational change of a nucleobase to an extrahelical position, is a key step in the enzymatic repair of damaged DNA. An assay that can detect the flipped-out species in free solution without covalent modification of the DNA would be desirable. The design and synthesis of a simple, sensitive, and rapid assay using specific noncovalent binding to pyrimidines by zinc-cyclen and a commonly used fluorescent reporter group, dansyl, is reported. The binding of the zinc-cyclen unit to a flipped-out thymine base results in a change in the fluorescent properties of the dansyl group that is distinct from nonspecific binding to duplex DNA or intercalation into either the flipped-in or flipped-out species. The assay was tested using fluorescence spectroscopy and detection at 533 ± 5 nm with normal and abasic duplex DNA as negative and positive controls. The data obtained are fitted to a one-site binding model to determine the equilibrium constant for the two-step process involving base flipping and binding to be ~10-6 M. Copyright
