3 research outputs found
Bodipy-Labeled Nucleoside Triphosphates for Polymerase Synthesis of Fluorescent DNA
New
fluorescent nucleosides and nucleoside triphosphate (dNTPs)
analogs bearing the F-Bodipy fluorophore linked through a short, flexible
nonconjugate tether were synthesized. The Bodipy-labeled dNTPs were
substrates for several DNA polymerases which incorporated them into
DNA in primer extension, nicking enzyme amplification reaction, and
polymerase chain reaction. The fluorescence of F-Bodipy is not quenched
upon incorporation in DNA and can be detected both in solutions and
on gels
A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation
Mapping
of weak and hence transient interactions between low-abundance
interacting molecules is still a major challenge in systems biology
and protein biochemistry. Therefore, additional system-wide acting
tools are needed to determine protein interactomics. Most important
are reagents that can be applied at any kind of protein interface
and the possibility to enrich cross-linked fragments with high efficiency.
In this study, we report the synthesis of a novel noncanonical amino
acid that features a diazirine group for ultraviolet cross-linking
as well as an alkyne group for labeling by click chemistry. This bifunctional
amino acid, called PrDiAzK, may be inserted into almost any protein
interface with minimal structural perturbation using genetic code
expansion. We demonstrate that PrDiAzK can be site-selectively incorporated
into proteins in both bacterial and mammalian cell cultures, and we
show that PrDiAzK allows protein labeling as well as cross-linking.
In addition, we tested PrDiAzK for proteome-wide incorporation via
stochastic orthogonal recoding of translation, implying potential
applications in system-wide mapping of protein–protein interactions
in the future
A Universal Nucleoside with Strong Two-Band Switchable Fluorescence and Sensitivity to the Environment for Investigating DNA Interactions
With the aim of developing a new tool to investigate
DNA interactions,
a nucleoside analogue incorporating a 3-hydroxychromone (3HC) fluorophore
as a nucleobase mimic was synthesized and incorporated into oligonucleotide
chains. In comparison with existing fluorescent nucleoside analogues,
this dye features exceptional environmental sensitivity switching
between two well-resolved fluorescence bands. In labeled DNA, this
nucleoside analogue does not alter the duplex conformation and exhibits
a high fluorescence quantum yield. This probe is up to 50-fold brighter
than 2-aminopurine, the fluorescent nucleoside standard. Moreover,
the dual emission is highly sensitive to the polarity of the environment;
thus, a strong shielding effect of the flanking bases from water was
observed. With this nucleoside, the effect of a viral chaperone protein
on DNA base stacking was site-selectively monitored