10 research outputs found
Aryne Compatible Solvents are not Always Innocent
Arynes are important
and versatile intermediates in a variety of
transformations. Commonly used solvents for aryne chemistry include
acetonitrile and dichloromethane. Although rarely reported, the reactive
nature of aryne intermediates makes them prone to side reactions,
which sometimes involve solvent participation. Acetonitrile and dichloromethane
are not always innocent solvents and can participate in aryne-based
reactions. These results are presented in the context of ongoing mechanistic
investigations of the triple aryne–tetrazine reaction
Aza-Glycine Induces Collagen Hyperstability
Hydrogen
bonding is fundamental to life on our planet, and nature
utilizes H-bonding in nearly all biomolecular interactions.
Often, H-bonding is already maximized in natural biopolymer
systems such as nucleic acids, where Watson–Crick H-bonds are
fully paired in double-helical structures. Synthetic chemistry allows
molecular editing of biopolymers beyond nature’s capability.
Here we demonstrate that substitution of glycine (Gly) with aza-glycine
in collagen may increase the number of interfacial cross-strand
H-bonds, leading to hyperstability in the triple-helical form.
Gly is the only amino acid that has remained intolerant to substitution
in collagen. Our results highlight the vital importance of maximizing
H-bonding in higher order biopolymer systems using minimally perturbing
alternatives to nature’s building blocks
Rational Design and Facile Synthesis of a Highly Tunable Quinoline-Based Fluorescent Small-Molecule Scaffold for Live Cell Imaging
Small-molecule
fluorescent probes are powerful tools for chemical biology; however,
despite the large number of probes available, there is still a need
for a simple fluorogenic scaffold, which allows for the rational design
of molecules with predictable photophysical properties and is amenable
to concise synthesis for high-throughput screening. Here, we introduce
a highly modular quinoline-based probe containing three strategic
domains that can be easily engineered and optimized for various applications.
Such domains are allotted for (1) compound polarization, (2) tuning
of photophysical properties, and (3) structural diversity. We successfully
synthesized our probes in two steps from commercially available starting
materials in overall yields of up to 95%. Facile probe synthesis was
permitted by regioselective palladium-catalyzed cross-coupling, which
enables combinatorial development of structurally diverse quinoline-based
fluorophores. We have further applied our probes to live-cell imaging,
utilizing their unique two-stage fluorescence response to intracellular
pH. These studies provide a full demonstration of our strategy in
rational design and stream-lined probe discovery to reveal the diverse
potential of quinoline-based fluorescent compounds
Synthesis and Conformational Dynamics of the Reported Structure of Xylopyridine A
Natural
products have served as a rich source for the discovery
of new nucleic acid targeting molecules for more than half a century.
However, our ability to design molecules that bind nucleic acid motifs
in a sequence- and/or structure-selective manner is still in its infancy.
Xylopyridine A, a naturally occurring molecule of unprecedented architecture,
has been found to bind DNA by a unique mode of intercalation. Here
we show that the structure proposed for xylopyridine A is not consistent
with the characterization in the original isolation report and does
not bind B-form DNA. Instead, we report that the originally proposed
structure for xylopyridine A represents a new class of conformationally
dynamic structure-selective quadruplex nucleic acid binder. The unique
molecular conformation locks out nonspecific intercalative binding
modes and provides a starting point for the design of a new class
of structure-specific nucleic acid binder
Synthesis and Conformational Dynamics of the Reported Structure of Xylopyridine A
Natural
products have served as a rich source for the discovery
of new nucleic acid targeting molecules for more than half a century.
However, our ability to design molecules that bind nucleic acid motifs
in a sequence- and/or structure-selective manner is still in its infancy.
Xylopyridine A, a naturally occurring molecule of unprecedented architecture,
has been found to bind DNA by a unique mode of intercalation. Here
we show that the structure proposed for xylopyridine A is not consistent
with the characterization in the original isolation report and does
not bind B-form DNA. Instead, we report that the originally proposed
structure for xylopyridine A represents a new class of conformationally
dynamic structure-selective quadruplex nucleic acid binder. The unique
molecular conformation locks out nonspecific intercalative binding
modes and provides a starting point for the design of a new class
of structure-specific nucleic acid binder
Structural Basis for Aza-Glycine Stabilization of Collagen
Previously,
we have demonstrated that replacement of the strictly
conserved glycine in collagen with aza-glycine provides a general
solution for stabilizing triple helical collagen peptides (Chenoweth,
D. M.; et al. <i>J. Am. Chem. Soc.</i> <b>2016</b>, <i>138</i>, 9751; <b>2015</b>, <i>137</i>, 12422). The additional hydrogen
bond and conformational constraints provided by aza-glycine increases
the thermal stability and rate of folding in collagen peptides composed
of Pro-Hyp-Gly triplet repeats, allowing for truncation to the smallest
self-assembling peptide systems observed to date. Here we show that
aza-glycine substitution enhances the stability of an arginine-containing
collagen peptide and provide a structural basis for this stabilization
with an atomic resolution crystal structure. These results demonstrate
that a single nitrogen atom substitution for a glycine alpha-carbon
increases the peptide’s triple helix melting temperature by
8.6 °C. Furthermore, we provide the first structural basis for
stabilization of triple helical collagen peptides containing aza-glycine
and we demonstrate that minimal alteration to the peptide backbone
conformation occurs with aza-glycine incorporation
Synthesis of 9‑Substituted Triptycene Building Blocks for Solid-Phase Diversification and Nucleic Acid Junction Targeting
Triptycenes have
been shown to bind nucleic acid three-way junctions,
but rapid and efficient methods to diversify the triptycene core are
lacking. An efficient synthesis of a 9-substituted triptycene scaffold
is reported that can be used as a building block for solid-phase peptide
synthesis and rapid diversification. The triptycene building block
was diversified to produce a new class of tripeptide–triptycenes,
and their binding abilities toward d(CAG)·(CTG) repeat junctions
were investigated
Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders
Recently, the utility
of triptycene as a scaffold for targeting
nucleic acid three-way junctions was demonstrated. A rapid, efficient
route for the synthesis of bridgehead-substituted triptycenes is reported,
in addition to solid-phase diversification to a new class of triptycene
peptides. The triptycene peptides were evaluated for binding to a
d(CAG)·(CTG) repeat DNA junction exhibiting potent affinities.
The bridgehead-substituted triptycenes provide new building blocks
for rapid access to diverse triptycene ligands with novel architectures
Ultrafast Solvation Dynamics and Vibrational Coherences of Halogenated Boron-Dipyrromethene Derivatives Revealed through Two-Dimensional Electronic Spectroscopy
Boron-dipyrromethene (BODIPY) chromophores
have a wide range of
applications, spanning areas from biological imaging to solar energy
conversion. Understanding the ultrafast dynamics of electronically
excited BODIPY chromophores could lead to further advances in these
areas. In this work, we characterize and compare the ultrafast dynamics
of halogenated BODIPY chromophores through applying two-dimensional
electronic spectroscopy (2DES). Through our studies, we demonstrate
a new data analysis procedure for extracting the dynamic Stokes shift
from 2DES spectra revealing an ultrafast solvent relaxation. In addition,
we extract the frequency of the vibrational modes that are strongly
coupled to the electronic excitation, and compare the results of structurally
different BODIPY chromophores. We interpret our results with the aid
of DFT calculations, finding that structural modifications lead to
changes in the frequency, identity, and magnitude of Franck–Condon
active vibrational modes. We attribute these changes to differences
in the electron density of the electronic states of the structurally
different BODIPY chromophores
Optochemical Control of Protein Localization and Activity within Cell-like Compartments
We report inducible dimerization
strategies for controlling protein
positioning, enzymatic activity, and organelle assembly inside synthetic
cell-like compartments upon photostimulation. Using a photocaged TMP-Haloligand
compound, we demonstrate small molecule and light-induced dimerization
of DHFR and Haloenzyme to localize proteins to a compartment boundary
and reconstitute tripartite sfGFP assembly. Using photocaged rapamycin
and fragments of split TEV protease fused to FRB and FKBP, we establish
optical triggering of protease activity inside cell-size compartments.
We apply light-inducible protease activation to initiate assembly
of membraneless organelles, demonstrating the applicability of these
tools for characterizing cell biological processes in vitro. This
modular toolkit, which affords spatial and temporal control of protein
function in a minimal cell-like system, represents a critical step
toward the reconstitution of a tunable synthetic cell, built from
the bottom up