Journal of the American Chemical Society,
Год журнала:
2020,
Номер
142(33), С. 14117 - 14124
Опубликована: Июль 22, 2020
To
understand
the
role
of
intracellular
metabolites
in
cellular
processes,
it
is
important
to
measure
dynamics
and
fluxes
small
molecules
living
cells.
Although
conventional
metabolite
sensors
composed
fluorescent
proteins
have
been
made
detect
some
metabolites,
an
emerging
approach
use
genetically
encoded
RNA.
Because
ability
rapidly
generate
metabolite-binding
RNA
aptamers,
RNA-based
potential
be
designed
more
readily
than
protein-based
sensors.
Numerous
strategies
developed
convert
green-fluorescent
Spinach
or
Broccoli
fluorogenic
aptamers
into
metabolite-regulated
Nevertheless,
red
fluorescence
particularly
desirable
because
low
level
background
However,
variant
aptamer,
Red
Broccoli,
does
not
exhibit
cells
when
imaged
with
its
cognate
fluorophore.
It
known
why
vitro
but
live
mammalian
Here,
we
develop
a
new
fluorophore,
OBI
(3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime-1-benzoimidazole),
which
binds
high
affinity
makes
resistant
thermal
unfolding.
We
show
that
enables
detected
Furthermore,
can
fused
S-adenosyl
methionine
(SAM)-binding
aptamer
sensor
imaging
SAM
These
results
reveal
functions
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Янв. 2, 2024
Abstract
The
hydrated
electron,
e
–
(aq)
,
has
attracted
much
attention
as
a
central
species
in
radiation
chemistry.
However,
less
is
known
about
at
the
water/air
surface,
despite
its
fundamental
role
electron
transfer
processes
interfaces.
Using
time-resolved
electronic
sum-frequency
generation
spectroscopy,
spectrum
of
interface
and
dynamics
are
measured
here,
following
photo-oxidation
phenoxide
anion.
spectral
maximum
agrees
with
that
for
bulk
shows
orbital
density
resides
predominantly
within
aqueous
phase,
agreement
supporting
calculations.
In
contrast,
chemistry
interfacial
differs
from
water,
diffusing
into
leaving
phenoxyl
radical
surface.
Our
work
resolves
long-standing
questions
highlights
potential
ubiquitous
interface.
Journal of Chemical Theory and Computation,
Год журнала:
2017,
Номер
13(6), С. 2561 - 2570
Опубликована: Май 4, 2017
The
probability
of
non-radiative
transitions
in
photochemical
dynamics
is
determined
by
the
derivative
couplings,
couplings
between
different
electronic
states
through
nuclear
degrees
freedom.
Efficient
and
accurate
evaluation
is,
therefore,
central
importance
to
realize
reliable
computer
simulations
reactions.
In
this
work,
for
multistate
multireference
second-order
perturbation
theory
(MS-CASPT2)
its
'extended'
variant
(XMS-CASPT2)
are
studied,
which
we
present
an
algorithm
their
analytical
evaluation.
computational
costs
evaluating
essentially
same
as
those
calculating
energy
gradients.
geometries
energies
calculated
with
XMS-CASPT2
small
molecules
at
minimum
conical
intersections
(MECIs)
good
agreement
computed
configuration
interaction.
As
numerical
examples,
MECIs
optimized
using
stilbene
a
GFP
model
chromophore
(the
4-para-hydroxybenzylidene-1,2-dimethyl-imidazolin-5-one
anion).
Molecular Biology of the Cell,
Год журнала:
2017,
Номер
28(7), С. 848 - 857
Опубликована: Март 30, 2017
Genetically
encoded
fluorescent
tags
are
protein
sequences
that
can
be
fused
to
a
of
interest
render
it
fluorescent.
These
have
revolutionized
cell
biology
by
allowing
nearly
any
imaged
light
microscopy
at
submicrometer
spatial
resolution
and
subsecond
time
in
live
or
organism.
They
also
used
measure
abundance
thousands
millions
cells
using
flow
cytometry.
Here
I
provide
an
introduction
the
different
genetic
available,
including
both
intrinsically
proteins
derive
their
fluorescence
from
binding
either
endogenous
exogenous
fluorophores.
discuss
optical
biological
properties
guidelines
for
choosing
appropriate
experiment.
Tools
tagging
nucleic
acid
reporter
molecules
detect
presence
biomolecules
briefly
discussed.
Science,
Год журнала:
2020,
Номер
367(6473), С. 76 - 79
Опубликована: Янв. 3, 2020
Electrostatics
guide
chromophore
twist
Photoisomerization—the
twisting
of
bonds
in
a
molecule
response
to
absorption
light—is
exploited
biology
sense
light
and
can
influence
the
photophysical
properties
fluorescent
proteins
used
imaging
applications.
Romei
et
al.
studied
this
behavior
by
introducing
unnatural
amino
acids
into
photoswitchable
green
protein
Dronpa2,
thus
systematically
altering
electronic
(see
Perspective
Hu
).
Crystal
structures
spectroscopic
analyses
series
these
variants
support
model
which
electrostatic
interactions
between
its
environment
barrier
heights
for
around
different
during
photoisomerization.
These
insights
may
future
design
with
desired
properties.
Science
,
issue
p.
76
;
see
also
26
The Journal of Chemical Physics,
Год журнала:
2018,
Номер
149(18)
Опубликована: Ноя. 8, 2018
The
field
of
computational
molecular
sciences
(CMSs)
has
made
innumerable
contributions
to
the
understanding
phenomena
that
underlie
and
control
chemical
processes,
which
is
manifested
in
a
large
number
community
software
projects
codes.
CMS
now
poised
take
next
transformative
steps
better
training
modern
design
engineering
methods
tools,
increasing
interoperability
through
more
systematic
adoption
agreed
upon
standards
accepted
best-practices,
overcoming
unnecessary
redundancy
effort
along
with
greater
reproducibility,
deployment
new
onto
hardware
platforms
from
in-house
clusters
mid-range
computing
systems
supercomputers.
This
turn
will
have
future
impact
on
be
created
address
grand
challenge
science
we
illustrate
here:
formulation
diverse
catalysts,
descriptions
long-range
charge
excitation
transfer,
development
structural
ensembles
for
intrinsically
disordered
proteins.
ACS Chemical Biology,
Год журнала:
2019,
Номер
14(6), С. 1077 - 1090
Опубликована: Апрель 17, 2019
Development
of
single-molecule
localization
microscopy
(SMLM)
has
sparked
a
revolution
in
biological
imaging,
allowing
“super-resolution”
fluorescence
below
the
diffraction
limit
light.
The
past
decade
seen
an
explosion
not
only
optical
hardware
for
SMLM
but
also
development
or
repurposing
fluorescent
proteins
and
small-molecule
probes
this
technique.
In
review,
written
by
chemists
chemists,
we
detail
history
collate
collection
with
demonstrated
utility
SMLM.
We
hope
it
will
serve
as
primer
probe
choice
well
inspiration
new
fluorophores
that
enable
imaging
samples
exquisite
detail.
Methods and Applications in Fluorescence,
Год журнала:
2019,
Номер
7(2), С. 022002 - 022002
Опубликована: Март 1, 2019
The
right
choice
of
a
fluorescent
probe
is
essential
for
successful
luminescence
imaging
and
sensing
especially
concerning
in
vivo
vitro
applications,
the
development
new
classes
have
gained
more
attention
last
years.
One
most
promising
class
are
upconversion
nanoparticles
(UCNPs)—inorganic
nanocrystals
capable
to
convert
near-infrared
light
high
energy
radiation.
In
this
review
we
will
compare
UCNPs
with
other
probes
terms
(a)
optical
properties
probes,
such
as
their
brightness,
photostability
excitation
wavelength;
(b)
chemical
dispersibility,
stability
under
experimental
or
physiological
conditions,
availability
modification
strategies
labelling;
(c)
potential
toxicity
biocompatibility
probe.
Thereby
want
provide
better
understanding
advantages
drawbacks
address
future
challenges
design
nanocrystals.
The Journal of Physical Chemistry Letters,
Год журнала:
2024,
Номер
15(9), С. 2325 - 2331
Опубликована: Фев. 22, 2024
Time-resolved
spectroscopy
is
an
important
tool
for
unraveling
the
minute
details
of
structural
changes
in
molecules
biological
and
technological
significance.
The
nonlinear
femtosecond
signals
detected
such
systems
must
be
interpreted,
but
it
a
challenging
task
which
theoretical
simulations
are
often
indispensable.
Accurate
transient
absorption
or
two-dimensional
electronic
spectra
are,
however,
computationally
very
expensive,
prohibiting
wider
adoption
existing
first-principles
methods.
Here,
we
report
artificial-intelligence-enhanced
protocol
to
drastically
reduce
computational
cost
simulating
time-resolved
spectra,
makes
affordable
polyatomic
increasing
size.
based
on
doorway–window
approach
on-the-fly
surface-hopping
simulations.
We
show
its
applicability
prototypical
molecule
pyrazine
produces
with
high
precision
respect
ab
initio
reference
while
cutting
by
at
least
95%
compared
pure
