Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression
Nature Structural & Molecular Biology,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 16, 2024
Language: Английский
AAV Genome Topology Decides ITR Secondary Structure
BioEssays,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 5, 2025
Intra-strand
base
pairing
is
possible
when
double-stranded
DNA
contains
inverted
repeats,
but
vanishingly
improbable
without
so-called
negative
superhelicity.
This
superhelicity
itself
conditional
upon
whether
the
molecule
can
retain
torsional
stress-a
question
of
"topology."
principle
has
been
uncontroversial
to
biophysicists
since
1980s
proven
challenging
for
outsiders
grasp
and
retain.
For
those
in
AAV
research,
this
constitutes
a
decades-long
missed
connection.
one
multitude
viruses
bearing
secondary-structure-forming
elements
on
their
termini.
Its
"inverted
terminal
repeats"
(ITRs)
self-anneal
into
relatively
large
hammerhead
structures
both
ends
dynamically
structured
genome
are
central
numerous
host
interactions
that
drive
viral
lifecycle.
A
standalone
article
such
as
therefore
warranted
promote
an
understanding
these
ideas
research
community
highlight
significance
basic
biology
virus
its
vector
gene
delivery
system.
Language: Английский
Application of a bivalent “click” approach to target tyrosyl-DNA phosphodiesterase 1 (TDP1)
RSC Medicinal Chemistry,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 1, 2025
Application
of
copper-catalyzed
azide–alkyne
cycloaddition
(CuAAC)
“click”
reactions
assemble
bivalent
proteolysis-targeting
chimeras
(PROTACs)
constituents
targeting
tyrosyl-DNA
phosphodiesterase
1
(TDP1).
Language: Английский
Topological epigenetics: The biophysics of DNA supercoiling and its relation to transcription and genome instability
Current Opinion in Cell Biology,
Journal Year:
2024,
Volume and Issue:
92, P. 102448 - 102448
Published: Dec. 12, 2024
Language: Английский
A convenient single-cell newly synthesized transcriptome assay reveals gene expression dynamics during early-stage T-cell activation
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 23, 2024
Abstract
Sequencing
newly
synthesized
transcriptome
alongside
regular
in
single
cells
enables
the
study
of
gene
expression
temporal
dynamics
during
rapid
chromatin
and
regulation
processes.
However,
existing
assays
to
profile
single-cell
require
in-house
technical
expertise
achieve
high
cellular
throughput,
limiting
their
widespread
application.
Here,
we
developed
NOTE-seq,
a
method
that
simultaneously
profiles
transcriptomes
cells.
NOTE-seq
integrates
4-thiouridine
labeling
RNA,
thiol-alkylation-based
chemical
conversion,
streamlined
workflow
on
10X
Genomics
platform,
offering
throughput
is
accessible
convenient
for
biology
laboratories
without
specialized
expertise.
Using
characterized
early-stage
T-cell
activation
Jurkat
naïve
T
cells,
identified
transcription
factors
regulons,
discovered
Fli-1
as
master
factor
upon
stimulation.
Interestingly,
chemotherapeutic
topoisomerase
inhibitor
affects
level
indicating
potential
complications
immune
system.
Language: Английский
Optical tweezers in biomedical research – progress and techniques
Journal of Medicine and Life,
Journal Year:
2024,
Volume and Issue:
17(11), P. 978 - 993
Published: Nov. 1, 2024
Optical
tweezers,
which
leverage
the
forces
exerted
by
radiation
pressure,
have
emerged
as
a
pivotal
technique
for
precisely
manipulating
and
analyzing
microscopic
particles.
Since
Arthur
Ashkin's
ground-breaking
work
in
1970s
subsequent
development
of
single-beam
optical
trap
1986,
capabilities
tweezers
expanded
significantly,
enabling
intricate
manipulation
biological
specimens
at
micro-
nanoscale.
This
review
elucidates
foundational
principles
trapping
their
extensive
applications
biomedical
sciences.
The
biomedicine
are
vast,
ranging
from
investigation
cellular
mechanical
properties,
such
cell
stretching,
membrane
elasticity,
stiffness,
to
single-molecule
studies
encompassing
DNA
protein
mechanics,
protein-DNA
interactions,
molecular
motor
functions,
pathogen-host
interactions.
Advancement
this
field
includes
integration
with
holography,
fluorescence
microscopy,
microfluidics,
enhancements
force
sensitivity
positional
accuracy.
These
tools
profoundly
impacted
study
drug
discovery
processes,
disease
diagnostics,
providing
unparalleled
insights
into
biophysical
mechanisms
underlying
health
pathology.
Language: Английский