5 research outputs found
Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces
The emerging Overhauser effect dynamic
nuclear polarization (ODNP)
technique measures the translational mobility of water within the
vicinity (5–15 Å) of preselected sites. The work presented
here expands the capabilities of the ODNP technique and illuminates
an important, previously unseen, property of the translational diffusion
dynamics of water at the surface of DNA duplexes. We attach nitroxide
radicals (i.e., spin labels) to multiple phosphate backbone positions
of DNA duplexes, allowing ODNP to measure the hydration dynamics at
select positions along the DNA surface. With a novel approach to ODNP
analysis, we isolate the contributions of water molecules at these
sites that undergo free translational diffusion from water molecules
that either loosely bind to or exchange protons with the DNA. The
results reveal that a significant population of water in a localized
volume adjacent to the DNA surface exhibits fast, bulk-like characteristics
and moves unusually rapidly compared to water found in similar probe
volumes near protein and membrane surfaces. Control studies show that
the observation of these characteristics are upheld even when the
DNA duplex is tethered to streptavidin or the mobility of the nitroxides
is altered. This implies that, as compared to protein or lipid surfaces,
it is an intrinsic feature of the DNA duplex surface that it interacts
only weakly with a significant fraction of the surface hydration water
network. The displacement of this translationally mobile water is
energetically less costly than that of more strongly bound water by
up to several <i>k</i><sub>B</sub><i>T</i> and
thus can lower the activation barrier for interactions involving the
DNA surface
Investigating Functional DNA Grafted on Nanodiamond Surface Using Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy
Nanodiamonds (NDs) are a new and
attractive class of materials
for sensing and delivery in biological systems. Methods for functionalizing
ND surfaces are highly valuable in these applications, yet reported
approaches for covalent modification with biological macromolecules
are still limited, and characterizing behaviors of ND-tethered biomolecules
is difficult. Here we demonstrated the use of copper-free click chemistry
to covalently attach DNA strands at ND surfaces. Using site-directed
spin labeling and electron paramagnetic resonance spectroscopy, we
demonstrated that the tethered DNA strands maintain the ability to
undergo repetitive hybridizations and behave similarly to those in
solutions, maintaining a large degree of mobility with respect to
the ND. The work established a method to prepare and characterize
an easily addressable identity tag for NDs. This will open up future
applications such as targeted ND delivery and developing sensors for
investigating biomolecules
Global Structure of a Three-Way Junction in a Phi29 Packaging RNA Dimer Determined Using Site-Directed Spin Labeling
The condensation of bacteriophage phi29 genomic DNA into
its preformed
procapsid requires the DNA packaging motor, which is the strongest
known biological motor. The packaging motor is an intricate ring-shaped
protein/RNA complex, and its function requires an RNA component called
packaging RNA (pRNA). Current structural information on pRNA is limited,
which hinders studies of motor function. Here, we used site-directed
spin labeling to map the conformation of a pRNA three-way junction
that bridges binding sites for the motor ATPase and the procapsid.
The studies were carried out on a pRNA dimer, which is the simplest
ring-shaped pRNA complex and serves as a functional intermediate during
motor assembly. Using a nucleotide-independent labeling scheme, stable
nitroxide radicals were attached to eight specific pRNA sites without
perturbing RNA folding and dimer formation, and a total of 17 internitroxide
distances spanning the three-way junction were measured using Double
Electron–Electron Resonance spectroscopy. The measured distances,
together with steric chemical constraints, were used to select 3662
viable three-way junction models from a pool of 65 billion. The results
reveal a similar conformation among the viable models, with two of
the helices (H<sub>T</sub> and H<sub>L</sub>) adopting an acute bend.
This is in contrast to a recently reported pRNA tetramer crystal structure,
in which H<sub>T</sub> and H<sub>L</sub> stack onto each other linearly.
The studies establish a new method for mapping global structures of
complex RNA molecules, and provide information on pRNA conformation
that aids investigations of phi29 packaging motor and developments
of pRNA-based nanomedicine and nanomaterial
Nitroxide Sensing of a DNA Microenvironment: Mechanistic Insights from EPR Spectroscopy and Molecular Dynamics Simulations
The behavior of the nitroxide spin labels 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline
(R5a) and 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) attached at a phosphorothioate-substituted
site in a DNA duplex is modulated by the DNA in a site- and stereospecific
manner. A better understanding of the mechanisms of R5a/R5 sensing
of the DNA microenvironment will enhance our capability to relate
information from nitroxide spectra to sequence-dependent properties
of DNA. Toward this goal, electron paramagnetic resonance (EPR) spectroscopy
and molecular dynamics (MD) simulations were used to investigate R5
and R5a attached as R<sub><i>p</i></sub> and S<sub><i>p</i></sub> diastereomers at phosphorothioate <sub>pS</sub>C<sub>7</sub> of dÂ(CTACTG<sub>pS</sub>C<sub>7</sub>Y<sub>8</sub>TTAG).
dÂ(CTAAAGCAGTAG) (Y = T or U). X-band continuous-wave EPR spectra revealed
that the dT<sub>8</sub> to dU<sub>8</sub> change alters nanosecond
rotational motions of R<sub><i>p</i></sub>-R5a but produces
no detectable differences for S<sub><i>p</i></sub>-R5a,
R<sub><i>p</i></sub>-R5, and S<sub><i>p</i></sub>-R5. MD simulations were able to qualitatively account for these
spectral variations and provide a plausible physical basis for the
R5/R5a behavior. The simulations also revealed a correlation between
DNA backbone B<sub>I</sub>/B<sub>II</sub> conformations and R5/R5a
rotational diffusion, thus suggesting a direct connection between
DNA local backbone dynamics and EPR-detectable R5/R5a motion. These
results advance our understanding of how a DNA microenvironment influences
nitroxide motion and the observed EPR spectra. This may enable use
of R5/R5a for a quantitative description of the sequence-dependent
properties of large biologically relevant DNA molecules
CRISPR–Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling
The RNA-guided CRISPR–Cas9
nuclease has revolutionized genome
engineering, yet its mechanism for DNA target selection is not fully
understood. A crucial step in Cas9 target recognition involves unwinding
of the DNA duplex to form a three-stranded R-loop structure. Work
reported here demonstrates direct detection of Cas9-mediated DNA unwinding
by a combination of site-directed spin labeling and molecular dynamics
simulations. The results support a model in which the unwound nontarget
strand is stabilized by a positively charged patch located between
the two nuclease domains of Cas9 and reveal uneven increases in flexibility
along the unwound nontarget strand upon scissions of the DNA backbone.
This work establishes the synergistic combination of spin-labeling
and molecular dynamics to directly monitor Cas9-mediated DNA conformational
changes and yields information on the target DNA in different stages
of Cas9 function, thus advancing mechanistic understanding of CRISPR–Cas9
and aiding future technological development