Stretching and Heating Single DNA Molecules with Optically Trapped Gold-Silica Janus Particles

Self-propelled micro- and nanoscale motors are capable of autonomous motion typically by inducing local concentration gradients or thermal gradients in their surrounding medium. This is a result of the heterogeneous surface of the self-propelled structures that consist of materials with different chemical or physical properties. Here we present a self-thermophoretically driven Au–silica Janus particle that can simultaneously stretch and partially melt a single double-stranded DNA molecule. We show that the effective force acting on the DNA molecule is in the ∼pN range, well suited to probe the entropic stretching regime of DNA, and we demonstrate that the local temperature enhancement around the gold side of the particle produces partial DNA dehybridization

Effect of Gender and Defensive Opponent on the Biomechanics of Sidestep Cutting

Purpose: Anterior cruciate ligament (ACL) injuries often occur in women during cutting maneuvers to evade a defensive player. Gender differences in knee kinematics have been observed, but it is not known to what extent these are linked to abnormal neuromuscular control elsewhere in the kinetic chain. Responses to defense players, which may be gender-dependent, have not been included in previous studies. This study determined the effects of gender and defense player on entire lower extremity biomechanics during sidestepping. Methods: Eight male and eight female subjects performed sidestep cuts with and without a static defensive opponent while 3D motion and ground reaction force data were recorded. Peak values of eight selected motion and force variables were, as well as their between-trial variabilities, submitted to a two-way (defense × gender) ANOVA. A Bonferroni-corrected alpha level of 0.003 denoted statistical significance. Results: Females had less hip and knee flexion, hip and knee internal rotation, and hip abduction. Females had higher knee valgus and foot pronation angles, and increased variability in knee valgus and internal rotation. Increased medial ground reaction forces and flexion and abduction in the hip and knee occurred with the defensive player for both genders. Conclusions: A simulated defense player causes increased lower limb movements and forces, and should be a useful addition to laboratory protocols for sidestepping. Gender differences in the joint kinematics suggest that increased knee valgus may contribute to ACL injury risk in women, and that the hip and ankle may play an important role in controlling knee valgus during sidestepping. Consideration of the entire lower extremity contributes to an understanding of injury mechanisms and may lead to better training programs for injury prevention

Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament

Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two recently developed magnetic tweezers assays, freely orbiting magnetic tweezers and magnetic torque tweezers, designed to measure the twist and torque of individual molecules. By directly monitoring changes in DNA twist on RAD51 binding, we determine the unwinding angle per RAD51 monomer to be 45°, in quantitative agreement with that of its bacterial homolog, RecA. Measurements of the torque that is built up when RAD51-dsDNA filaments are twisted show that under conditions that suppress ATP hydrolysis the torsional persistence length of the RAD51-dsDNA filament exceeds that of its RecA counterpart by a factor of three. Examination of the filament's torsional stiffness for different combinations of divalent ions and nucleotide cofactors reveals that the Ca2+ ion, apart from suppressing ATPase activity, plays a key role in increasing the torsional stiffness of the filament. These quantitative measurements of RAD51-imposed DNA distortions and accumulated mechanical stress suggest a finely tuned interplay between chemical and mechanical interactions within the RAD51 nucleoprotein filament

Torsional sensing of small-molecule binding using magnetic tweezers

DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3 ± 1° and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment

DNA fluctuations reveal the size and dynamics of topological domains

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here, we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real time and at the single-molecule level. Our approach is based on quantifying the extension fluctuations—in addition to the mean extension—of supercoiled DNA in magnetic tweezers (MT). Using a combination of high-speed MT experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime, the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how the transient (partial) dissociation of DNA-bridging proteins results in the dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our results to further the understanding and optimization of magnetic tweezer measurements and to enable quantification of the dynamics and reaction pathways of DNA processing enzymes in the context of physiologically relevant forces and supercoiling densities

The free energy landscape of retroviral integration

Retroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the replication cycle. Yet, strand transfer is intrinsically iso-energetic and it is not clear how efficient integration can be achieved. Here we investigate the dynamics of strand transfer and demonstrate that consecutive nucleoprotein intermediates interacting with a supercoiled target are increasingly stable, resulting in a net forward rate. Multivalent target interactions at discrete auxiliary interfaces render target capture irreversible, while allowing dynamic site selection. Active site binding is transient but rapidly results in strand transfer, which in turn rearranges and stabilizes the intasome in an allosteric manner. We find the resulting strand transfer complex to be mechanically stable and extremely long-lived, suggesting that a resolving agent is required in vivo

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold

SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be 2-N-(3-dimethylaminopropyl)-N-propylamino]-4-2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene-1-phenyl-quinolinium and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5~μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5~μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold

Additional roles of a peripheral loop–loop interaction in the Neurospora VS ribozyme

Many RNAs contain tertiary interactions that contribute to folding the RNA into its functional 3D structure. In the VS ribozyme, a tertiary loop–loop kissing interaction involving stem–loops I and V is also required to rearrange the secondary structure of stem–loop I such that nucleotides at the base of stem I, which contains the cleavage–ligation site, can adopt the conformation required for activity. In the current work, we have used mutants that constitutively adopt the catalytically permissive conformation to search for additional roles of the kissing interaction in vitro. Using mutations that disrupt or restore the kissing interaction, we find that the kissing interaction contributes ∼1000-fold enhancement to the rates of cleavage and ligation. Large Mg2+-dependent effects on equilibrium were also observed: in the presence of the kissing interaction cleavage is favored >10-fold at micromolar concentrations of Mg2+; whereas ligation is favored >10-fold at millimolar concentrations of Mg2+. In the absence of the kissing interaction cleavage exceeds ligation at all concentrations of Mg2+. These data provide evidence that the kissing interaction strongly affects the observed cleavage and ligation rate constants and the cleavage–ligation equilibrium of the ribozyme