Torque and Topology of Braided DNAs under Tension

Double helix DNAs become intertwined around one another during replication and recombination.Here we used magnetic tweezers to make braided DNA molecules and measured their torques under various catenations(Ca)at forces ranging from 0.3 to 8 pN.Images of braided DNA constructs under tensions were captured by scanning electron microscopy which showed major and minor grooves of DNAs and plectonemes of the braids.When the two DNA molecules were braided,the extension decreased as the catenation increased from 0 to 50 turns.We used a thermodynamic Maxwell relation to deduce the torque by integrating the change in the braid extension as a function of the force.The torque increased with the catenation,force and intertether distance until the catenation reached a buckling point.Under the condition of 2 pN force and Ca=20,the torque was computed to be 31,21 and 15 pN nm for the braids of which the intertether distances were 54%,31%and 26%of the DNA contour length,respectively.At an 8.03 pN holding force,the torque was computed to be 76 pN nm as the catenation increased from 0 to 30 turns,or as the catenation density varied from 0 to 0.053.The torque reached a plateau when the catenation increased above 20,indicating formation of braid-plectonemes.The twist modulus increased with the catenation prior to reaching a peak.Before reaching the peak,the moduli were higher than those of a single twisted DNA under the same catenation and applied force.Our experimental data agrees well with the calculation results by a recently developed semiflexible polymer model.Our measurements of the nonlinear torque of the braid establish new fundamental properties of DNA intertwining,which is key to understanding DNA replication and gene expression.The speaker will also introduce briefly other projects in the Xiao group including direct measurements of theforce spectrum of single unlabeled proteins such as adhesive nano-fibers for biofilm,the screening of integrin-targeted peptides drugs by single cell approaches,and the micromechanical approach for determining the survival rate of stem cells.

Force Spectrum of Single CsgA Nanofiber Reveal Surprising Properties

CsgA protein monomers consist of aβ-helix of five repeat units possessing several conservative residues and thus,inherently fibrillate.CsgA protein monomers could self-assemble into hierarchical nanofiber structure cross multiple scales after expression and secretion by E.Coli cells.Previous researches show that CsgA nanofibers could provide adhesion,stiffness,and mechanical homogeneity for the biofilms,host cells’fibronectin binding for internalization,or protection against phage attack.CsgA nanofibers have obtained various applications in material science and synthetic biology.To illustrate,CsgA nanofibers have characteristics of intrinsic hierarchical structures across multiple scales,robustness in harsh environments and programmable functionality via biological tools.Studying the force spectrum or mechanical properties of the nanofiber can provide fundamental information of self-assembly process and ultra-stability in extreme conditions.Single molecule techniques such as atomic force microscopy,optical tweezers,and magnetic tweezers have been widely applied to study proteins.In these studies,proteins are usually chemically conjugated or genetically constructed to have a tag such as histidine,cysteine or biotin.Genetic engineering requires modification of the plasmids encoding the specific protein,and also involve special protein expression and purification.Such study needs collaboration from multi-disciplinary.It normally studies one protein at a time which gives out clear signal but lacks throughput and efficiency.Here we have established a simple method to measure all kinds of proteins without labels.The carboxyl terminus of a protein is attached to the amine group on a magnetic bead,and the amine terminus of the protein is attached to glutaraldehyde on the glass slide.Then we used magnetic tweezers to manipulate and stretched the bead and protein.Extension versus rotation relation was used to identify a single protein or protein fibril.The fiber under tension is also observed by Scanning Electronic Microcopy which convinces that single CsgA-His fibril is linked to a microbead.The peak of diameter distribution is around 15 nm.The fracture of fibers was observed in real time on SEM.Force-extension curves of single fibers are obtained in real time.The force-extension curves generally agree with the worm like chain model.The persistence lengths from the fitting are from 0.9 to 49.8 nm.The elongation ratio increases gradually with force until reaches a plateau.The maximum elongation ratio of 78 nanofibers were made into an elongation ratio distribution diagram,more than half of CsgA-His nanofibers has an elongation ratio from 0 to 2,some are distributed in 2~10,and a few are distributed in 10~18.The maximum elongation ratio of CsgA-His nanofibers is 17.1,indicating that the fibril’s flexibility is much higher than DNA or silk fiber.For forces less than 20 pN,the extension was reversible.With a 42.1 pN holding force,the extension jumped in steps of from 30 to 365 nm and was irreversible.At the scale tested,the jumps corresponded to the unfolding of multiple beta sheets in the fiber.Work for CsgA-His nanofibers during stretching increase with the normalized strain fractions.The experimental data agree with a theoretical prediction for a single CsgA protein from a SMD calculation.Therefore,our results provide key information for the understandings of CsgA protein nanofiber assembly and biofilm robustness.

Physical Models for Interactions Between Single Von Willebrand Factor A1 Domain and GPIbα

Von Willebrand Factor(VWF)is a concatameric glycoprotein that plays a key role in rapid hemostasis and thrombosis.VWF has different functional domains that can bind to various molecules such as collagen,hemostatic factorⅧ,integrin,and platelet glycoprotein lbα(GPlbα)to achieve multiple biological functions.During hemostasis,the A1 domain of VWF binds to GPIbαwhere platelets accumulate in the injured vascular endothelium.Due to forces generated by the hemodynamic gradient flow,the relations of bond-dissociation rates versus forces show that the lifetime of molecular bond has multiple states under the external force.We processed the experimental data of receptor-ligand in a single molecule obtained from optical tweezers by two different methods,including a Dudko-Hummer-Szabo equation,and another method combining force4ime history and force induced bond rupture.Then we used a recently developed physical equation regarding protein unfolding rate to fit our results.The lifetime of the bond between A1 and GPlbαobtained by the above mentioned two methods shows a'three-stage'change upon gradually increasing the external force.When the external force was below 8 pN,the lifetime of the bond deceased as the external force increased,which is a typical expression of a catch bond.The lifetime of the bond started to increase when the external force increased from 8 to 11 pN,and then decrease again when the external force increased to above 11 pN.Kim et al.used different processing methods and proposes a'flex-bond'model:the lifetime of the bond will decrease as the external force increases,then suddenly increase to a peak,and continue to decrease with the increase of force.A recently developed model based on the structural-elastic properties of molecules fits our data well,indicating that the bond formed by Al and GPlbαhas a catch-bond phenomenon in a certain interval of external forces,and a flex bond in other force intervals.In conclusion,A1-GPIbαbond will have a'slip-catch-slip'bond tendency.Our result provides a alternative understanding about the role of Al-GPlbαinteractions in the mechanism of hemostasis.

Force-Regulated Adhesion and Activation Study of Integrin Targeting Polypeptides

Integrins are heterodimeric cell surface receptors that bind to ligands on another cell,e.g.intercellular adhesion molecule 1(ICAM-1),or the extracellular matrix.Integrins play an important role in immune system,and they participate in inflammation,thrombosis,and proliferation,migration and apoptosis of tumor cells.They mediate adhesion and transduce signals across the membrane usually under the influence of forces.A recent study has shown that integrins bind and activate transforming growth factorβisoform(TGF-β)which is involved in tumor suppression and growth,and blocking the binding of TGF-βto integrin can inhibit tumor growth.RGD(arginine-glycine-aspartate)small peptide,which competitively inhibits ligand binding to integrins,has been approved as an injectable drug.However,when the RGD is used to block cancer-related extracellular signaling pathways,it will also cause activation of integrins for a period,and stimulate the transduction of intracellular signals constantly.Therefore,it is necessary to explore for new drugs that can selectively control conformational state of integrins without activating or blocking all of them.In this study,we selected two small peptides,KQAGDV and RTDLDSLRT,that combined with integrins and do not contain an RGD sequence.The non-RGD polypeptide RTDLDSLRT has been reported to have a binding site with integrins and the binding affinity is on nanomolar scale.For the motif of the fibrinogen y chain C-terminal KQAGDV,it can adhere to the head of the integrins.The micropipette aspiration technique and electron microscopy techniques were used to study the adhesion and activation of integrins by peptides,respectively.Micropipette aspiration technique was used to investigate the adhesion frequency of peptide and integrin on Jurkat cell.The pressure system was used to supply a controllable negative pression to the microtube,and two micropipettes were used to absorb red blood cells and Jurkat cells,respectively.The red blood cells were coated with small peptides and can serve as a force sensor after being sucked when two cells were connected.The binding kinetics of integrin and peptides interactions was determined by fitting the curves constructed using adhesion probability between two cells as a function of time.The curves were fitted using a small system probabilistic kinetic model to estimate a pair of kinetic parameters,including the zero force reverse rate kr0,and the cellular binding affinity Acmrm1Ka0.The adhesion frequency yielded P(t)=75%and 57%for RGD and KQAG DV peptides,respectively.We obtained Acmrm1Ka0=1.40 and kr0=0.32 s-1,for RGD,and Acmrm1Ka0=0.85 and kr0=0.54 s-1 for KQAGDV.The RGD peptide has a higher adhesion frequency and lower dissociation rate than the KQAGDV peptide.Electron microscopy techniques was used to observe the activation of integrins by peptides.Jurkat cell expressing integrins was bound to a magnetic bead and bottom plate which were coated with different integrin-binding peptides.Then,we manipulated the beads in a controlled direction by changing the magnetic field nearby,and the forces were applied to the cell.The target cells were fixed and then observed by scanning electron microscope or transmission electron microscope.Jurkat cells contain abundant flexible microvilli of which there are many parallel bundles of actin filaments inside.By electron microscopy analysis,the cell connected with magnetic bead coated with RGD were found to be protruded and the size of microvilli increased up to#-fold of the length of the KQAGDV sample.The microvilli exhibited a curved agglomerate structure under a force-free condition.Moreover,a higher proportion of cells were activated in the presence of RGD than KQAGDV.In conclusion,the binding affinity of KQAGDV to integrin is weaker than RGD,and KQAGDV can bind with integrins effectively with a lower activated proportion.Our results indicate the peptides may selectively bind to integrins without activating them.