The Experts below are selected from a list of 225 Experts worldwide ranked by ideXlab platform
Venigalla B Rao - One of the best experts on this subject based on the ideXlab platform.
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In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine.
Proceedings of the National Academy of Sciences of the United States of America, 2013Co-Authors: Pan Tao, Marthandan Mahalingam, Bernard S Marasa, Zhihong Zhang, Ashok K Chopra, Venigalla B RaoAbstract:The bacteriophage T4 DNA packaging machine consists of a molecular motor assembled at the portal vertex of an icosahedral head. The ATP-powered motor packages the 56-µm-long, 170-kb viral genome into 120 nm × 86 nm head to near Crystalline Density. We engineered this machine to deliver genes and proteins into mammalian cells. DNA molecules were translocated into emptied phage head and its outer surface was decorated with proteins fused to outer capsid proteins, highly antigenic outer capsid protein (Hoc) and small outer capsid protein (Soc). T4 nanoparticles carrying reporter genes, vaccine candidates, functional enzymes, and targeting ligands were efficiently delivered into cells or targeted to antigen-presenting dendritic cells, and the delivered genes were abundantly expressed in vitro and in vivo. Mice delivered with a single dose of F1-V plague vaccine containing both gene and protein in the T4 head elicited robust antibody and cellular immune responses. This "progene delivery" approach might lead to new types of vaccines and genetic therapies.
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Adenine Recognition Is a Key Checkpoint in the Energy Release Mechanism of Phage T4 DNA Packaging Motor
Journal of molecular biology, 2011Co-Authors: Kiran Kondabagil, Bonnie Draper, Venigalla B RaoAbstract:Abstract ATP is the source of energy for numerous biochemical reactions in all organisms. Tailed bacteriophages use ATP to drive powerful packaging machines that translocate viral DNA into a procapsid and compact it to near-Crystalline Density. Here we report that a complex network of interactions dictates adenine recognition and ATP hydrolysis in the pentameric phage T4 large “terminase” (gp17) motor. The network includes residues that form hydrogen bonds at the edges of the adenine ring (Q138 and Q143), base-stacking interactions at the plane of the ring (I127 and R140), and cross-talking bonds between adenine, triphosphate, and Walker A P-loop (Y142, Q143, and R140). These interactions are conserved in other translocases such as type I/type III restriction enzymes and SF1/SF2 helicases. Perturbation of any of these interactions, even the loss of a single hydrogen bond, leads to multiple defects in motor functions. Adenine recognition is therefore a key checkpoint that ensures efficient ATP firing only when the fuel molecule is precisely engaged with the motor. This may be a common feature in the energy release mechanism of ATP-driven molecular machines that carry out numerous biomolecular reactions in biological systems.
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the small terminase gp16 of bacteriophage t4 is a regulator of the dna packaging motor
Journal of Biological Chemistry, 2009Co-Authors: Abdulrahman S Alzahrani, Kiran Kondabagil, Song Gao, Noreen Kelly, Manjira Ghoshkumar, Venigalla B RaoAbstract:Tailed bacteriophages and herpes viruses use powerful molecular motors to translocate DNA into a preassembled prohead and compact the DNA to near Crystalline Density. The phage T4 motor, a pentamer of 70-kDa large terminase, gp17, is the fastest and most powerful motor reported to date. gp17 has an ATPase activity that powers DNA translocation and a nuclease activity that cuts concatemeric DNA and generates the termini of viral genome. An 18-kDa small terminase, gp16, is also essential, but its role in DNA packaging is poorly understood. gp16 forms oligomers, most likely octamers, exhibits no enzymatic activities, but stimulates the gp17-ATPase activity, and inhibits the nuclease activity. Extensive mutational and biochemical analyses show that gp16 contains three domains, a central oligomerization domain, and N- and C-terminal domains that are essential for ATPase stimulation. Stimulation occurs not by nucleotide exchange or enhanced ATP binding but by triggering hydrolysis of gp17-bound ATP, a mechanism reminiscent of GTPase-activating proteins. gp16 does not have an arginine finger but its interaction with gp17 seems to position a gp17 arginine finger into the catalytic pocket. gp16 inhibits DNA translocation when gp17 is associated with the prohead. gp16 restricts gp17-nuclease such that the putative packaging initiation cut is made but random cutting is inhibited. These results suggest that the phage T4 packaging machine consists of a motor (gp17) and a regulator (gp16). The gp16 regulator is essential to coordinate the gp17 motor ATPase, translocase, and nuclease activities, otherwise it could be suicidal to the virus.
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A virus DNA gate: Zipping and unzipping the packed viral genome
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Venigalla B RaoAbstract:Tailed bacterial viruses (bacteriophages) are ubiquitously distributed in nature and are likely the most abundant organisms on the biosphere (1). Spending most of their time outside of the host, a bacterial cell, in often hostile external environments, they come to “life” upon encountering the receptor molecules on the host cell surface. The virus consists of a head (capsid) into which the DNA (genome) is packaged and a tail that delivers the genome into the bacterium. The capsid is pressurized because of packing of highly negatively-charged, relatively rigid dsDNA to near-Crystalline Density (≈500 μg/mL). The internal capsid pressure, ≈6 MPa or >10 times that of bottled champagne (2), provides a driving force for delivery of viral genome into host cell. One of the longstanding questions in phage biology has been how these viruses contain the DNA pressure and trigger release only upon recognition of a specific host cell. In this issue of PNAS, a study by Lhuillier et al. (3) describes the pseudoatomic structure of a DNA gate from the Bacillus subtilis bacteriophage SPP1, which “zips” the capsid after the genome is packaged and unzips it when the virus is ready to infect the host. It is a compelling story, which began with the first in vitro virus assembly experiments described by Edgar and Wood >40 years ago (4) and is applicable not only to phages but also to large eukaryotic viruses such as herpes viruses.
Paul J. Jardine - One of the best experts on this subject based on the ideXlab platform.
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Slow and steady wins the race: physical limits on the rate of viral DNA packaging.
Current opinion in virology, 2019Co-Authors: Paul J. JardineAbstract:During the assembly of dsDNA viruses such as the tailed bacteriophages and herpesviruses, the viral chromosome is compacted to near Crystalline Density inside a preformed head shell. DNA translocation is driven by powerful ring ATPase motors that couple ATP binding, hydrolysis, and release to force generation and movement. Studies of the motor of the bacteriophage phi29 have revealed a complex mechanochemistry behind this process that slows as the head fills. Recent studies of the physical behavior of packaging DNA suggest that surprisingly long-time scales of relaxation of DNA inside the head and jamming phenomena during packaging create the physical need for regulation of the rate of packaging. Studies of DNA packaging in viral systems have, therefore, revealed fundamental insight into the complex behavior of DNA and the need for biological systems to accommodate these physical constraints.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature Physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses, molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ∼50–100 nm prohead shells^ 1 , 2 . Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA–DNA interactions^ 3 . Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems^ 4 , 5 , 6 , 7 , 8 . Experiments in which conditions are changed during packaging to switch DNA–DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles^ 5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles^ 9 , 10 . The molecular motors that package DNA into viruses stall frequently under conditions promoting DNA–DNA attraction. Single-molecule experiments suggest the stalling is due to a nonequilibrium jamming transition induced by the attractive interactions.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ~50-100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10.
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Structure of the RNA claw of the DNA packaging motor of bacteriophage φ29
Nucleic acids research, 2012Co-Authors: Elena Harjes, Paul J. Jardine, Marc C. Morais, Shelley Grimes, Wei Zhao, Aya Kitamura, Hiroshi MatsuoAbstract:Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-Crystalline Density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33-35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.
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Bacteriophage phi29 Translocates DNA Along A Left-Handed Helical Path During Packaging
Biophysical Journal, 2010Co-Authors: Craig L. Hetherington, Paul J. Jardine, Shelley Grimes, Aathavan Karunakaran, Dwight L. Anderson, Carlos BustamanteAbstract:Bacteriophage phi29 employs a homomeric ring of RecA-like ATPases in order to package its dsDNA genome into the capsid at near-Crystalline Density. Previous single-molecule measurements of packaging have revealed the coordination of motor subunits, the step size of the motor, and the sensitivity of the motor to substrate modifications, thereby suggesting structural and kinetic models for the mechanism of translocation. However, traditional single-molecule experiments measure only the projection of the motor's motion onto the DNA longitudinal axis.We directly observe that phi29 translocates DNA along a left-handed helical path by monitoring rotation of a bead attached to the side of the substrate DNA in a laser tweezers. Simultaneously, the response to applied torque is measured. This novel experiment probes the details of force and torque generation by the packaging motor. Combining these measurements with angstrom-scale laser tweezers observations of motor stepping suggests specific geometric models for the interaction of the motor and DNA during translocation.The rotor bead technique introduced here allows tracking of the complete three-dimensional trajectory of a dsDNA translocase in action. It also permits the application of torque in a laser tweezers apparatus using commercially-available microspheres.
Shelley Grimes - One of the best experts on this subject based on the ideXlab platform.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature Physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses, molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ∼50–100 nm prohead shells^ 1 , 2 . Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA–DNA interactions^ 3 . Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems^ 4 , 5 , 6 , 7 , 8 . Experiments in which conditions are changed during packaging to switch DNA–DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles^ 5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles^ 9 , 10 . The molecular motors that package DNA into viruses stall frequently under conditions promoting DNA–DNA attraction. Single-molecule experiments suggest the stalling is due to a nonequilibrium jamming transition induced by the attractive interactions.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ~50-100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10.
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Structure of the RNA claw of the DNA packaging motor of bacteriophage φ29
Nucleic acids research, 2012Co-Authors: Elena Harjes, Paul J. Jardine, Marc C. Morais, Shelley Grimes, Wei Zhao, Aya Kitamura, Hiroshi MatsuoAbstract:Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-Crystalline Density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33-35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.
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Bacteriophage phi29 Translocates DNA Along A Left-Handed Helical Path During Packaging
Biophysical Journal, 2010Co-Authors: Craig L. Hetherington, Paul J. Jardine, Shelley Grimes, Aathavan Karunakaran, Dwight L. Anderson, Carlos BustamanteAbstract:Bacteriophage phi29 employs a homomeric ring of RecA-like ATPases in order to package its dsDNA genome into the capsid at near-Crystalline Density. Previous single-molecule measurements of packaging have revealed the coordination of motor subunits, the step size of the motor, and the sensitivity of the motor to substrate modifications, thereby suggesting structural and kinetic models for the mechanism of translocation. However, traditional single-molecule experiments measure only the projection of the motor's motion onto the DNA longitudinal axis.We directly observe that phi29 translocates DNA along a left-handed helical path by monitoring rotation of a bead attached to the side of the substrate DNA in a laser tweezers. Simultaneously, the response to applied torque is measured. This novel experiment probes the details of force and torque generation by the packaging motor. Combining these measurements with angstrom-scale laser tweezers observations of motor stepping suggests specific geometric models for the interaction of the motor and DNA during translocation.The rotor bead technique introduced here allows tracking of the complete three-dimensional trajectory of a dsDNA translocase in action. It also permits the application of torque in a laser tweezers apparatus using commercially-available microspheres.
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The bacteriophage φ29 portal motor can package DNA against a large internal force
Nature, 2001Co-Authors: Douglas E. Smith, Shelley Grimes, Dwight L. Anderson, Sander J. Tans, Steven B. Smith, Carlos BustamanteAbstract:As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage φ29 packages its 6.6-µm long, double-stranded DNA into a 42 × 54 nm capsid^ 1 by means of a portal complex that hydrolyses ATP^ 2 . This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-Crystalline Density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 µm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force–velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to ∼50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.
Douglas E. Smith - One of the best experts on this subject based on the ideXlab platform.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature Physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses, molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ∼50–100 nm prohead shells^ 1 , 2 . Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA–DNA interactions^ 3 . Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems^ 4 , 5 , 6 , 7 , 8 . Experiments in which conditions are changed during packaging to switch DNA–DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles^ 5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles^ 9 , 10 . The molecular motors that package DNA into viruses stall frequently under conditions promoting DNA–DNA attraction. Single-molecule experiments suggest the stalling is due to a nonequilibrium jamming transition induced by the attractive interactions.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ~50-100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10.
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The bacteriophage φ29 portal motor can package DNA against a large internal force
Nature, 2001Co-Authors: Douglas E. Smith, Shelley Grimes, Dwight L. Anderson, Sander J. Tans, Steven B. Smith, Carlos BustamanteAbstract:As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage φ29 packages its 6.6-µm long, double-stranded DNA into a 42 × 54 nm capsid^ 1 by means of a portal complex that hydrolyses ATP^ 2 . This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-Crystalline Density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 µm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force–velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to ∼50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.
Nicholas Keller - One of the best experts on this subject based on the ideXlab platform.
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Single Molecule Dynamics of Viral DNA Packaging Using Optical Tweezers
2016Co-Authors: Nicholas KellerAbstract:Author(s): Keller, Nicholas Andreas | Advisor(s): Smith, Douglas E | Abstract: Viral DNA packaging is a required step in the lytic cycle of many DNA viruses. A DNA polymer is packaged into a pre-formed capsid to a near Crystalline Density state by a powerful molecular motor that is fueled by ATP hydrolysis. To accomplish this task, the motor must generate enough force to match the resistance forces that arise from tight polymer confinement. These forces are due to entropy loss, bending energy, and electrostatic repulsion. Despite recent advances in the fields of viral DNA packaging and ejection, there are still many questions that remain unanswered. Does the packaged DNA undergo non-equilibrium dynamics? Do partly attractive DNA-DNA interactions as mediated by polyamines enhance or inhibit packaging? What affect does the conformational history of the packaged DNA have on the subsequent packaging dynamics? Which residues of the motor are responsible for generating force? And finally, is the force driving viral DNA ejection similar in magnitude to the package force? In this work, I present experimental studies that shed light on these questions. The packaging of single DNA molecules into single empty pro-capsids was measured using a custom-built dual optical tweezers system. Using the bacteriophage phi29 and T4 systems, I and my research collaborators pioneered new techniques in optical tweezers for investigating the dynamics of DNA packaging and force generation of a viral packaging motor. Using these techniques, we discovered many new findings in the areas of polymer confinement, non-equilibrium dynamics, DNA condensation, and enzyme kinetics.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature Physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses, molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ∼50–100 nm prohead shells^ 1 , 2 . Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA–DNA interactions^ 3 . Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems^ 4 , 5 , 6 , 7 , 8 . Experiments in which conditions are changed during packaging to switch DNA–DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles^ 5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles^ 9 , 10 . The molecular motors that package DNA into viruses stall frequently under conditions promoting DNA–DNA attraction. Single-molecule experiments suggest the stalling is due to a nonequilibrium jamming transition induced by the attractive interactions.
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Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging
Nature physics, 2016Co-Authors: Nicholas Keller, Paul J. Jardine, Shelley Grimes, Douglas E. SmithAbstract:In many viruses molecular motors forcibly pack single DNA molecules to near-Crystalline Density into ~50-100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10.