Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session G22: Biopolymers: Nucleic Acids and Structural |
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Sponsoring Units: DBIO DSOFT Chair: Ralf Bundschuh, Ohio State Univ - Columbus Room: 303 |
Tuesday, March 3, 2020 11:15AM - 11:27AM |
G22.00001: Autonomous synthesis and assembly of a ribosomal subunit on a chip Michael Levy, Reuven Falkovich, Shirley S. Daube, Roy H. Bar-Ziv Ribosome biogenesis is an efficient and complex assembly process that has not been reconstructed outside a living cell so far, yet is the most critical step for establishing a self-replicating artificial cell. |
Tuesday, March 3, 2020 11:27AM - 11:39AM |
G22.00002: The formation of filopodia bridge and intercellular nanotube : A Critical rule of torque and restorative force. O-chul Lee, Minhyeok Chang, Jaeho Oh, Jong-Bong Lee, Jae-Hyung Jeon In mammalian cells, a network of intercellular membrane nanotubes enables long-distance communication which is an intercellular transfer of cytoplasmic molecules and even organelles and viruses. The main component in filopodia which constitutes membrane intercellular nanotubes is consists of bundled actin filamentous. Also, several studies have confirmed the dynamic behavior of the filopodia which are undergoing restorative force by myosin II and torque by myosin V. Using a fluorescence imaging method, we have found that filopodia grown from two adjacent cells form the helical structure resulting. To understand the mechanism of forming the intercellular nanotube, we model a filopodium as a bundle of wormlike chains whose net persistence length is consistent with the value measured by our optical tweezers experiment. In this study, we quantitatively investigate the conformation, stability, and dynamics of the filopodia in comparison with the experiment by using the Langevin dynamics simulation. From the simulation results, we propose a region of a magnitude of tension and torque applied to the filopodia to form the nanotube |
Tuesday, March 3, 2020 11:39AM - 11:51AM |
G22.00003: A novel coarse-grained energy functions for RNA folding DONG ZHANG, Shi-Jie Chen Coarse-grained models combined with effective sampling techniques are now poised to address a wide range of problems in biological systems. An accurate coarse-grained force field is crucial for quantitative modeling of structure, dynamics, and function. We recently developed a novel approach to extract RNA coarse-grained energy functions from the structural database. The key ingredient of the approach is to stepwise build the correlations between the different interactions and the inherent chain connectivity and excluded volume interactions through an iterative construction of the reference states. The novel approach allows us to extract energy functions from the inverse Boltzmann law. The validity of this approach is supported by the close agreement between the simulated distributions for all the structural parameters and those observed from the experimental structure database. Benchmark tests on tertiary structure folding and 3D structure predictions show comparable or much improved predictions than existing coarse-grained models. This novel method for the treatment of many-body correlation effects can be easily transferred to other computational biology problems. |
Tuesday, March 3, 2020 11:51AM - 12:03PM |
G22.00004: Non-ergodic transport and conformational dynamics of DNA in biomimetic cytoskeleton networks Jonathan Garamella, gina aguirre, Kathryn Regan, Ryan J. McGorty, Rae M Robertson-Anderson Macromolecular crowding is an increasingly relevant biophysical phenomenon that affects drug delivery, protein function, and intracellular transport. Of particular interest is the influence that cytoskeletal filaments have on the transport and conformational dynamics of large DNA molecules. Here, we use single-molecule conformational tracking (SMCT) to elucidate the transport properties and conformational dynamics of linear and relaxed circular (ring) DNA in in vitro composite networks of actin and microtubules with variable types of crosslinking. Specifically, we investigate the impact of crosslinking actin to actin, microtubules to microtubules, and actin to microtubules. While both linear and ring DNA undergo anomalous subdiffusion in all networks, the transport properties are heavily influenced by DNA topology. Linear DNA chains are compacted and display a single mode of subdiffusion, while ring DNA polymers are swollen and exhibit biphasic subdiffusion suggestive of transient threading by the biomimetic cytoskeleton. These results are bolstered by non-Gaussian van Hove distributions and non-ergodic behavior of both DNAs, with the transport of ring DNA molecules becoming less ergodic than their linear counterparts at longer times. |
Tuesday, March 3, 2020 12:03PM - 12:15PM |
G22.00005: Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures Ralf Bundschuh, Elan Shatoff RNA-protein interactions play an important role in regulating gene expression. Since RNA-protein interactions are affected by RNA secondary structure, single nucleotide polymorphisms in the vicinity of protein binding sites can affect these interactions. This provides a mechanism for single nucleotide polymorphisms outside coding regions and outside the actual protein binding sites to convey a phenotype. Here, we use a modified version of the Vienna RNA folding package and PAR-CLIP data for HuR (ELAVL1) in humans to characterize the genome-wide effect of single nucleotide polymorphisms on HuR binding and show that they can have a many-fold effect on the affinity of HuR binding to RNA transcripts from tens of bases away. We also find that the effect of single nucleotide polymorphisms on protein binding appears to be under selection, with the minor alleles tending to make it harder for a protein to bind. |
Tuesday, March 3, 2020 12:15PM - 12:27PM |
G22.00006: COARSE-GRAINED MODELING OF DNA PLECTONEME FORMATION IN THE PRESENCE OF BASE-PAIR MISMATCHES Parth Rakesh Desai, Siddhartha Das, Keir C Neuman Defects in double stranded DNA can arise from mismatched base pairs. In vivo, these must be rapidly repaired since they affect a variety of cell processes. Here we use molecular dynamics to study the effect of mismatched bps on DNA supercoiling. Magnetic tweezers-based studies of DNA supercoiling have shown that in DNA harboring a single mismatch, the plectoneme always localizes at the mismatch. These studies were conducted at relatively high salt concentrations (>0.5M). Theoretical studies have predicted that under physiological salt concentrations of ~0.2M, plectoneme localization becomes probabilistic. However, both approaches are currently limited to positively supercoiled DNA. We develop a simulation framework using the oxDNA model to study the effect of mismatches on both positively and negatively supercoiled DNA. We find that for a positively supercoiled DNA, the oxDNA framework can reproduce the experimentally observed plectoneme pinning at high force and high salt concentrations. Under physiological salt concentrations (0.2M), we find that the plectoneme localization at the mismatch becomes probabilistic. The utility of the simulation approach is highlighted by the ability to quantify the effect of mismatches on the motion of plectonemes along the DNA molecule. |
Tuesday, March 3, 2020 12:27PM - 12:39PM |
G22.00007: A quantitative model of temperature actuated DNA origami nanocaliper constructs Kyle Crocker, Joshua Johnson, Carlos E Castro, Ralf Bundschuh Manipulation of temperature can be used to actuate gold nanoparticle incorporated into DNA origami nanocalipers. We develop a physical model of this system that uses partition function analysis of the interaction between the nanocaliper and nanoparticle to predict the probability that the nanocaliper is open at a given temperature. The model agrees well with experimental data, and the comparison between model and experiment reveals surprising insights into the nanocaliper-nanoparticle system. For instance, geometric constraints on the system are suggested. Additionally, the model predicts experimental conditions that allow the actuation temperature of the nanocaliper to be tuned over a wide range of temperatures from 20oC to 60oC. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices. |
Tuesday, March 3, 2020 12:39PM - 12:51PM |
G22.00008: A dynamic model of DNA Supercoiling Biao Wan, Jin Yu, Xinliang Xu The dynamics of DNA supercoiling is important for many biological functions of DNA, such as gene expression regulation. In this investigation we first studied DNA supercoiling generation through a Brownian dynamics simulation of DNA, which is modeled as a discrete worm-like chain. Two well-separated time scales are observed: mechanical balance along the DNA can be regarded as instantaneous (10-3∼10-2ms) when compared to the global configuration change of the DNA supercoil structure (>100ms). Based on this time separation, we developed a new model where the fast mechanical balancing dynamics are coarse grained. While the numerical simulation of DNA supercoil dynamics based on this model can be shown to fully reproduce DNA dynamical behavior above millisecond time scale, the computational efficiency is great improved. In our example of a DNA segment of 6000 base pairs, simulation based on the new model is times faster than the original Brownian dynamics simulations, making numerical study of DNA dynamics at biologically relevant time scales (e.g.1∼10 sec ) possible. |
Tuesday, March 3, 2020 12:51PM - 1:03PM |
G22.00009: Real-Time Tracking and Quantification of Transposible Element Activity Davneet Kaur, Gloria Lee, Nicholas Sherer, Elliot Urriola, Hneil Kim, Chi Xue, K. Michael Martini, Nigel Goldenfeld, Thomas E Kuhlman Transposable elements (TEs), or jumping genes, are DNA sequences that can change their position in a genome using a cut-and-paste or copy-and-paste mechanism. They are fundamental building blocks of all genomes, accounting for large fractions of genomic masses, and may have played a major role in the emergence of genetic diversity and function. Even so, many open questions remain regarding their differential abundance among organisms, the functions of their individual proteins, rates of protein activity and transposition and the effects of TEs on their hosts. To address these unanswered questions, we have constructed and released inducible TEs in bacteria to quantify their rates of activity and physiological effects on their hosts. To quantify dynamics, we've designed fluorescent visualization and quantification techniques to make real time high resolution observations of protein expression and transposition events as they occur in living cells. We show that we can obtain a deeper understanding of the roles of TEs and their individual proteins through our analysis. |
Tuesday, March 3, 2020 1:03PM - 1:15PM |
G22.00010: Simulating the Polarization Effects of Gas-Phase Nucleic Acids Christopher Myers, Alan Chen
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Tuesday, March 3, 2020 1:15PM - 1:27PM |
G22.00011: Existence of the B-Form DNA helix in nanoDNA liquid crystals and its variation due to aggregate assembly Gregory Smith, Tommaso Fraccia, Mikhail Zhernenkov, Tommaso Bellini, Noel Anthony Clark
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Tuesday, March 3, 2020 1:27PM - 1:39PM |
G22.00012: Constructing Out-of-plane Auxetic Response in Paper Prateek Verma, Anselm C Griffin, Meisha Shofner It is known that several kinds of paper (including the common copy paper) increase in thickness when stretched. Previously, we examined several commercially available papers and found this behavior in some of them. We also devised, utilizing a few other reports, a mechanistic explanation for the origin of this auxetic response. In this research, we apply our understanding of this mechanism to construct auxetic paper handsheets. Key structural parameters of a nonwoven cellulose fiber network in paper –fiber length, sheet thickness and crosslinking density, that were previously predicted to affect the magnitude and sign of Poisson’s ratio, were altered to produce a range of handsheets. It was found that longer fibers, crosslinking density, extent of refining, and sheet thickness significantly affect the magnitude of auxetic response in paper. |
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