Autonomous and tunable biomaterials

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Mechanics of DNA-based biopolymer composites

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Transport in biomimetic crowded environments

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Ring polymers and topological polymer blends

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Design and characterization of topologically active DNA-based materials

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Autonomous and tunable biomaterials

  • People: Gloria Lee, Gregor Leech, Christopher Currie
  • Funding: Keck Foundation

This collaborative research project aims to push the frontier of science and engineering by creating a novel class of autonomous materials that can harness energy-driven, molecular-scale biological ratchets to perform programmable motion and work. Biology has already engineered “autonomous” systems that can sense, compute, remember, and react to stimuli. The composite cytoskeletal network of protein filaments - including actin, microtubules, and their associated motor proteins - is one key example. While future technological demands will require such autonomous, active materials, humans currently have no capability to design or build such non-equilibrium, multicomponent systems. Inspired by biology, we are addressing this need by coupling multi-component cytoskeleton networks to the robust timekeeping of circadian oscillators to create a class of biomaterials that rhythmically alter their mechanical properties. We create tunable composites of actin filaments and microtubules and incorporate motor proteins and cyanobacteria clock proteins to induce self-sustaining stiffening and softening cycles. Fusing the information processing and signaling capabilities of circadian clocks with the mechanical tunability and versatility of the cytoskeleton has the potential to create an entirely new class of autonomously active materials that can not only intelligently respond to external signals, but also anticipate future demands. Beyond the practical goal of creating a new platform of smart biomaterials, this work elucidates the fundamental principles underlying dynamically self-regulating biomolecular networks.

Mechanics of DNA-based biopolymer composites

  • People: Karthik Reddy Peddireddy, Pawan Khanal
  • Funding: Air Force Office of Scientific Research

Most naturally occurring biomaterials, such as cytoskeleton, are heterogeneous biopolymer blends (composites) that display captivating and useful scale-dependent viscoelastic properties that are completely controlled by polymer topology, stiffness, size and concentration. Thus, biopolymer blends are powerful platforms for developing dynamic, hierarchical, multifunctional materials. However, understanding the underlying macromolecular dynamics, interactions, and stress propagations that lead to the unique macroscale mechanics is critical to precisely spatiotemporally tuning composites to have desired material properties. Our lab designs blends of DNA and proteins with systematically varied topologies, stiffnesses, sizes and concentrations. We characterize and link together molecular dynamics and mechanical properties of these blends to determine the molecular properties necessary to achieve specific novel material properties, thereby enabling a bottom-up approach to biomaterial design. Using DNA, one of the most well-controlled and tunable polymer platforms in existence, allows for precise modulation of mechanics over an unparalleled parameter space. We are currently focused on biologically inspired composites of (i) circular and linear DNA and (ii) DNA and cytoskeleton proteins. This research also includes developing new microscopy and microrheology techniques to directly connect stresses induced in biopolymer blends to corresponding molecular deformations and network rearrangement.

Transport in biomimetic crowded environments

  • People: Gregor Leech, Gloria Lee
  • Funding: NIH

We are investigating how the properties of intracellular environments control macromolecular dynamics and organization, including anomalous transport, conformational fluctuations, and clustering. The intracellular milieu is crowded by a myriad of interacting macromolecules that are heterogeneously distributed and exhibit wide-ranging non-equilibrium dynamics. For example, the complex cytoskeletal network of proteins, including actin, microtubules, and their associated motor and binding proteins, actively generates stresses and drives cytoplasmic rearrangement. However, understanding how cytoskeletal activity impacts the intracellular transport and distribution of macromolecules and complexes diffusing through these networks remains a grand challenge. Preventing progress on this open question is the daunting complexity of the intracellular environment, making it challenging to attribute various macromolecular transport modes and distributions to specific intracellular interactions or components. While in vitro studies can address this challenge, they are often too simplified to accurately capture in vivo phenomena. To bridge the gap between in vivo and in vitro studies, we are developing a powerful platform that combines active, non-equilibrium cytoskeleton networks, in and out of vesicle confinement, with cutting-edge microscopy methods and image analysis algorithms to comprehensively characterize the dynamics and spatial distributions of macromolecules in tunable biomimetic environments. We are specifically focused on the dynamics of large DNA molecules within confined cytoskeleton networks that are engineered to tunably contract, rearrange, coarsen, and flow on demand. Understanding how DNA moves through the dynamic, crowded cell will enable engineering of environments to block viral genome transport, facilitate design and delivery of gene therapies, and provide insights into how macromolecules or complexes are sterically sequestered, actively driven together or mixed. Our complex yet tunable system and results will serve as a powerful benchmark for in vivo studies probing intracellular dynamics, and our designed microscopy and analyses will be immediately transferable to such studies.

Ring polymers and topological polymer blends

  • People: Karthik Peddireddy, Pawan Khanal, Philip Neill
  • Funding: Air Force Office of Scientific Research, NSF

Understanding the dynamics of circular polymers and their mixtures with linear polymers remains an important challenge in soft materials and complex fluids. In addition to polymer physics, circular DNA plays a critical role in essential life processes and new biotechnologies such as single-cell DNA sequencing. The question remains: how does polymer topology impact the flow properties of semi-dilute and entangled polymeric fluids? This research focuses on elucidating the dynamics of large ring polymers and their interactions with linear and supercoiled polymers. We characterize the rheological properties of ring-linear and supercoiled-ring polymer blends using DNA polymers that span a wide range of concentrations, molecular weights, and relative fractions of topologies. We couple linear and nonlinear optical tweezers microrheology with single-molecule tracking, macrorheology and differential dynamic microscopy to understand the dynamics of ring polymers using custom-designed DNA constructs. We span concentrations from semi-dilute to highly entangled, with a focus on the poorly understood crossover regimes straddling each well-defined regime. As part of this research, our lab also focuses on developing and optimizing methods for synthesizing and purifying highly concentrated solutions of ring and linear DNA of wide-ranging lengths, which we happily share with other labs.

Design and characterization of topologically active DNA-based materials

  • People: Natalie Crist, Philip Neill
  • Funding: Air Force Office of Scientific Research

The frontier of materials research is to engineer non-equilibrium active materials that can sense, respond, and morph to create active work. Such materials can enable resilient self-healing aircraft and bridges; adaptable self-activating PPE; responsive purification, filtration and flow control in pipelines; and manless search-and-rescue devices that can move and change shape on-demand. Our unique approach to this problem is to use time-varying macromolecular topology to control the rheological and structural properties of composite biomaterials. DNA is the ideal candidate for this strategy as it naturally exists in different topological states – supercoiled, circular and linear – with enzymes that can convert one topology to another. Further, DNA is highly compatible with wide-ranging environments, making it an ideal conduit to confer mechanical tunability into other biological or synthetic materials. In this research we capitalize on these unique robustness features of DNA to engineer and interrogate active biomaterials that can self-alter their mechanics and structure by enzymatically-driven topological conversion of DNA. We are creating concentrated solutions of supercoiled and circular DNA and integrating enzymes that alter their topological state in a tunable time-dependent manner. In future work we will incorporate these dense topologically-active DNA solutions into systems of rigid biopolymer rods and nano-colloids. This highly adaptable and transferrable approach to active matter can be incorporated into numerous materials to produce novel non-equilibrium properties and responses. This line of research also involves designing a suite of optical tweezers microrheology and microscopy techniques to precisely characterize the time-varying rheological and structural properties of the active systems during enzymatic activity. These techniques are broadly applicable to the wide variety of active materials currently under intense investigation.