Research in the Molecular Systems Lab    Dept. Systems Biology Harvard Medical School Wyss Institute for Biologically Inspired Engineering

Overview: Engineering programmable molecular systems inspired by biology

We are a group of scientists with a shared interest in engineering programmable molecular systems inspired by biology. We currently focus on engineering information directed self-assembly of nucleic acid (DNA/RNA) structures and devices, and on exploiting such systems to do useful molecular work. Such de novo designed systems are composed of small synthetic monomers capable of conditional configuration change and can be programmed to self-assemble, move, and compute. They can potentially serve as programmable controllers for the spatial and temporal arrangements of diverse functional molecules (e.g. fluorophores, proteins), which will enable us to develop applications in imaging, sensing, diagnostics, and therapeutics.

Our molecular mechanism research currently focuses on developing DNA bricks as a general framework for constructing nanostructures with prescribed molecular geometry and kinetics. By interfacing these DNA structures with technologically relevant functional molecules, we are developing applications in digital fabrication of inorganic materials, bioimaging (in particular super-resolution imaging), and biosensing. In addition to making DNA structures in test tubes, we are also interested in making RNA structures in living cells and use them as programmable sensors and controllers for cellular behavior.

Figure: Research overview. For [P.x], see paper [x] on Publications page.

DNA bricks (and beyond)

We are generally interested in discovering, inventing, and developing fundamental molecular mechanisms that will enable precisely prescribed spatial and dynamic control of digital information bearing molecules, such as DNA and RNA.

We recently invented a general framework for programming the self-assembly of short synthetic DNA strands into prescribed target shapes or demonstrating their prescribed dynamic behavior. Using short DNA strands that we call "DNA bricks", we have demonstrated the modular construction of sophisticated 1D (Science, 321:824, 2008), 2D (Nature, 485:623, 2012) and 3D (Science, 338:1177, 2012) structures on the 100-nanometer scale with nanometer precision, as well as extended 2D crystals with prescribed depths that grow to micron sizes (Nature Chemistry, 2014). Additionally, using hairpin-shaped reconfigurable ``toehold bricks", we have demonstrated diverse, dynamic behavior such as catalytic circuits, triggered assembly, and autonomous locomotion (Nature, 451:318, 2008).

We are interested in further developing the DNA brick framework to improve its scalability, versatility, robustness, reliability, and general applicability. We are also interested in developing other enabling methods for encoding programmable spatial and dynamic behavior into DNA molecules, which may differ substantially from the DNA brick framework [e.g. the tripod polyhedra (Science, 334:65, 2014)].

We are also interested in generalizing the principle of digital information directed self-assembly beyond the molecular scale. For a specific example on digital assembly across scales, see our recent collaborative work on DNA directed self-assembly of "gel bricks" (Nature Communications, 4:2275, 2013).

Digital fabrication with DNA

A synthetic DNA structure by itself may not be technologically useful. We are interested in developing general strategies to translate the precise spatial control of DNA structures to diverse technologically relevant materials. We currently focus on using DNA structures as templates to direct the synthesis of shape-controlled inorganic materials. For example, in three recent collaborative projects, we have demonstrated the synthesis of shaped-controlled (1) inorganic dioxide structures by growing a conforming coating over a DNA structure ( J. Am. Chem. Soc., 135:6778, 2013), (2) graphene structures by using metalized DNA structures as lithography masks (Nature Communications, 4:1663, 2013), and (3) 3D inorganic structures casted using DNA nano-structure molds (Science, 2014).

We are interested in developing methods that will enable us to precisely specify the shape, composition, and function of inorganic structures using the digital information stored in self-assembling DNA molecules. We are interested in developing DNA based "molecular genomes" for nano-electronics and photonics devices.

Engineering imaging probes with prescribed molecular geometry and kinetics

Microscopy has emerged as a central tool for studying biology. At the heart of microscopic technology is the imaging probe, which transduces invisible biological information to an imageable signal. Present imaging probes are mostly engineered by manipulating their optical, chemical, and physical properties. Our key observation is that the precise spatial and temporal control over the synthetic DNA structures offers an unprecedented opportunity for engineering single-molecule imaging probes with explicitly designed molecular geometry and kinetics, which in turn provides a novel platform for developing transformative imaging capabilities. Our lab's imaging research thus focuses on engineering imaging probes with prescribed molecular geometry and kinetics.

One particularly interesting direction is to engineer imaging probes based on "triggered molecular geometry". The idea is that upon detecting a molecular signal (e.g. a target mRNA or a protein), the probe produces a prescribed, imageable molecular shape. The shape can be imaged directly; alternatively, it can serve as a spatial organizer or amplification scheme for other imaging entities such as fluorophores. As the first step towards this goal, we have recently developed a static version of such geometrically-encoded fluorescent probes. Specifically, we engineered a DNA based rigid nanorod and attached particular fluorophores to designated regions of the rod. Using this method, we made 216 distinct, geometrically encoded, fluorescent barcodes, providing a powerful tool for highly multiplexed single-molecule imaging (Nature Chemistry, 4:832, 2012). Another exciting direction that we currently focus on is to engineer kinetic probes for multiplexed super-resolution imaging (see below).

Super-resolution imaging via programmable autonomous blinking

Our research on engineering the molecular kinetics of imaging probes currently focuses on developing a super-resolution technique that utilizes the programmable autonomous blinking behavior of the imaging probe. Super-resolution microscopy enables biologists to see the previously invisible by circumventing the classical diffraction limit, and holds promise to broadly transform biomedical research. However, current methods offer only limited resolution and multiplexing power, and tend to require either expensive instrumentation or specialized experimental conditions.

We aim to develop a super-resolution imaging method using programmable nucleic acid-based probes that will allow precise molecular control of their autonomous blinking behavior and will thus enable high spatial resolution and multiplexing power (Nature Methods, 11:313, 2014; Science, 334:65, 2014). The technique will be simple to implement and easy to use. If successful, the new technique will bring the performance, applicability and usability of super-resolution imaging to a new level in practicality and will help transform research practice in diverse biomedical fields.

Programmable molecular instruments

Life at its finest scale can be viewed as dynamic self-assembling molecular systems. We are interested in interfacing our synthetic nucleic acid structures with biological molecular systems. By probing and directing the spatial and dynamical molecular behaviors in biological systems, these synthetic DNA/RNA devices can provide powerful experimental and therapeutic tools to address fundamental biomedical problems.

We are interested in engineering synthetic DNA/RNA devices that can sense a biological signal (e.g. mRNA, protein, small molecules) and either produces a readout observable by a human user or actuates a biological response. As a specific example, we have recently developed a simple DNA probe for robust and specific detection of single-base change in single-stranded DNA and RNA targets (Nature Chemistry, 4:208, 2012). Another direction is to engineer genetically encodable RNA nano-devices to probe and program the internal states of living cells (see below).

Probing and programming biology with synthetic RNA nanostructures

In addition to making DNA nanostructures in test tubes, we are also interested in making synthetic RNA nanostructures in living cells. The vision is to use these rationally designed RNA nanostructures as genetically encodable sensors and controllers to ``probe and program biology''.

We are collaboratively pursuing two directions, synthetic organization and synthetic regulation. (1) Synthetic organization refers to the spatial arrangement of functional molecules in the cells. We currently focus on engineering RNA scaffolds assembled from transcribable ``RNA bricks'' to position protein enzymes for useful functions. (2) In synthetic regulation, we aim to program the information flow in biology. As a specific example, we have recently invented a de-novo-designed gene expression regulator called ``toehold switch'' that implements a general molecular function: if detect RNA A, then translate gene B. We invented toehold switches for programming information flow in living cells (Cell, 2014), and the extended to work in vitro for constructing paper-based synthetic gene-networks (Cell, 2014). Such programmable molecular functions have broad implications in biosensing, imaging, and potentially in diagnostics and therapeutics. We are interested in developing these RNA switches as embedded information processing units in living cells for sensing and modulating complex intra-cellular gene expression profiles, and are exploring their utilities for developing biomedical applications.

See our publications here.