Ramesh Subramani

Bio: Ramesh Subramani is an academic researcher from Katholieke Universiteit Leuven. The author has contributed to research in topics: Materials science & Self-healing hydrogels. The author has an hindex of 9, co-authored 13 publications receiving 1936 citations. Previous affiliations of Ramesh Subramani include National Research Foundation of South Africa & University of Copenhagen.

Self-assembly of a nanoscale DNA box with a controllable lid.

Abstract: By exploiting the unique structural motifs and self-recognition properties of DNA, it is possible to generate self-assembled DNA nanostructures of specific shapes. Here, a previously described DNA 'origami' method has been extended into three dimensions to create an addressable DNA box on the nanometre scale that can be opened by an externally supplied DNA key'.

Single-molecule chemical reactions on DNA origami

Abstract: DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

The influence of swelling on elastic properties of polyacrylamide hydrogels

Abstract: Polyacrylamide (PAM) hydrogels are commonly used as substrates for cell mechanical and mechanobiological studies because of their tunable stiffness and ease of handling. The dependence of bulk rheological and local elastic properties (assessed by Atomic Force Microscopy, or AFM) of PAM hydrogels on its composition and polymerization temperature has been extensively studied. PAM hydrogels swell when immersed in media, but the influence of swelling on local elastic properties is poorly characterized. Direct measurements of the effect of swelling on PAM elastic properties are scarce. We report here, for the first time, the direct measurements of volumetric swelling and local elastic properties of PAM gels throughout the post-polymerization swelling process until equilibrium. First, local and global elastic properties (measured by rheology), were obtained during polymerization in the absence of swelling, and showed good agreement with each other. Four PAM hydrogel compositions were characterized thus, with corresponding storage shear moduli (as measured immediately after polymerization) of 4,530 Pa (termed stiffest), 2,900 Pa (stiff), 538 Pa (soft), and 260 Pa (softest). Next, all compositions were subjected to swelling in phosphate buffered saline. Swelling ratios and local elastic moduli were measured at 0, 3, 6, 9, 12, and 24 h post-polymerization for the soft and softest compositions, and once daily till 6 days post-polymerization for all four compositions. For the stiffest and stiff gels, swelling ratio, and local elastic modulus changed negligibly with time, while for the soft and softest gels, substantial changes between Day 0 and Day 1 were found for both swelling ratio (increased by 21.6 and 133%, respectively), and local elastic modulus decreased (by 33.7 and 33.3%, respectively), substantially. Experimental data were analyzed by a model that combined ideal elastomer mechanics and poroelastic swelling kinetics model. Model predictions confirmed the validity of present measurements with respect to past studies where swelling and elastic properties were not measured simultaneously. The present study underlines the important effect swelling can have on PAM elastic properties and provides detailed quantitative data to guide the duration taken to reach equilibrium—a useful information for cell mechanics experiments. In addition, the simultaneous measurements of swelling and local elastic moduli provide novel data for the validation of theoretical models.

A novel secondary DNA binding site in human topoisomerase I unravelled by using a 2D DNA origami platform.

Abstract: The biologically and clinically important nuclear enzyme human topoisomerase I relaxes both positively and negatively supercoiled DNA and binds consequently DNA with supercoils of positive or negative sign with a strong preference over relaxed DNA. One scheme to explain this preference relies on the existence of a secondary DNA binding site in the enzyme facilitating binding to DNA nodes characteristic for plectonemic DNA. Here we demonstrate the ability of human topoisomerase I to induce formation of DNA synapses at protein containing nodes or filaments using atomic force microscopy imaging. By means of a two-dimensional (2D) DNA origami platform, we monitor the interactions between a single human topoisomerase I covalently bound to one DNA fragment and a second DNA fragment protruding from the DNA origami. This novel single molecule origami-based detection scheme provides direct evidence for the existence of a secondary DNA interaction site in human topoisomerase I and lends further credence to the theo...

Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors.

Abstract: Perfusion bioreactors regulate flow conditions in order to provide cells with oxygen, nutrients and flow-associated mechanical stimuli. Locally, these flow conditions can vary depending on the scaffold geometry, cellular confluency and amount of extra cellular matrix deposition. In this study, a novel application of the immersed boundary method was introduced in order to represent a detailed deformable cell attached to a 3D scaffold inside a perfusion bioreactor and exposed to microscopic flow. The immersed boundary model permits the prediction of mechanical effects of the local flow conditions on the cell. Incorporating stiffness values measured with atomic force microscopy and micro-flow boundary conditions obtained from computational fluid dynamics simulations on the entire scaffold, we compared cell deformation, cortical tension, normal and shear pressure between different cell shapes and locations. We observed a large effect of the precise cell location on the local shear stress and we predicted flow-induced cortical tensions in the order of 5 pN/μm, at the lower end of the range reported in literature. The proposed method provides an interesting tool to study perfusion bioreactors processes down to the level of the individual cell’s micro-environment, which can further aid in the achievement of robust bioprocess control for regenerative medicine applications.

A logic-gated nanorobot for targeted transport of molecular payloads

Abstract: We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. The device can be loaded with a variety of materials in a highly organized fashion and is controlled by an aptamer-encoded logic gate, enabling it to respond to a wide array of cues. We implemented several different logical AND gates and demonstrate their efficacy in selective regulation of nanorobot function. As a proof of principle, nanorobots loaded with combinations of antibody fragments were used in two different types of cell-signaling stimulation in tissue culture. Our prototype could inspire new designs with different selectivities and biologically active payloads for cell-targeting tasks.

Dynamic DNA nanotechnology using strand-displacement reactions

Abstract: The programmable and reliable hybridization of DNA strands has enabled the preparation of a wide variety of structures. This Review discusses how, in addition to these static assemblies, the process of displacing — and ultimately replacing — strands also makes possible the construction of dynamic systems such as logic gates or autonomous walkers.

Challenges and opportunities for structural DNA nanotechnology

Abstract: DNA molecules have been used to build a variety of nanoscale structures and devices over the past 30 years, and potential applications have begun to emerge. But the development of more advanced structures and applications will require a number of issues to be addressed, the most significant of which are the high cost of DNA and the high error rate of self-assembly. Here we examine the technical challenges in the field of structural DNA nanotechnology and outline some of the promising applications that could be developed if these hurdles can be overcome. In particular, we highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in diagnostics and therapeutics for human health.

Programmable materials and the nature of the DNA bond

Abstract: For over half a century, the biological roles of nucleic acids as catalytic enzymes, intracellular regulatory molecules, and the carriers of genetic information have been studied extensively. More recently, the sequence-specific binding properties of DNA have been exploited to direct the assembly of materials at the nanoscale. Integral to any methodology focused on assembling matter from smaller pieces is the idea that final structures have well-defined spacings, orientations, and stereo-relationships. This requirement can be met by using DNA-based constructs that present oriented nanoscale bonding elements from rigid core units. Here, we draw analogy between such building blocks and the familiar chemical concepts of "bonds" and "valency" and review two distinct but related strategies that have used this design principle in constructing new configurations of matter.