Krishnan Y.,National Center for Biological science |
Bathe M.,Massachusetts Institute of Technology
Trends in Cell Biology | Year: 2012
Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone. © 2012 Elsevier Ltd.
Saha S.,National Center for Biological science
Nature Nanotechnology | Year: 2015
The concentration of chloride ions in the cytoplasm and subcellular organelles of living cells spans a wide range (5–130 mM), and is tightly regulated by intracellular chloride channels or transporters. Chloride-sensitive protein reporters have been used to study the role of these chloride regulators, but they are limited to a small range of chloride concentrations and are pH-sensitive. Here, we show that a DNA nanodevice can precisely measure the activity and location of subcellular chloride channels and transporters in living cells in a pH-independent manner. The DNA nanodevice, called Clensor, is composed of sensing, normalizing and targeting modules, and is designed to localize within organelles along the endolysosomal pathway. It allows fluorescent, ratiometric sensing of chloride ions across the entire physiological regime. We used Clensor to quantitate the resting chloride concentration in the lumen of acidic organelles in Drosophila melanogaster. We showed that lumenal lysosomal chloride, which is implicated in various lysosomal storage diseases, is regulated by the intracellular chloride transporter DmClC-b. © 2015 Nature Publishing Group
Howes M.T.,University of Queensland |
Mayor S.,National Center for Biological Science |
Parton R.G.,University of Queensland
Current Opinion in Cell Biology | Year: 2010
Eukaryotic cells deftly coordinate an array of endocytic pathways beyond the classical clathrin-mediated endocytic route. Although the existence of clathrin-independent endocytic pathways has been accepted for some time, only recently have tools been developed that specifically delineate their fine details, including molecular composition and ultrastructural morphology. Identification of the salient features of distinct pathways has concomitantly attributed them with specific roles during important cellular processes. Insight from model organisms confirms these roles and suggests maintenance of crucially adapted functions across species. Among other roles, clathrin-independent endocytosis has now been linked to plasma membrane repair, cellular spreading, cellular polarization, and modulation of intercellular signaling. The field is now primed to identify how these pathways function within physiologically relevant environments. © 2010 Elsevier Ltd.
Mayor S.,National Center for Biological science
Cell | Year: 2011
Caveolae are protein-driven membrane invaginations that regulate both the physical and chemical composition of the plasma membrane. Sinha et al. (2011) now show that caveolae are membrane reservoirs that are used to rapidly buffer against changes in membrane tension. © 2011 Elsevier Inc.
Bhalla U.S.,National Center for Biological science
Current Opinion in Neurobiology | Year: 2014
Neurons perform far more computations than the conventional framework of summation and propagation of electrical signals from dendrite to soma to axon. There is an enormous and largely hidden layer of molecular computation, and many aspects of neuronal plasticity have been modeled in chemical terms. Memorable events impinge on a neuron as special input patterns, and the neuron has to decide if it should 'remember' this event. This pattern-decoding decision is mediated by kinase cascades and signaling networks over millisecond to hour-long timescales. The process of cellular memory itself is rooted in molecular changes that give rise to life-long, stable physiological changes. Modeling studies show how cascades of synaptic molecular switches can achieve this, despite stochasticity and molecular turnover. Such biochemically detailed models form a valuable conceptual framework to assimilate the complexities of chemical signaling in neuronal computation. © 2013 .
National Center For Biological Science | Date: 2012-05-09
The present disclosure relates to delivering neutral bioimaging molecules encapsulated within icosahedral DNA capsules in vivo and in vitro. The present disclosure also discloses the entrapment of neutral bioimaging molecules like FITC dextran within the cavity of a DNA polyhedron without any molecular recognition or chemical conjugation between host (DNA icosahedron) and cargo (like FITC Dextran). This DNA polyhedron is structurally well defined and shows high encapsulation efficiency. The present disclosure also relates to complex formed due to the encapsulation of neutral bioimaging agents within icosahedral DNA capsules.
National Center For Biological Science | Date: 2015-09-16
Disclosed are nucleic acid-based molecular switches that respond to changes in pH. The switches may be used in DNA nanodevices. The switches may also act as sensors for measuring the pH of a sample, including cells, regions thereof, and whole organisms. The switch includes an A-motif that forms at acidic pH. Also disclosed are compositions and methods for measuring the pH of cells or regions thereof, such as vesicles, the nucleus, mitochondrial matrix, or the Golgi lumen.
National Center For Biological Science | Date: 2013-11-12
The instant disclosure provides for a method of identifying and isolating pluripotent stem cells and distinguishing pluripotent stem cells from differentiating/differentiated cells, using the property of endogenous blue fluorescence emitted from intracellular lipid bodies which serves as an endogenous marker for the pluripotent state.
National Center For Biological Science | Date: 2013-06-11
The present technology provides a cell based assay for identifying compounds that modulate store-operated ionic calcium levels using itpr mutant cell lines, such as itpr-ku cells, which have abnormal ionic calcium levels.
National Center For Biological Science | Date: 2012-10-11
The present disclosure relates to a nucleic acid assembly (NAA), comprising sensor domain and handle domain; an assembly interfaceable motif (AIM) sequence optionally along with intracellular targeting motif (ITM) sequence; and an AIM-NAA complex. It also relates to a vector comprising assembly interfaceable motif sequence optionally along with intracellular targeting motif sequence and a cell comprising the vector. Further, the instant disclosure also provides a method to obtain the nucleic acid assembly, method of intracellular targeting and kit thereof.