Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines

Controlling the size and shape of DNA condensates is important in vivo and for the improvement of nonviral gene delivery. Here, we demonstrate that the morphology of DNA condensates, formed under a variety of conditions, is shifted completely from toroids to rods if the bacterial protein HU is present during condensation. HU is a non-sequence-specific DNA binding protein that sharply bends DNA, but alone does not condense DNA into densely packed particles. Less than one HU dimer per 225 bp of DNA is sufficient to completely control condensate morphology when DNA is condensed by spermidine. We propose that rods are favored in the presence of HU because rods contain sharply bent DNA, whereas toroids contain only smoothly bent DNA. The results presented illustrate the utility of naturally derived proteins for controlling the shape of DNA condensates formed in vitro. HU is a highly conserved protein in bacteria that is implicated in the compaction and shaping of nucleoid structure. However, the exact role of HU in chromosome compaction is not well understood. Our demonstration that HU governs DNA condensation in vitro also suggests a mechanism by which HU could act as an architectural protein for bacterial chromosome compaction and organization in vivo

Graphene and amyloid peptide binding and its implications in Alzheimer's disease

A poster discussing the relation of graphene and amyloid peptide binding to Alzheimer's disease

Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin

Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs

Graphene & Graphene Oxide and amyloid peptide binding and its implications in Alzheimer’s disease

Alzheimer’s disease is a neurodegenerative disease caused by the incorrect cleaving of the transmembrane Amyloid Precursor Protein into the neurotoxic Aβ40 and Aβ42 fragments2. These fragments are soluble oligomers with a random coil conformation that can impair synapses or neurotransmission; they may also aggregate into parallel and antiparallel beta sheets to form amyloid plaques, which can block or distort signaling between neuronal pathways7. Aβ fibrils self-assemble into parallel and antiparallel beta sheets on hydrophobic graphite, but not on hydrophilic mica5,6. Aβ fibrils also assemble on graphene, which irreversibly captures fibrils3, suggesting grapheme might have a role in the study of Alzheimer’s amyloid plaque. These studies characterize binding between amyloid beta peptide fibrils and graphene using Raman spectroscopy, scanning electron microscopy (SEM), and circular dichroism (CD). The goal is to provide evidence that graphene can attract free floating Aβ fibrils and Aβ plaque. Both studies currently use diphenylalanine peptide, a self-assembling model peptide for Aβ fibrils

Fabrication and Experimental Analysis of Axially Oriented Nanofibers

A novel design of a laboratory built axially rotating collector (ARC) having capability to align electrospun nanofibers have been described. A detailed morphological comparison of such nanofibers orientation and their geometry is done using scanning electron microscopy (SEM). For comparison various polymeric solutions were electrospun on conventional static collector as well as ARC. The average diameter of polyvinyl alcohol (PVA) nanofibers was found to be 250 nm while polycaprolactone (PCL) nanofibers were found to be within a range of 600–800 nm. Conducting nanoparticles such as graphene and multi-walled carbon nanotubes (MWNTs) mixed with polymer solutions shown to have a significant influence on the overall geometry of these nanofibers and their diameter distribution. It is evident from the SEM analysis that both graphene and MWNTs in polymer solution play a crucial role in achieving a uniform diameter of nanofibers. Lastly, the formation of the aligned nanofibers using ARC has been mathematically modeled and the electromagnetic field governing the process has been simulated