Lecture 5. Biomolecular Self-assembly (and Detection)
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1 Lecture 5. Biomolecular Self-assembly (and Detection) Instructor: Prof. Zhiyong Gu (Chemical Engineering & UML CHN/NCOE Nanomanufacturing Center)
2 Lecture 6: Biomolecular Self-assembly Table of Contents Definitions Fundamentals and principles p Examples of biomolecular self-assembly Nanostructure fabrication by bimolecular self-assembly Case study: Biosensing and detection by nanowires
3 Biomolecular Self-assembly Definitions A biomolecule is a chemical compound that naturally occurs in living organisms. Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur. Other elements sometimes are incorporated but are much less common. DNA Proteins Cell Membrane
4 DNA Self-Assembly Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. The DNA double helix is held together by hydrogen bonds between the bases attached to the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). DNA self-assembly is the most advanced and versatile system known for programmable construction of patterned systems on the molecular scale Reif, Duke Univ.
5 DNA Assisted Self-Assembly of Nanowires Electroanalysis 19, 2007, No. 22,
6 Nanostructure Fabrication by Bimolecular Self-assembly DNA Based Nanoparticles Assembly Nature, 382, (1996)
7 Protein Self-Assembly (Folding) Protein structures Primary structure: amino acid sequence Secondary structure: regularly repeating local structures stabilized by hydrogen bonds alpha helix (α-helix) β sheet (also β-pleated sheet) From Wikipedia
8 Protein Self-Assembly (Folding) Protein structures Tertiary structure: the overall shape of a single protein molecule; l the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, ti most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even posttranslational modifications. Quaternary structure: the shape or structure that results from the interaction of more than one protein molecule, usually called protein subunits in this context, which function as part of the larger assembly or protein complex. From Wikipedia
9 Antibody-Antigen Interactions Antibody Structuret Antibodies are immune system-related proteins called immunoglobulins. Each antibody consists of four polypeptides two heavy chains and two light chains joined to form a "Y" shaped molecule. The amino acid sequence in the tips of the "Y" varies greatly among different antibodies. This variable region, composed of amino acids, give the antibody its specificity for binding antigen. This image represents the structure of an antibody's variable region (Fab) complexed with an antigen, in this case hen egg white lysozyme. y
10 Antibody-Antigen Interactions The hypervariable (HV) regions of a Fab, representing both light and heavy chains, are highlighted in purple. The antigen is green. The part of the antigen in direct contact with the antibody is called the antigenic determinant, or epitope In this view, the HV regions of the Fab have been deleted. The framework (FR) regions of the antibody do not contact the antigen.
11 Nanostructure Fabrication by Bimolecular Self-assembly Biotin-Avidin Linker for Nanowire Assembly Nano Lett., 2004, 4,
12 Cell Membranes (Lipid Bilayer) Illustration of a cell membrane Diagram of the arrangement of amphipathic lipid molecules to form a lipid bilayer. The polar yellow head groups separate the grey hydrophobic tails from the aqueous cytosolic and extracellular environments
13 Vesicles Vesicle is a relatively small and enclosed compartment, separated from the cytosol by at least one lipid bilayer. If there is only one lipid bilayer, they are called unilamellar vesicles; otherwise they are called multilamellar. Vesicles store, transport, or digest cellular products and waste. Biological Cell Schematic showing the cytoplasm, with its components (or organelles), of a typical animal cell. Organelles: (1) nucleolus (2) nucleus (3) Example: Bio-mimetic i lipid/pda id/pdavesicles ribosome (4) vesicle (5) rough endoplasmic reticulum (6) Golgi apparatus (7) cytoskeleton A schematic description of a chromatic vesicle composed of (8) smooth endoplasmic reticulum (9) phospholipids (black) and polydiacetylene (PDA) (blue). mitochondria (10) vacuole (11) cytosol (12) These particles form bio-mimetic bilayersconstituting a useful lysosome (13) centriole. platform for studying membrane processes, such as peptidemembrane interactions, pore formation, drug permeation through lipid barriers, and others.
14 Vesicles Made by Block Copolymers Journal of Polymer Science: Part B: Polymer Physics, Vol. 42, (2004)
15 Vesicles Made by Block Copolymers Journal of Polymer Science: Part B: Polymer Physics, Vol. 42, (2004)
16 Vesicles Made by Block Copolymers Journal of Polymer Science: Part B: Polymer Physics, Vol. 42, (2004)
17 Case Study: Nanowire-Based Biosensors Materials Today, 2005, 20 Nanomedicine, 1(1), (2006)
18 Case Study: Nanowire-Based Biosensors (A) Schematic of a field-effect transistor (FET); (B) schematic of electrically-based sensing using FET devices. The binding of a charged or polar biological or chemical species to the chemically modified gate dielectric is analogous to applying a voltage using a gate electrode as shown in A. (C) A nanowire device configured as a sensor with antibody receptors (green) and binding of a protein with net negative charge yields an increase in the conductance. (D) A prototype nanowire sensor biochip with integrated microfluidic sample delivery Nanomedicine, 1(1), (2006)
19 Case Study: Nanowire-Based Biosensors (A) Schematic of a single virus binding and unbinding to the surface of a silicon nanowire device modified with antibody receptors; (B) simultaneous conductance and optical data for a silicon nanowire device with a lowdensity of antibody receptor units (C) high-density of anti-body (D) schematic of multiplexsed single virus detection. Nanomedicine, 1(1), (2006)
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