Natural Biological assembly at nanoscale slides
- 1. Topic: Natural biological assembly at the nanoscale
- 2. Contents: • Introduction • Self assembly of DNA • Self assembly of protein • Applications of natural biological self assembly at nanoscale
- 3. What is biological assembly? Biological assembly (also sometimes referred to as the biological unit) is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule.
- 4. Characteristic features of natural bioassemblies at Nanoscale • Well-organized architectures with a broad selection of sizes at the nanometer scale. • Monodispersed particles with uniform size and shape. • Variability of genomic sequence, through which the composition and surface properties can be controlled through recombinant technology. • Economic large-scale production in gram or even in kilogram quantities.
- 5. Preparations • Biological assembly may be built from: 1. One copy of the asymmetric unit 2. Multiple copies of the asymmetric unit 3. A portion of the asymmetric unit • Hemoglobin is used to demonstrate each of these cases:
- 6. Biological assembly composed of one copy of the asymmetric unit Biological assembly composed of multiple copies of the asymmetric unit Multiple biological assemblies in the asymmetric unit
- 8. Manipulation of DNA 1. Strand displacement, is the displacement of a single strand of DNA from a double helix by an incoming strand with a longer complementary region to the template strand.
- 9. 2. DNA restriction is the cleaving of phosphodiester bonds between the nucleotide subunits at specific locations determined by short (4-8 base) sequences by a class of enzymes called nucleases.
- 10. 3. DNA ligation is the re-joining of nicked double stranded DNA by repairing the phosphodiester bond between nucleotides by the class of enzymes known as ligases. 4. DNA polymerases are a class of enzymes that catalyze the polymerization of nucleoside triphosphates into a DNA strand. 5. Deoxyribozymes (DNAzymes) are a class of nucleic acid molecules that possess enzymatic activity for example, cleave specific target nucleic acids.
- 11. Why use DNA to assemble molecular-scale devices? 1. A variety of geometries can be achieved by carefully programming DNA sequences to interact among themselves in a predictable manner 2. The structure of most complex DNA nanostructures can be reduced to determining the structure of short segments of dsDNA 3. Design of DNA nanostructures can be assisted by software
- 12. 4. The solid-phase chemical synthesis of custom ssDNA is now routine and inexpensive 5. The assembly of DNA nanostructures is a very simple experimental process 6. The assembled DNA nanostructures can be characterized by a variety of techniques
- 13. Self-assembled DNA tiles and lattices 1. DNA nanostructures i. Stem-loop : a ssDNA that loops back to hybridize on itself ii. Sticky end : an unhybridized ssDNA that protrudes from the end of a double helix. iii. Holliday junction : two parallel DNA helices form a junction with one strand of each DNA helix crossing over to the other DNA helix.
- 14. DNA tiles and lattices • A DNA tile is a DNA nanostructure that has a number of sticky ends on its sides, which are termed pads. • A DNA lattice is a DNA nanostructure composed of a group of DNA tiles that are assembled together via hybridization of their pads
- 16. DNA origami • First proposed and implemented by Paul W. K. Rothemund in 2006 , in which he folded a long viral single-stranded DNA (ssDNA) molecule to create DNA structures of arbitrary shapes • The term origami refers to the Japanese folk art of folding paper into a special shape
- 17. • Method is based on folding of the large ssDNA (usually the 7.3 kilobase genome of the M13 bacteriophage) with an excess of smaller complementary strands (typically 32 bases). • These small strands are called “staple” strands and are complementary to at least two distinct segments of the long ssDNA
- 18. Schematic illustration of DNA folding in origami construction
- 20. Three dimensional DNA origami A cube like hollow box with a hinged lid that can be open and closed by a DNA strand as a key was constructed and imaged
- 22. Protein self assembly • Proteins are biologically significant molecules that maintain the functional integrity of cells. • Proteins are created from amino acids – The 20 amino acids found in nature have unique properties. • Some are acidic some are basic and some are neutral.
- 23. Types of protein self assembly • There are two types of molecular self- assembly. • Intra-molecular and • Intermolecular. • The term ‘self-assembly’ commonly refers to the intermolecular self-assembly while the intramolecular self-assembly is referred to as ‘folding’.
- 24. General Amino Acid Structure • Variation in the R group leads to acidic and basic and neutral amino acids.
- 25. Protein self assembly • Primary Structure: it is determined by the sequence of amino acids. • Secondary structure: it involves localized domains of the proteins that interact to form alpha helices or beta sheets • Tertiary structure: involves interactions between the various domains lead to formation of a supramolecular structure
- 26. Protein self assembly • The highest level of protein structure is the quaternary structure. • Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex • The secondary, tertiary and quaternary structures of a protein can be ‘denatured’ while the primary structure can only be hydrolyzed
- 27. Protein self assembly • The highest level of protein structure is the quaternary structure. • Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex • The secondary, tertiary and quaternary structures of a protein can be ‘denatured’ while the primary structure can only be hydrolyzed
- 28. Ferritin protein cages • Ferritins are globular protein complexes that are vital to iron homeostasis. • The ferritin protein family can self-assemble into protein cages of two types. i. Maxi-ferritins have nearly 24 identical protein subunits that self-assemble into a spherical cage with an octahedral symmetry. ii. Mini-ferritins that have tetrahedral symmetry, hollow assemblies composed of 12 monomers.
- 29. Peptide nanofibres • Peptide nanofibres can be obtained from a modified amyloid-beta peptide when assembly is done in water. • When assembly is done in methanol, nanotubes are formed. • The different morphologies arise from changes in the hydrogen-bonding capacity of the solvent, which may modify the propensity for beta-sheets to twist.
- 30. Peptide nanofibres • They can also be produced by alternating hydrophobic and hydrophilic amino acid residues (self-complementary repeats) that have a tendency to adopt a beta-sheet structure.
- 31. • A team of researchers at the University of Massachusetts at Amherst has succeeded in self-assembling superstructures by simply mixing together proteins and nanoparticles. Protein-Nanoparticle co-engineering approach
- 32. Gold NP with arginine ligend Protein bearing GFP and an anionic tail Mix them in proper ratio ArNP combine with protein Ordered nanostructure is formed by electrostatic interactions
- 33. Hierarchical organization of engineered proteins and nanoparticles in complex superstructures.
- 34. Therapeutic Benefits • This structures can deliver the proteins to the cytosol of cells, where they can then be directly transported to the cell nucleus. • This strategy is a new way to treat a wide range of genetic abnormalities, including chronic inflammation, cerebrovascular disorders and cancer.
- 35. Nanocage of Icosahedral shape • Researchers also made an icosahedral protein nanostructures with dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. • These nanostructure interact with living cell in the same way the virus interact.
- 36. Applications of natural biological self assembly at nanoscale
- 37. Diagnostics and Sensing Optical sensor: Self-assembled DNA nanostructures loaded with intercalator dyes for tracking and labelling biomolecules like proteins. Electrochemical sensors: Detection of phenolic compounds peptide nanotubes at the surface of gold electrodes
- 38. Gene and drug delivery • Delivery of drug by viruses. • Nanofilaments loaded with doxorubicin penetrate breast cancer cells promote apoptosis Information technologies • DNA-based logic circuits using only single stranded DNA as inputs and outputs
- 39. Detection of pollutants DNA strand functionalized at ends by FRET probes designed for the selective sensing of mercury (hairpin formation) lead (aptamer formation) • Building nanostructures with porosity and gas sorption properties using peptidic residues such as Dialanine selectively absorb oxygen over Xerogel was then used to absorb iodine vapors Chemical storage
- 41. Thank You