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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

7. Self assembly of
DNA

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

19. 2Dimensional DNA origami

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

21. Self assembly of
proteins

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