Nanobiotechnology

BIOT F422
II SEMESTER 2021 - 22

Course Handout (Part II)

Date: 17.01.2022

Scope and objective of the course:

The course deals with the principles and application of nano- and
micro-fabrication methods to build tools for exploring the
biological systems. The course includes interdisciplinary aspects of
biology and nanotechnology on the principles of microfabrication
techniques with a focus on nanoparticles, drug delivery systems,
and interactions with molecular and cellular level for biomedical
and biological research applications.
Text Books:
1. The Nanobiotechnology Handbook, (2010) YubingXie, CRC Press,
ISBN 9781439838693
2. NanoBioTechnology - BioInspired Devices and Materials of the
Future (2008) Shoseyov, Oded, Levy, Ilan, Humana Press, ISBN 978-1-
59745-218-2

Reference books:
1. Nanobiotechnology; concepts, applications and Perspectives,
Edited by C. M. Niemeyer and C. A. Mirkin, Wiley VCH ISBN 3-527-
30658-7
2. Nanobiotechnology II; more concepts and applications, Edited by
C. M. Niemeyer and C. A. Mirkin, Wiley VCH ISBN 3-527-30658-7
3. Bionanotechnology: Global Prospects (2008) David E. Reisner, CRC
Press; 1 edition, ISBN 978-0849375286
4 Bionanotechnology: Lessons from Nature (2004), David S.
Goodsell, Wiley-Liss; 1 edition ISBN: 978-0-471-41719-4
Lec. No. Learning objectives Contents References@
(Chapters)
1-3 Introduction to Introduction and Overview of Tb2,Ch1, Rb2
Nanobiotechnology Nanobiotechnology,
4-9 Self-assembling Synthesis and assembly of nanoparticles Tb1 Ch1,
nanostructures and nanostructures using bio-derived
templates: Coiled coil peptides, Protein,
DNA, Polysaccharides, Lipid membranes,
Viruses
10-13 Protein based S layers, Engineered nanopores, Ferritin, Rb1 Ch
nanostructures bacteriorhodopsin and its applications 13,14,23,24
14-18 DNA based DNA-Gold nanoparticle conjugates, DNA-
nanostructures Protein nanostructures, DNA based metallic
nanowires and networks, DNA-
nanomechnaical devices
19-20 Microbial Biosynthesis using bacteria, yeast, fungi, Chap 9
nanoparticle plant extracts
production
21-24 Bacterial magnets Magnetosomes: Nanoscale magnetic iron Chap 10
minerals in bacteria, Applications
25-30 Nanostructures for Nanocarrier mediated delivery of Tb1 Ch5, Tb2
Medicinal therapeutic and imaging agents, contrast Ch12-15
Applications agents for MMR, Nanoscale control of
cellular environment for tissue
engineering.
31-34 Nanostructures for Nanoparticles for electrochemical N2 Chap 7,
analytics bioassays, Luminescent semiconductor 8, 9
quantum dots in biology, surface
plasmon resonance biosensors
35-37 Nanomotors Biological Nanomotors, Biologically Chap 20, 21
inspired hybrid devices
38-40 Toxicity and Patent Nanotoxicity, Responsible Tb1 Ch6,
issues nanotechnology, Patenting inventions in Rb1 Ch27
bionanotechnology
EC Evaluation Duration Weightage Date & Time Venu
No Components e
.
1 Mid Sem 90 min 30% 10/03/22
(4:00 to

To be announced
5:30pm)
2 Quiz/ Seminar -- 30 % To Be
Announced
5 Compre Exam 3h 40% 12/05/22

later
(FN)
 Feynman: "There is plenty of room at the
bottom"
Seminal speech on December 1959 at CalTech

• " Why can’t be compress 24 volumes of

Encyclopedia Britannica on a pin head ?“

• " The biological example of writing

information on a small scale has inspired
me to think of something that should be
possible "

In 1990, IBM scientists wrote the logo IBM

using 35 xenon atoms on nickel.
The scale of things - nanometers and more
 What are nanomaterials?
Materials ranging in size from 1-100nm in at
least one dimension

The small size of nanomaterials influences the

way that these substances behave in the
environment because of quantum effects and
surface-to-volume ratios
Unique optical, chemical, electronic and photoelectrochemical
properties as at the nano scale, "quantum effects" dictate the
physical and chemical properties of the material

Lighting up the world with QDs

 Nanogold – different colors for
different sizes

The nanoscale size translates to unique optical properties because the

movement of the gold electrons are restricted, and therefore
interactions with light change.
Other unique properties that can result from
quantum effects include
 enhanced reactivity
 improved catalysis
 tunable wavelength sensing ability
 increased mechanical strength
 improved electrical conductivity
 stronger oxidative and reductive potential.
High surface area/volume ratio lead to quantum size effects
Nanotechnology isn’t something that was created in
the past few years, the past few decades, or even the
past few centuries. Nanostructures existed on this
earth long before intelligent life even appeared. It is
fascinating to think that nature was the first
nanoengineer.
 Nano-dimensions in Biology

DNA Proteins
Proteins

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 Nano- dimensions in Biology
Cont….
Self-assembled structures; biological membranes

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 Nano-dimensions in Biology
Cont….

ATP synthase
a highly complex
molecular machine
powered by an ion flux

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 Nano-dimensions in Biology
Cont….
Bacterial flagellar
motor:
about 45 nm in diameter
and is assembled from
about 20 different
kinds of parts.
.

5 http://www.evolutionnews.org/2012/09/visualizing_the064761.htmlBITS Pilani, K K Birla Goa Campus

Diatoms; range of intricate
morphologies
Diatoms are a major group of
algae, and are one of the most
common types of phytoplankton

Encased within a unique cell

wall made of nanostuctured
granular silica called frustules,
which have an array of pores
and branches.

The positioning and size of the

pores and branches are species-
specific, and therefore,
genetically determined

Chem. Soc. Rev., 2011, 40, 849–859 BITS Pilani, K K Birla Goa Campus
 Sponges
 Multicellular organisms which have
bodies full of pores and channels
allowing water to circulate through them
 Sponges take advantage of high levels of
environmental silicon to build robust
structures of amorphous silica. These
structures, called spicules, range from 1
mm to 3 m in length and microns to
millimeters in diameter, exhibit a low
elastic modulus and high fracture
toughness
 Produce a variety of intricate skeletal
elements that currently cannot be
duplicated in the laboratory or by industry

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Magnetotactic bacteria

Magnetotactic bacteria
contain magnetic particles
composed of greigite (Fe3S4)
or magnetite (Fe3O4)
The crystals are chemically
pure, single-domain magnets
with high magnetic coercivity
Magnetospirillum gryphiswaldense These magnetic particles are
cell, showing magnetite crystals used for navigation
arranged in a chain.

Schuler et al, Appl. Microbiol. Biotechnol., 1999, 52, 464–473

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Magnetotactic bacteria,
cont….

Electron micrographs of
crystal morphologies and
intracellular organization of
magnetosomes found in
various magnetotactic
bacteria

Schuler et al, Appl. Microbiol. Biotechnol., 1999, 52, 464–473

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 Thus, living organisms provide sophisticated
examples of assembly with unprecedented
control over distinct shapes and sizes over
multiple length scales from the nanometer to the
micrometer scales

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The first signs of
nanotechnology in
mankind’s era dates back
to ancient Egypt. It has
been noted that the ruby
red glasses the Egyptian’s
produced contained gold
nanoparticles

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The Lycurgus Cup is a Roman
glass cage cup

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Damascus steel

 Steel used in Middle

Eastern swordmaking
 1100 to 1700 AD.
 The blades were
reputed to be not only
tough and resistant to
shattering, but capable
of being honed to a
sharp and resilient
edge.

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Advanced metallurgy of the
ancient Indians

More than 1600 years

back, to build an iron
pillar of this huge size in a
single forge
It is 100% corrosion
resistant inspite of the
fact that it is 98% iron!

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Modern Nanotechnology
Information Technology Energy
• More efficient and cost
• Smaller, faster, more
effective technologies for
energy efficient and
energy production
powerful computing
− Solar cells
and other IT-based − Fuel cells
systems − Batteries
− Bio fuels

Medicine Consumer Goods

• Cancer treatment • Foods and beverages
−Advanced packaging materials,
• Bone treatment sensors, and lab-on-chips for
• Drug delivery food quality testing
• Appetite control • Appliances and textiles
• Drug development −Stain proof, water proof and
• Medical tools wrinkle free textiles
• Diagnostic tests • Household and cosmetics
• Imaging − Self-cleaning and scratch free
products, paints, and better
cosmetics

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 Applications
Tumor targeting and drug delivery

Dendrimer complex
docking on cellular
folate receptors

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 Applications
Tumor targeting and drug delivery

A new thin-film coating developed at MIT can deliver controlled drug doses
to specific targets in the body when an electric potential is applied. The
films are made from alternating layers of two materials: a negatively
charged pigment and a positively charged drug molecule,
36 BITS Pilani, K K Birla Goa Campus
 Applications
Molecular diagnostics

 Detecting target DNA using AuNPs-probe conjugate

 Hybridization leads to cross-linking of AuNPs which change color
from red to purple.
 Detection of pathogens such as H5N1 virus, Mycobacterium and
Cryptosporidium
 Sensitivity higher than conventional PCR-based diagnostics

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 Gene delivery

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 Photothermal therapy

Von Maltzahn G et al Cancer Res. 2009. 69. 3892–3900.

43 BITS Pilani, K K Birla Goa Campus

 Magnetically Controlled Drug
Release
magnetic nanoparticles can be used as
an external and remotely controlled
trigger for controlled drug release. The
thermal energy can open the gates of
any kind of organic or inorganic carriers
which contain drugs for therapy

44 Yoo et al, Accounts of Chemical Research, 2011, 44, BITS Pilani, K K Birla Goa Campus
 Applications:
DNA based nanodevice

Two double-crossover molecules (red and blue) connected by a bridge element (yellow)
that can be converted from B-DNA (top) to Z-DNA (bottom) by the addition of a positively
charged cobalt compound (and converted back again by its removal) form the basis of a
DNA nanomechanical device. The change is monitored by attached fluorescent dyes
represented by the stippled circles.
http://www.foresight.org/Updates/Update36/Update36.1.html BITS Pilani, K K Birla Goa Campus
 DNA sequencing with
nanopores
a-hemolysin pore (very first, natural
pore)
(~2nm diameter)

Axial View Side View

Nanopore in membrane
DNA in buffer
Voltage clamp
Measure current

42 BITS Pilani, K K Birla Goa Campus

 Applications
Quantum dot with cytochrome
Organic transformation through photoactivation of the QDs

Excitation of CdS–cytochrome P450 enzyme hybrids resulted in the hydroxylation of

myristic acid to α- and β-hydroxymyristic acid products via activation of P450 enzyme
by superoxide and hydroxyl radicals generated from quantum dot excitation
Ipe et al, Angew. Chem. Int. Ed, 2005
37 BITS Pilani, K K Birla Goa Campus
 Applications
Enzyme entrapment

Immobilized 90% of the enzyme activity from the precursor solution and
retained 100% of its activity. This loading efficiency was in contrast to that of
sol–gel methods of enzyme entrapment in silica, in which less than 10% of
initial enzyme activity is entrapped, and where loading was restricted to 0.1–
5% w/w.

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BITS Pilani, K K Birla Goa Campus
 Self-assembled
macromolecular templates
Container like protein architectures
eg: viral capsids and ferritin.
Have three distinct interfaces that
can be synthetically exploited.
The subunits can be modified both
chemically and genetically to
impart designed functionality to
different surfaces of the cage.
synthetic flexibility allows for the
introduction of multifunctionality in
a single cage.

37 BITS Pilani, K K Birla Goa Campus

 Capsids

Cowpea chlorotic mottle virus in closed conformation induced by low pH

and/or high concentration of metal ions, and in a swollen conformation
induced by high pH and/or low concentration of metal ions. Swelling results in
the formation of 2 nm pores
39 BITS Pilani, K K Birla Goa Campus