ROOPAVATH UDAY KIRAN
M.Tech 1st year
• DNA based Nanoelectronics
• DNA mediated assembly of Metal
• Sequence specific Molecular Lithography
• DNA detection with Metallic nanoparticles
• The combination of biological elements with
electronics is of great interest for many
• Inspired by biological signal processes
• To explore ways of manipulating, assembling,
and applying biomolecules and cells on
integrated circuits, joining biology with
The overall goal
• To create bioelectronic devices for biosensing
• Drug discovery
• Curing diseases
• To build new electronic systems based on
biologically inspired concepts
• Having tools similar in size to biomolecules
enables us to manipulate, measure, and (in the
future) control them with electronics, ultimately
connecting their unique functions.
Recent advances in the field
• Electrical contacting of redox proteins with
• The use of DNA or proteins as templates to
assemble nanoparticles .
• Use of nanoelectrodes, nano-objects, and
nanotools in living cells and tissue, for both
fundamental biophysical studies and cellular
signaling detection and nanowires.
• Functional connection of neuronal signal
processing elements and electronics in order to
build brain–machine interfaces and future
Deoxyribonucleic acid (DNA)
• Deoxyribonucleic acid (DNA) is a nucleic acid that
contains the genetic instructions for the
development and function of living organisms.
• DNA is a long polymer made from repeating units
called nucleotides. The DNA chain is 22 to 24 Å
wide and one nucleotide unit is 3.3 Å long.
• DNA polymers can be enormous molecules
containing millions of nucleotides. For instance,
the largest human chromosome is 220 million
base pairs long.
DNA FOR MOLECULAR DEVICES
• The two- and three-dimensional assembly of complex objects
(cubes, octahedral, etc.) made with DNA (Seeman 1998, 2003) onto
organized chips to recognize and position other biological
materials, with applications in diagnostics and medicine.
• To explore the conductivity of DNA, Alternatively, if measurable
currents cannot be sustained by DNA molecules, another
interesting strategy is to realize hybrid objects (metal
nanoparticles/ wires, proteins/antibodies, etc.) in which electrons
move and carry current flows, templated by DNA helices at
selected locations This route also allows to embed conducting
objects into the hybrid architectures, to realize, e.g., a carbon
nanotube DNA-templated nanotransistor
Both of these ways could lead to the development of DNA based
WHAT IS KNOWN ABOUT DNA’S ABILITY
TO CONDUCT ELECTRICAL CURRENTS?
• We just point out here the salient results that
motivated the pursuit of optimized
measurement setups on one hand, and of
DNA-derivatives and mimics beyond native-
DNA on the other hand.
• The desired “mutants” should exhibit
enhanced conductivity and/or other
exploitable functions, whereas maintaining
the inherent recognition and structuring
traits of native Watson-Crick DNA that are
demanded for self-assembling.
The molecules used for electronic applications
need to express three main features:
(a) Structuring, namely, the possibility to tailor
their structural properties (composition,
length, etc.) “on demand”.
(b) Recognition, namely, the ability to attach
them to specific sites or to other target
(c) Electrical functionality, namely, suitable
conductivity and control of their electrical
• One of the main challenges with such molecules,
however, is the control of their electrical conductivity.
• Early work in this field has yielded seemingly
controversial results for native-DNA, showing electrical
behaviours from insulating through semiconducting to
conducting, with even a single report of proximity-
• Indeed, recent reviews of the experimental literature
highlighted that the variety of available experiments
cannot be analyzed in a unique way; for instance,
electrical measurements conducted on single molecules,
bundles, and networks, are not able to reveal a uniform
interpretation scheme for the conductivity of DNA,
because they refer to different materials or at least
DNA - templated electronics
• Sequence-specific molecular lithography.
• The protein RecA, which is normally responsible for
homologous recombination in Escherichia coli
bacteria, is utilized as a sequence-specific resist,
analogous to photoresist in conventional
• The patterning information is encoded in the
underlying DNA substrate rather than in glass masks.
• Facilitates precise localization of molecular devices
on the DNA substrate and formation of molecularly
A possible scheme for the DNA templated
assembly of molecular-scale electronics
• Homologous recombination
• Addresses three major challenges on the way to
I. Precise localization of a large number of
devices at molecularly accurate addresses on
II. Construction, inter-device wiring.
III. It wires the molecular network to the
macroscopic world, thus bridging between the
nanometer and macroscopic scales.
There are four major obstacles to the
realization of this concept.
• Biological processes need to be adopted and modified
to enable the in-vitro construction of stable DNA
junctions and networks with well-defined connectivity.
• The hybridization of electronic materials with
biological molecules needs to be advanced to the point
where precise localization of electronic devices on the
network is made possible.
• Appropriate nanometer-scale electronic devices need to
be developed. These devices should be compatible
with the assembly and functionalization chemistry.
• Since DNA molecules are insulating, they need to be
converted into conductive wires.
• Homologous recombination is a protein-mediated
reaction by which two DNA molecules, possessing same
sequence homology, crossover at equivalent sites.
• RecA is the major protein responsible for this process in
• RecA proteins are polymerized on a probe DNA molecule
to form a nucleoprotein filament, which is then mixed
with the substrate molecules.
• The nucleoprotein filament binds to the DNA substrate at
homologous probe–substrate locations.
• Note that RecA polymerization on the probe DNA is not
sensitive to sequence. The binding specificity of the
nucleoprotein filament to the substrate DNA is dictated by
the probe’s sequence and its homology to the substrate
DNA molecules were first aldehyde-derivatized by reacting
them with glutaraldehyde.
Sample was incubated in an AgNO3 solution.
The reduction of silver ions by the DNA-bound aldehyde in
the unprotected segments of the substrate molecule resulted
in tiny silver aggregates along the DNA skeleton.
The aggregates catalyzed subsequent electroless gold
Continuous highly conductive gold wire
• RecA-mediated recombination can be harnessed to
generate the molecularly accurate DNA junctions
required for the realization of elaborate DNA scaffolds.
• Two types of DNA molecules which were 15 kbp and
4.3 kbp long respectively, were prepared.
• The short molecule was homologous to a 4.3 kbp
segment at one end of the long molecule.
• The RecA was first polymerized on the short
molecules and then reacted with the long molecules.
• The recombination reaction led to the formation of a
stable, three-armed junction with two 4.3 kbp-long
arms and an 11 kbp-long third arm.
• Through the fast increasing knowledge about
biomolecules and their interaction with other
biomolecules, the study of those
biorecognition events has become more and
• One of the most remarkable technologies that
had a strong impact on DNA detection is
probably the DNA chip (or gene chip)
• This allows researchers to conduct thousands
or even millions of different DNA sequence
tests simultaneously on a single chip or array.
The DNA chip technology also comes with
• The miniaturized probe spots on a DNA chip need
expensive fabrication procedures, which are also
used in microfabrication.
• The readout of the DNA arrays must be
miniaturized. Finally, the detection scheme must be
sensitive enough to detect just a few copies of
target and selective enough to discriminate between
target DNAs with slightly different compositions.
Solution to the above demerit - DNA Labelling :
• DNA labeled with fluorescent dyes in combination
with confocal fluorescence imaging of DNA chips has
provided the high sensitivity needed
• For instance, nowadays many hundreds of diseases
are diagnosable by the molecular analysis of DNA.
• Mainly the DNA hybridization reaction is used for
the detection of unknown DNA, where the target
(unknown single-stranded DNA; ssDNA) is
identified, when it forms a double-stranded
(dsDNA) helix structure with it complementary
probe (known ssDNA).
• By labeling of either the target DNA or the probe
DNA, the hybridization reaction can be detected by
radiochemical, fluorescence, electrochemical,
microgravimetric, enzymatic, and
• Fluorescence labeling also allows multicolor
labeling, making possible the multiplexed
detection of differently labeled single-stranded
DNA targets on one array.
• However, fluorescent dyes have significant
• Susceptible to photobleaching
• Broad emission and absorption bands, which
limit the number of dyes.
These disadvantages have limited the use of DNA
chips mainly to specialized laboratories
DNA Detection using Metal Nanoparticles
• These new detection schemes are based on the
unique properties of metal nanoparticles, such as
Large optical extinction and scattering coefficients.
Catalytic activity, and surface electronics.
metal nanoparticles have approached as alternative
labels in a variety of DNA detection schemes.
• Most notably, gold nanoparticles have been used for
the DNA detection, because they can be easily
modified with biomolecules.
• However, other metal nanoparticles, such as Ag, Pt,
and Pd, have also been used for DNA detection
Label-Free, Fully Electronic Detection of DNA with a
Field-Effect Transistor Array
• Field-effect sensors, especially FETs, offer an alternative
approach for the label-free detection of DNA with a direct
electrical readout .
• Recently, the detection limit of potentiometric field-
effect sensors was enhanced such that single nucleotide
polymorphisms (SNPs) were successfully detected.
• The sensors used the field-effect at the electrolyte-oxide-
semiconductor (EOS) interface, which was firstly
described for ion-selective field-effect transistors (ISFET).
• Typically, the response of such devices is interpreted as
shift of the flat-band voltage of the field effect structure
• Most of these sensor chips were operated as
potentiometric ISFETs and used the ion-selectivity of the
solid–liquid interface or artificial molecular membranes,
which were attached to the FET gate structure.
• In this context, the dc as well as the ac readout of the
FETs has been reported and the influence of a
biomembrane attached to the transistor gate structure
has been described.
The ISFET structure can be highly integrated to multichannel
sensors by using standard industrial processes.
• A miniaturized, low-cost, fast readout, highly integrated,
and addressable multichannel sensor with sensitivity high
enough to detect SNPs, would be the ideal device for
genetic testing and medical diagnostics.
Last but not least
• the other way to pursue DNA-based
nanoelectronics is by looking at derivatives that
may exhibit intrinsic conductivity better than the
double helix. One of the most appealing
candidates in the guanine quadruple helix G4-
• Other viable candidates are DNA hybrids with
metal ions and double helices in which the native
bases are substituted with more aromatic bases
that may improve the longitudinal π-overlap
Applications of Hybrid Nanobioelectronic systems
• Nanoelectronics for the future. The fascinating
world of the bio–self-assembly provides new
opportunities and directions for future electronics,
opening the way to a new generation of
computational systems based on biomolecules and
biostructures at the nanoscale.
• Life sciences. Rapid pharmaceutical discovery and
toxicity screening using arrays of receptors on an
integrated circuit, with the potential to develop
targeted “smart drugs.”
• Medical diagnostics. Rapid, inexpensive, and
broad-spectrum point-of-use human and animal
screening for antibodies specific to infections
• Environmental quality. Distinguishing dioxin isomers for
cleaning up polluted sites, improving production
efficiency of naturally derived polysaccharides such as
pectin and cellulose, and measuring indoor air quality
for “sick” buildings.
• Food safety. Array sensors for quality control and for
sensing bacterial toxins.
• Crop protection. High-throughput screening of pesticide
and herbicide candidates.
• Military and civilian defense. Ultrasensitive, broad-
spectrum detection of biological warfare agents and
chemical detection of antipersonnel land mines,
screening passengers and baggage at airports, and
providing early warning for toxins from virulent bacterial
• Nanobioelectronics - for Electronics,Biology,
and Medicine – Edited by Andreas
Offenhausser and Ross Rinaldi.
• Nanobiotechnology Concepts, Applications
and Perspectives Edited by Christof M.
Niemeyer and Chad A. Mirkin.
• Yubing Xie - The nanobiotechnology
handbook-CRC Press – Taylor - Francis (2013)