Physics of Nano-Bio Systems
Pik-Yin Lai 黎璧賢
Department of Physics & Center for Complex Systems,
National Central University, Chung-Li, Taiwan 320
Email: pylai@phy.ncu.edu.tw
•Introduction: DNA, proteins, molecular biology
•Biopolymers/DNA
•Single molecule Force experiments.
•Elastic models of DNA & DNA mechanics
•Charge Transport in DNA
•DNA microarray
•Nano-technology & DNA bio-sensor
•DNA as nano-materials
2005
Cell
Nucleus
Chromosome
Chromatin
Double-stranded biopolymer, 2 sugarphosphate chains (backbones) twisted
around each other forming a RH (B-form)
double helix.
Brief Molecular biology
• Molecular Biology of the Cell
Central Dogma
Proteins
Bonding &
Forces in bio-systems
•Van der Waals: ~2.5kT
•Ionic: ~250kT
•Covalent: ~100-300kT
•H-bonds: ~5-10kT
•Hydrophobic: ~few kT
Room Temp:
1kT~ 4x10^-21 J
Some common Biomolecular chains
Spectrin
Globular actin
Intermediate filament
F-actin
Microtubule
Linear mass
density
persistence
length
Actin filaments, microtubules are stiff in cellular scales
--- thermal fluctuations not important
base pairs: A-T & C-G
Watson-Crick Base Pairs
•Hydrogen bonded base pairs: A-T & C-G
•A-T: 2 H-bonds; C-G: 3 H-bonds
•10.5bps/turn, helix pitch ~3.4nm.
•helical structure is further stabilized by
vertical stacking interactions (induceddipole--induced-dipole) between the
aromatic bases
11
12
• ~10 to 10 bps in a human DNA
Nature review: 50 years of DNA
Mechanics/Elasticity of Single Bio-molecules
• To investigate the conformational changes
in single bio-molecules, may provide
significant insight into how the molecule
functions.
• How forces at the molecular level of the
order of pN underlie the varied chemistries
and molecular biology of genetic materials?
Force scales
• Size of bead/cell, d~2 micron
• thermal agitation sets the lower limit to force
measurements;
• Langevin force~10fN/Hz
• Weight of a cell ~ 10fN
• Entropic forces ~kT/nm ~ 4 pN
• Non-covalent bond~eV; elastic forces~eV/nm=160pN
• Force to break covalent bond~ eV/A~1600pN
1/2
Experimental Tools in Force expts.
•Micro-mechanical springs (fibers,micro-pipette,cantilevers),
•Hydrodynamic drag
•Optical or magnetic tweezers
•Scanning force/Atomic force microscopy
•Imaging techniques and Fluorescence microscopy
Strick et al., Science 271, 1835 (96);
Ann. Rev. Biophys. 29, 523 (00)
Scanning force microscopy
•Commercial SFM tips can have stiffness low as ~10mN/m;
can measure forces as low as 10pN.
•Etched optical fibre/glass microneedles are ultra-soft, ~1.7 mN/m;
force precision of ~1 pN
Optical Traps
Polarizability of bead, c
F= grad (p . E)=2c(grad E)E
net force acts radially towards the
more intense beam & vertically
towards the focus.
Calibrate by Brownian motion & fluid flow
near infrared lasers for biomolecules
single beam gradient trap
dual counter propagating beam trap
optical tweezers
Optical tweezers
Bustamante et al., Science 258, 1122 (92);
Biophys. J. 79, 1155 (00)
Micropipette aspiration
Pipette diameter~1~10mm
Suction P~1 Pa to 50kPa; f~1 pN to 1mN
Biointerface force probe
Force-Induced Transition of an overwound DNA to P-DNA
•positively supercoiled DNA reveals the existence of a
sharp transition at f~ 3 pN
•P-DNA corresponds to an overwound structure with
2.62 base pairs per turn.
•The bases are exposed tothe solvent with the
phosphate backbone allowed to wind at the center,
Biological implications of torque-induced transitions
• Many proteins interacting with DNA modify its twist (e.g.
histones).
• DNA overwinds/underwinds during transcription as the
RNA polymerase progresses on its substrate.
• during replication, helicases unwind the molecule to make
way for the replication complex.
• torsional stress in the molecule thus depends on the
balance between the generation
• of torsional stress (for example, during transcription or
replication) and its relaxation by topoisomerases.
• conceivable that the cell uses the torsional
• stress signal might control the expression of nearby genes.
Some experiments suggest that the wave of unwinding left
behind the transcription complex may turn on other genes
Unzipping DNA
•Measure force to unpair two bases
•Stick-slip response
•Prototype for DNA sequencing, need
higherresoultion
•Complexed with protein can make filament
stifferhigher sensitivity
Stretching Proteins
•undergo independent folding/unfolding transitions as the
polypeptide is stretched.
•display a typical sawtooth pattern, due to the coexistence in
the stretched protein of folded and unfolded domains.
•Pulling rate dependent: ~20pN to unfolding titin at 60nm/s
(optical tweezers); ~150pN at 1000nm/s (AFM)
•Two-level model.
Unfolding pathway of spectrin
a-helical domain
•Little common between force and temp.
induced unfolding pathways
Paci & Karplus
PNAS 97, 6521 (2000)
Unfolding pathway of Immunoglobulin
b-sandwich domain
•Important differences between force and temp.
induced unfolding pathways, but common
features of folding cores
Paci & Karplus
PNAS 97, 6521 (2000)
Interactions among different Bio-molecules
• To investigate the formation of
DNA/protein complex
• How stresses affect biological process? (e.g.
transcription, replication, unwrapping DNA
from nucleosome, RNA/RecA polymerase,
gene expression…..)
Physicist’s view of the DNA chain
Double helix stabilized by H-bonds (bp interactions)
Polymer of persistence length ~50nm under low force (<10pN):Entropic
elasticity. Complicated at high forces: cooperative behavior
Elasticity of dsDNA affect its structure and can influence the biological
functions
Worm-like chain model (stiff chain)
|t|=1
inextensible
single strand
Rod-like chain model (twisted stiff chain)
Marko et al., Science 256, 506, 1599 (94);
Bouchiat et al., PRL 80, 1556 (98)
Fitting from expts:
A=53nm;
Can account for some supercoiling properties of DNA
Phenomenological model, no description of underlying
mechanism.
Stretching a single dsDNA
lo =B-form contour length
Low force regime described well by
worm-like chain (WLC) model.
Abrupt increase in length at ~65pN
from B-form DNA to S-form DNA
dsDNA model with bending and bp stacking interactions
Zhou, Zhang & Ou-Yang. PRL (99); PRE (00)
ZZO model
Bending:
•ro =backbone arclength
Base-pair stacking:
between adjacent bps
•Asymmetric potential: a
free DNA is RH
•ro cosjo=0.34nm, eqm.
distance between 2 stacks
e=14kT, averaged value
take to be sequence indep.
Stretching force:
Twisting:
Low force: WLC is accurate
High force:
ZZO model: Good agreement with force experiment data.
dsDNA w/ bp stacking  wormlike-rod chain
(at low force)
Zhou & Lai, Chem .Phys. Lett. 346, 449 (01)
Since WLRC is a generic phenomenological model which
describe the low force elastic behavior well, any good
microscopic model must reduce to it at low force/torque.
cosj measures the extend the backbones are folded w.r.t.
central axis
Comparing Tw in both models:
In force-free state: jm minimizes V(j) and
for low force/torque: j is not far away from jm
B-form to S-form Transition under a Stretching force
Lai & Zhou, J. Chem. Physics 118, 11189 (2003)
Force Experiments
Stretching a single end-grafted DNA
S-form
B-form
•Abrupt increase of 1.7 times in contour length of dsDNA near
65pN.
•Thermal fluctuations unimportant near onset of transition.
ZZO model for double-stranded DNA
H. Zhou, Z. Yang, Z-.c. Ou-Yang, PRL 82, 4560 (99)
j=folding angle
Classical mechanics approach
•(thermal effects can be neglected since the DNA is quite straight near
the onset of BS)
•All lengths in units of R, energy in units of k/R f=fz, dimensionless
2
force b=fR /2k, t=(sinqcosf,sinq,sinf,cosq)
Minimizing Ebs: Euler Lagrange eqns.
B.C.s:
to // f,
jo non-zero
q(s)=0
Effective potential
•Behavior governed by the minima of U(j) in the long L limit.
First order phase transition at bt
2
b=fR /2k
Detail configurations of the strands can be explicitly calculated.
First-order elongation:Stretch by untwisting
b=0.073
b=0.075
Untwisting upon stretching
•Untwist per contour length from BS, DTw/Lo~-100 deg. /nm;
•Almost completely unwound ~ 34deg./bp
•Torque ~ 60 pN nm
Direct observation of DNA rotation during
transcription by Escherichia coli RNA
polymerase Harada et al., Nature 409 , 113 (2001)
•DNA motor: untwisting gives
rise to a torque
•BS transition provides a
switch for such a motor.
G > 5 pN nm from hydrodynamic drag estimate
Relative Extension
qo=10 deg. jo=53 deg. L=10
Transition to S-form occurs at f~45pN (c.f. expt.: ~65pN)
Relatvie extension Z/Lo increases by 1.7 times from BS. (c.f. expt.
~1.65 times)
Including external Torque
Torque couple with Linking number
Left-handed Z-form DNA obtained for large negative external torque
Z-form
S-form
B-form
Left to right: Torque increasing from –ve to +ve values
Z-DNA is left-handed, its bases seem to zigzag. One turn
spans 4.6 nm, comprising 12 base pairs. The DNA
molecule with alternating G-C sequences in alcohol or high
salt solution tends to have such structure.
In a solution with higher salt concentrations or with
alcohol added, the DNA structure may change to an
A form, which is still right-handed, but every 2.3 nm
makes a turn and there are 11 base pairs per turn.
Electrical properties of Single Bio-molecules
• Electronic excitations and motion of electric charges are
well known to play a significant role in a wide range of
bio-macromolecules
• DNA is negatively charged
• Electron transfer involving the DNA double helix is
thought to be important in radiation damage and repair and
in biosynthesis
• the double helix may mediate charge transfer between
different metal complexes
• DNA can be viewed as a one dimensional well conducting
molecular wire
• Molecular electronics /devices
Direct measurement of electrical
transport through DNA molecules
Porath et al. Nature 403, 635 (2000)
•Electrical transport measurements on micrometer-long DNA
`ropes', and also on large numbers of DNA molecules in films,
have indicated that DNA behaves as a good linear conductor.
•10.4nm-long, (30bps) double-stranded poly(G)-poly(C) DNA
molecules connected to two metal nano-electrodes
•After a DNA molecule was trapped from the solution, the
device was dried in a flow of nitrogen and electrical transport
was measured. No current was measured between the bare
electrodes before trapping
Semiconducting behavior in poly-A & poly-C
Porath et al. Nature 403, 635 (2000)
•By contrast, for poly-A or poly-C DNA, large-bandgap
semiconducting behavior. Nonlinear current-voltage curves
that exhibit a voltage gap at low applied bias. This is observed
in air as well as in vacuum down to cryogenic temperatures.
•Electronic interactions between the bases in the DNA
molecule lead to a molecular band where the electronic states
are delocalized over the entire length of the molecule.
•Electron transport in the hopping and band models is
facilitated when the Fermi level of the electrode is aligned
with the band edge by applying the bias voltage. Once
electrons are injected, transport occurs through hopping or
band conduction.
•charge carrier transport being mediated by the molecular
energy bands of DNA.
Electron transport is indeed due to DNA trapped between the electrodes
•Dashed curve: after incubation of the same sample for 1 h in a solution with 10 mg ml1 DNAse I enzyme (5mM Tris-HCl, 5mM MgCl2, 10 mg ml-1 DNAse I (pH 7.5)).
Double-stranded DNA was cut by the enzyme.
•Inset: two curves measured in a complementary experiment where the procedure was
repeated but in the absence of the Mg2+ ions that activate the enzyme and in the
presence of 10mM EDTA (ethylenediamine tetraacetic acid) that complexes any
residual Mg ions. The curve did not change.
•DNA was indeed cut by the enzyme in the original experiment.
Porath et al. Nature 403, 635 (2000)
Voltage gap widens with increasing
temperature
Porath et al. Nature 403, 635 (2000)
3 plausible transport models
Porath et al. Nature 403, 635 (2000)
•Black and red lines : with and without an applied bias voltage.
•Tunneling barriers : the contact between the DNA and the metal electrodes.
•Model 1 : common uni-step tunneling, as in electron-transfer studies
(ruled out since tunneling distance is too large: 8nm)
•Model 2 : sequential hopping between localized states associated with
basepairs—1d diffusion (unlikely due to the high field used & the large etransfer rate observed)
Model 3 : molecular band conduction due to electronic interaction that
leads to de-localization over the entire DNA (facilitated when the Fermi
level of the electrode is aligned with the band edge by applying the bias
voltage. Once electrons are injected, transport occurs through hopping or
band conduction.)
Direct measurement of hole transport
dynamics in DNA
Lewis et al. Nature 406, 51 (2000)
• oxidative damage to double helical DNA and the design of DNAbased devices for molecular electronics depend upon the
mechanism of electron and hole transport in DNA.
• Electrons and holes can migrate from the locus of formation to trap
sites and such migration can occur through either a single-step
‘‘super-exchange’’ mechanism or a multi-step charge transport
‘‘hopping’’
• The rates of single-step charge separation and charge recombination
processes are found to decrease rapidly with increasing transfer
distances, whereas multi-step hole transport processes are only
weakly distance dependent.
• spectroscopic measurements of photo-induced electron transfer in
synthetic DNA
• to investigate the distance-dependent
electron transfer in DNA utilizing hairpinformation bis(oligonucleotide)
• stilbene(St) serves as a linker between two
complementary oligonucleotides,
• The singlet St selectively photo-oxidizes G,
but not A,C,T, resulting in the formation of
the St- & G+ radicals.
• By monitoring the formation and decay of
St- , the dynamics of charge separation and
charge recombination can be determined by
transient spectroscopy over a large dynamic
range (sub-ps) to ms).
• The hairpins that contain three G:C base pairs
were designed to probe the dynamics of hole
transport from G+1, formed upon
photoinduced charge separation, to a GG step
separated from G+1 by one T:A base pair.
Kinetic scheme for e/hole transport
ta
Lewis et al. Nature 406, 51 (2000)
•charge separation: kcs, charge recombination: kcr,
• hole transport( kt & k-t ).
•occurrence of hole transport from G+ to GG would be expected to
increase ta as a consequence of the longer distance between the anion
and cation radicals and slower charge recombination for GG+ versus G+.
•The value of ta for 2G3 ~2G, : failure of hole transport to compete
with charge recombination in 2G3 (kcr>kt).
ta for 4G3 > 4G: occurrence of efficient hole transport (kt > kcr).
•rate constant for hole transport lies between the values of kcr for 2G and
4G (10^10/s> kt .>2x10^7/2)
Charge Transport along DNA
Tran et al. PRL 85, 1564 (2000)
•Microwave Cavity expt.: does not require contacts to be attached
to the specimen under study
•probe the temperature dependence of the conductivity associated
with the DNA double helix at high frequencies.
•The conductivity was evaluated from the measured loss(W) of
highly sensitive resonant cavities operating at 12 and 100 GHz:
l-DNA extracted from E. coli
“DNA in buffer”: DNA lyophilized in buffer
“dry DNA” : purified DNA
lyophilized buffer only
Temperature dependence of s
•High T: temperature driven charge
transport processes.
• D=0.33 eV & s0= 1200/(V cm) for
buffer environment,
• D =0.3 eV & s0 1900/(V cm) for the
dry l-DNA.
• s0 for DNA in buffer is comparable
to organic semiconductors
•due to carrier excitations across
single particle gaps or is due to
temperature driven hopping transport
processes.
• l-DNA: random bpdisorder
localized e states conduction by
1d hopping exp[-D/kT]
DNA Fishing by nano-probe
• a nano-probe of 20nm in diameter, 1 mm long on the tip of
a glass needle of 1 in diameter and covered with
aluminium.
• Then we coated the nano-probe with an amorphous teflon
film, and strip it on the tip of the nano-probe with electron
beam in an SEM. Avidin was fixed on the bald tip to fish a
biotin labeled DNA fiber. In this case, avidin-biotin
interaction was utilized because it is a very strong
biological binding.
• We made an experiment of DNA fishing; pipeted
bacteriophage T4-DNA (54 mm long) solution (0.2ng/ml )
on a slide glass; pipeted YOYO-1 lodide; set the probe as
to put its tip inside the solution; covered with a cover
glass,; and observed with an inverted fluorescent
microscope.
• As a result, the tip of the probe hooked up a single DNA
fiber flowing in the solution.
•a) SEM view of the tip of the nano-probe
made by 3D-EBD method on the glass needle
with hydrophobic coating .
•b) Schematic of DNA-fishing Experiment;
we fixed the nano-probe on the X-Y-Z
microstage moved its tip into the solution of
the DNA fibers, pipetted on a slide-glass fixed
on the stage of microscope, and observed
from below with a inverted fluorescent
microscope.
•Fluorescent microscopic view of the DNA
fishing;
• a)Nano-probe before experiment
• b)Fished a T4 phage DNA fiber of 50 m
long by the nano-probe
DNA as nano-materials
• “The nucleic-acid ‘system’ that operates in
terrestrial life is optimized (through evolution)
chemistry incarnate. Why not use it ... to allow
human beings to sculpt something new, perhaps
beautiful, perhaps useful, certainly unnatural.”
Roald Hoffmann, writing in American Scientist,
1994
• powerful molecular recognition system can be
used in nanotechnology to direct the assembly of
highly structured materials with specific nanoscale
features,
Branched DNA
• To produce interesting materials from DNA, synthesis is required in multiple
dimensions branched DNA is required. Branched DNA occurs naturally in living
systems, as ephemeral intermediates formed when chromosomes exchange
information during meiosis, the type of cell division that generates the sex cells
(eggs and sperm). Prior to cell division, homologous chromosomes pair, and the
aligned strands of DNA break and literally cross over one another, forming
structures called Holliday junctions. This exchange of adjacent sequences by
homologous chromosomes — a process called recombination — during the
formation of sex cells passes genetic diversity onto the next generation.
• The Holliday junction contains four DNA strands (each member of a pair of aligned
homologous chromosomes is composed of two DNA strands) bound together to
form four double-helical arms flanking a branch point. The branch point can relocate
throughout the molecule, by virtue of the homologous sequences. In contrast,
synthetic DNA complexes can be designed to have fixed branch points containing
between three and at least eight arms.
• Other modes of nucleic acid interaction aside from sticky ends available. For
example, Tecto-RNA molecules, held together loop–loop interactions, or paranemic
crossover (PX) DNA, cohesion derives from pairing of alternate half turns in interwrapped double helices. These new binding modes represent programmable
cohesive interactions between cyclic single-stranded molecules do not require
cleavage to expose bases to pair molecules together.
Holliday junction
Seeman, Nature 421, 427 (2003)
Assembly of branched DNA molecules.
a, Self-assembly of branched DNA molecules into a two-dimensional crystal. A DNA
branched junction forms from four DNA strands; those strands colored green and blue
have complementary sticky-end overhangs labeled H and H8, respectively, whereas
those colored pink and red have complementary overhangs V and V8, respectively. A
number of DNA branched junctions cohere based on the orientation of their
complementary sticky ends, forming a square-like unit with unpaired sticky ends on the
outside, so more units could be added to produce a two-dimensional crystal.
b, Ligated DNA molecules form interconnected rings to create a cube-like structure.
The structure consists of six cyclic interlocked single strands, each linked twice to its
four neighbors, because each edge contains two turns of the DNA double helix. For
example, the front red strand is linked to the green strand on the right, the light blue
strand on the top, the magenta strand on the left, and the dark blue strand on the bottom.
It is linked only indirectly to the yellow strand at the rear.
•
•
•
•
a, Schematic drawings of DNA double crossover
(DX) units. In the meiotic DX recombination
intermediate, labeled MDX, a pair of homologous
chromosomes, each consisting of two DNA
strands, align and cross over in order to swap
equivalent portions of genetic information; ‘HJ’
indicates the Holliday junctions. The structure of
an analogue unit (ADX), used as a tiling unit in
the construction of DNA two-dimensional arrays,
comprises two red strands, two blue crossover
strands and a central green crossover strand.
b, The strand structure and base pairing of the
analogue ADX molecule, labeled A, and a variant,
labeled B*. B* contains an extra DNA domain
extending from the central green strand that, in
practice, protrudes roughly perpendicular to the
plane of the rest of the DX molecule.
c, Schematic representations of A and B* where
the perpendicular domain of B* is represented as
a blue circle. The complementary ends of the
ADX molecules are represented as geometrical
shapes to illustrate how they fit together when
they self-assemble. The dimensions of the
resulting tiles are about 4216 nm and are joined
together so that the B* protrusions lie about 32
nm apart.
d, The B* protrusions are visible as ‘stripes’ in
tiled DNA arrays under an atomic force
microscope.
Two-dimensional DNA arrays.
Seeman, Nature 421, 427 (2003)
A rotary DNA nanomachine
Seeman, Nature 421, 427 (2003)
• rotary DNA nanomachine
• a, The device works by producing two different conformations, depending on
which of two pairs of strands (called ‘set’ strands) binds to the device
framework. The device framework consists of two DNA strands (red and blue)
whose top and bottom double helices are each connected by single strands.
Thus, they form two rigid arms with a flexible hinge in between and the loose
ends of the two strands dangling freely. The two states of the device, PX (left)
and JX2 (right), differ by a half turn in the relative orientations of their
bottom helices (C and D on the left, D and C on the right). The difference
between the two states is analogous to two adjacent fingers extended, parallel
to each other (right), or crossed (left). The states are set by the presence of
green or yellow set strands, which bind to the frame in different ways to
produce different conformations. The set strands have extensions that enable
their removal when complementary strands are added (steps I and III). When
one type of set strand is removed, the device is free to bind the other set
strands and switch to a different state (steps II and IV).
• b, The PX–JX2 device can be used to connect 20-nm DNA trapezoid
constructs. In the PX state, they are in a parallel conformation, but in the JX2
state, they are in a zig-zag conformation, which can be visualized on the right
by atomic force microscopy.
Seeman, Nature 421, 427 (2003)
•Applications of DNA scaffolds.
•a, Scaffolding of biological macromolecules. A DNA box (red) is
shown with protruding sticky ends that are used to organize boxes into
crystals. Macromolecules are organized parallel to each other within the
box, rendering them amenable to structure determination by X-ray
crystallography.
•b, DNA scaffolds to direct the assembly of nanoscale electrical circuits.
Branched DNA junctions (blue) direct the assembly of attached
nanoelectronic components (red), which are stabilized by the addition
of a positively charged ion.
Turbulent Drag Reduction and
Degradation of DNA PRL 89, 088302 (2002)
with H.J. Choi & C.K. Chan
• Drag Reduction: minute amount of polymer can reduce the
drag of the turbulent flow of the solution.
• Mechanism of DR is still unknown!
• Turbulence is also not fully understood.
• Polymers broken by strong turbulent flow--- degradation
• Large length scale of DNA (~10 microns) can probe the
larger turbulence structures. Obtain information about the
nature of turbulence: space filling factor, intermittency…
• Experiment: polymers/DNA in rotating disk apparatus under
strong turbulence. Re~ 10^6
• Our results suggest that the mechanism for turbulent
degradation of DNA is different from that of the normal
flexible long-chain polymers.
The double-stranded DNA is found to be a good drag reducer
when compared with the other normal linear polymers.
Fitting of time dependence of DR
gives an estimate of the
space-filling factor of turbulence.
dsDNA is cut into two equal halves
• Gel electrophoresis : -l-DNA: 48,502bp 23.1 kbp
(marker)
• Mechanical degradation of DNA is also different from
that of the normal linear-chain polymers: DNA is
always cut in half by the turbulence.
• Kolmogorov cascade picture of turbulence:
energy/time/mass (e) cascade down to disspative
length scale:
• Free draining chain (strongly stretched), force is
maximal at mid-point:
• Breaking strength of dsDNA ~500pN.
• Expt: e~ 0.1W/g, L~ 16 mm; Fmax ~ 1000pN
Drag reducing power disappears when dsDNA
denatures to form two single-strand molecules.
•Strong advection flow in turbulence
leads to strong distortion of chain in
small length scale: flexible polymer
are degraded.
•Large persistence length of dsDNA
gives rise to strong bending rigidity
is eventually stretched by tensile force.
DNA Chips
• result of achievements in two fields: molecular biology and
microfabrication technology
• Specific complementary interactions in double-stranded DNA
basepairs: A-T, C-G
• Strong cohesion & stiff due to double-helix structure
• Powerful molecular recognition scheme: 4^N diversity for a Nbp sticky-end
• First commercial in 1996, now more than 20 companies
• quickly and inexpensively detect the presence of a whole array of
genetically based diseases and conditions, including AIDS,
Alzheimer's disease, cystic fibrosis, and some forms of cancer.
• could make it possible to conduct widespread disease screening
cost-effectively, and to monitor the effectiveness of patient
therapies more effectively.
• Technique would promise for personalized medical care.
A hand-held DNA Chip device, made by
Nanogen, Inc. The circles at the top are sample
ports. The wires guide electric fields over the
DNA array, located on the light blue diamond.
DNA Microarrays
• using one of the strands to test for its biochemical mate; this is the basis of a gene
probe. The process of one strand of DNA matching up with its counterpart strand is
called hybridization.
• DNA chips are designed to identify hybridization products in the same fashion as
with traditional sequencers. Once hybridization has been completed, phosphorescent
chemicals that bind to the hybridized sequences are scanned with a light source,
making it easy to detect their presence with automated colorimetric or fluorimetric
equipment
• The concept is simply that of miniaturizing the gene sequencing technologies
already being developed, so that many assays and their related procedures can be
performed together. DNA chips will give researchers the ability to analyze
thousands of genes at once, and may also make it possible to conduct very elaborate
diagnostic procedures in such small settings as a physician's office or even with
mobile equipment used at the point of care.
• nano- and microscale fabrication techniquesin computer chip manufacturing: the
application of organic structures (e.g., segments of DNA and reagents) onto a
substrate of inorganic materials. Unlike computer chips, which use silicon-based
wafers, DNA microarrays are fabricated onto glass or plastic wafers or are placed in
tiny glass tubes and reservoirs.
Graphical illustration
DNA chip Fabrication techniques
•combines solid-phase chemical synthesis with photolithographic
fabrication techniques employed in the semiconductor industry.
Using a series of photolithographic masks to define chip exposure
sites, followed by specific chemical synthesis steps, the process
constructs high-density arrays of oligonucleotides, with each probe
occupying a predefined position in the array. Multiple probe arrays
are synthesized simultaneously on a large glass wafer.
•Another manufacturing approach involves the deposition of gene
probes onto the chip substrate using a tiny droplet sprayer that
resembles an ink-jet printer. Manufacturers spray a chemical solution
containing the gene probes in a pattern onto the chip substrate, in the
same fashion as in other clinical lab tests.
•Some companies use robots to deposit the gene probes onto the
substrate.
Biosenser using Luminescent
Conjugate Polymers
• Alan Heeger
Nano-particles in DNA bio-sensors