Editorial Board Member
Dr. Sheereen Majd
Department of Bioengineering
Pennsylvania State University
USA
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Biography
• Dr. Majd received her B.S. in Mechanical Engineering from Amirkabir
Institute of Technology, Tehran, in 2003. She completed her Ph.D. in
Biomedical Engineering at the University of Michigan, Ann Arbor, in
2009. Her doctoral work, under the supervision of Prof. Michael Mayer,
focused mainly on studying molecular processes on biological
membranes
such
as
lipid-protein
interactions,
drug-membrane
interactions, and membrane-associated enzymatic reactions using
engineering- and nanotechnology-based platforms.
> > >2
• After a short postdoctoral training at the University of Michigan, Dr.
Majd joined the Department of Bioengineering at the Pennsylvania
State University as an Assistant Professor in January of 2011. She
currently has a courtesy appointment in Department of Engineering
Science and Mechanics. Research efforts and interests in Dr. Majd’s
group lie at the interface of membrane biophysics, electrophysiology,
biomateri¬als, micro/nano fabrication, and biosensing for diagnostic
and therapeutic applications. Currently, the main focus of her research
group is the molecular processes within and across cell membranes and
the role of these molecular events in normal and diseased cellular
functions.
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Research Interests
• Membrane Biophysics and Model Membranes
• Biological and Synthetic Nanopores for Sensing and Single Molecule
Characterization
• Cell and Biomolecular Microarrays for Sensing and Cell Studies
• Hydrogel Micro/Nano Structures for Biological Studies
• Lipid-Enveloped Particles for Gene and Drug Delivery
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Publications
• Many publication of Dr. Sheereen Majd can be viewed at Sciencedirect
& Google Scholar (Hyperlinked)
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Biomolecular
Detection Systems
Fundamentals
of Detection
•
Bio-molecular detection systems, in general, have the following sub-blocks:
Molecular Biology
Biochemistry
Biochemical
Uncertainties
Biological
Sample
Biological
Assay
Fabrication/
Synthesis Processes
Circuit
Design
Fabrication and
Process Variation
Electronic Noise
Quantization Noise
Transducer/
Interface
Detection
Circuitry
Example:
Signal
Processing
Detection
Data
ADC
DNA
Microarrays
Photodiode
Image Sensor
Analog to Digital Conversion
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Affinity-Based Biosensors
•
Exploit the affinity of certain biomolecules for each other to capture and
Linker
Capture DNA probes
detect:
Target DNA
Captured
DNA
1 Sample exposure
2 Incubation
3 Detection
* There are different transduction methods for “counting” the binding events, e.g.,
fluorescence, electrochemical, chemi-luminescence …
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Parallel Affinity-Based Sensing
•
For simultaneous detection of multiple targets, use affinity-based sensors in
parallel:
Biological
sample
Planar solid
surface
Capturing
probe (A)
Capturing
sites
Capturing
probe (B)
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DNA Microarrays
DNA microarrays are massively parallel affinity-based biosensor arrays:
Fluorescent
Tag
10,000 spots
•
Target
DNA (A)
DNA
Probe (A)
20-100µm
A
B
50-300µm
Target
DNA (B)
DNA
Probe (B)
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Applications of DNA Microarrays
•
Recall central dogma:
•
DNA microarrays interrupt the information flow and measure gene expression
levels
•
frequently, the task is to measure relative changes in mRNA levels
•
this gives information about the cell from which the mRNA is sampled (e.g.,
cancer studies)
•
Other applications:
•
single nucleotide polymorphism (SNP) detection
•
simultaneous detection of multiple viruses, biohazard / water testing
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Sensing in DNA Microarrays
•
When complementary ssDNA molecules get close to each other, electrostatic
interactions (in form of hybridization bonds) may create dsDNA
Energy
ACGT
Hydrogen
bonds
TGCA
ACGT
ΔE
TGCA
CTGA
GACT
CTGA
GACT
•
Because of thermal energy, the binding is a reversible stochastic process
•
Relative stability of the dsDNA structures depend on the sequences
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Stability of dsDNA: Melting Temperature
•
The melting temperature (Tm) of a DNA fragment: the temperature at which
50% of the molecules form a stable double helix while the other 50% are
separated into single strand molecules
Energy
ACGT
Hydrogen
bonds
TGCA
ACGT
TGCA
dsDNA
50%
•
ssDNA
50%
Melting temperature is a function of DNA length, sequence content, salt
concentration, and DNA concentration
•
For sequences shorter than 18 ntds, there is a simple (Wallace) heuristic:
Tm  2( A  T )  4(G  C )
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Nonspecific Binding (Cross-hybridization)
•
Depending on sequences, non-specific binding may also happen:
AC
G
AG
T
TG
Not a perfect
match
Energy
CA
AG
TG
•
CA
CA
ΔE2
T
CA
T
G
T
AC
G
TG
TG
G
ΔE1
ΔE1
>
ΔE2
(Bond stability) 1
>
(Bond stability) 2
So, non-specific binding is not as stable as specific binding
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Non-specific binding in microarrays
•
Non-specific binding (cross-hybridization) manifests as interference:
(A)
Probe (A)
S A  f ( A, B, C )
(B)
Probe (B)
(C)
Probe (C)
•
Interference may lead to erroneous conclusions
•
Useful signal is affected by the interfering molecules, false positives possible
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Road to a Model: Underlying Physics
The kinetics of reactions depends on:
1. The frequency that the reactive species (e.g., molecules) get close to each other
2. If in close proximity, can thermal energy “facilitate” microscopic interactions
ssDNA (1)
ssDNA (2)
Energy
ssDNA (1)
ssDNA (2)
State 2
Molecules activated
dsDNA (1+2)
ΔE2
ΔE1
State 1
Molecules close
State 0
Molecules bind
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The Number of Captured Targets: A Random Process
Captured Analytes
x(t )
The number of captured molecules forms a continuous-time Markov process
Captured
Targets at t1
E[ x(t )]   x
E [ x (t )]
E[ x(t )]   x
Time (hours)
E [ x (t )]
2σ x
x(t1 )
Distribution of Captured Particles
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Microarrays
The steps involved in an experiment:
1 Sample Preparation
3 Incubation
4 Detection
2 Array Fabrication
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Thank You..!
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