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S f fBioMEMS and Bionanotechnology: Interface of Biology and Engineering at the micro and nanoscale

Rashid Bashir

Electrical and Computer Engineering & BioengineeringMicro and Nanotechnology LaboratoryUniversity of Illinois, Urbana-Champaignhttp://libna.micro.uiuc.edu/

1

On Size and Scale ! Top-Down Fab

System on A board

10mm

100mm

c an

d

A board

System on a chip

Tissue

Organs

Siz

e 100µm

1mm

oele

ctro

nic

ME

MS

p

Ants

eatu

re S

1µm

10µmMEMS

Mic

ro

Most Bacteria

Plant and Animal Cells

Fe

10

100nm

µ

27nm Feat.of MOS -T

(in 2009)

ctro

nics

os

cale

or

sVirus

10nm

1nm CNT, QD,NS, NWs, AAO

Gate Insulator

Nano-pores

Nan

oele

can

d N

ano

Sen

soProteinsHelical Turn of DNA

C-C Bond

0.1nm

2Bottoms-UpChemical

, ,

Bottoms -UpBiological

Atoms

BioMEMS and Bionanotechnology

Apply micro-systems and nanotechnology to develop novel devices and systems that have a biomedical impact or are

bio-inspired

Diagnostics Bio-inspired

bio-inspired

g pFabrication

BiMicro &

Nanotechnology

Therapeutics Bio-Electronics

Biology, Medicine

gyand Systems

Bio-inspiredMaterials

Tissue Engineering

Micro-devices forCell Biology

3

Microfluidic-Based BioChips !

Point-of-Care or Point-of-Test BioSensors

Abbott/iSTAT(Glucose)

Accuteck(LDH, Theophylline)

Microfluidic-Based BioChips !• Disposable, one-time-use devices• Highly sensitive• Detection and monitoring of target entities,

Abbott/iSTAT(gases, ions, markers) Pregnancy Tests

disease, and state of health

Nanowiresensor

DNA or RNAMolecules

Source Drain

Functionalized Nanosensor Array

Nanowiresensor

DNA or RNAMolecules

Source Drain

Functionalized Nanosensor Array

Functionalized Nanosensor Array

GateGate

• At Bedside, Doctor’s office, Home• Increased need to detect targets of disease for disease managementg g• Increased need to manage disease at the individual level

• Largest ever aging population• Resource-limited settings – global health• Better management of diagnostics/health care cost

Integrated Chips for Detection ofg pMicroorganisms and Cells

Lab on a chip for Nanopore On-Chip PCR

(optical/Temp/Chem

Micro-scaleImpedance

On-chipDielectro-

Ab-based

MEMSFilters

Glass cover Pin 70

0µm

Lab-on-a-chip for Detection of Live

Bacteria

pSensors for

DNA Detection

(optical/electrical)

Chem.-mediated

ImpedanceMeas.

Dielectrophoresis

basedCapture

Filters

hν

In/Out ports Cavities/ Wells

Epoxy adhesive

Dielectrophoresis Silicon Nanowires and Nanoplates for

GenomicDetection

Cell Lysing

Culture/Growth

Conc.Sorting

SelectiveCapture

Filters

Filters an Traps for Biological Entities

Micro-Mechanical Cantilevers for

Trapping/Lysing of Bacteria/Viruses In

Nano-Mechanical Cantilever Sensors

DNA and Protein Detection

Detection

Cantilevers for Detection of Spores

Bacteria/Viruses In Microfluidic Devices

Cantilever Sensors for Detection of

Viruses

“Lab on a Chip” with microfluidics and micro/nanosensors

Micro-fluidic Devices as ‘Petri-dish on a Chip’ for bacterial Culture

• Micro-fluidic “Bacterial culture” and “biomolecular detection” on a silicon chip

• Applications in food, pharmaceuticals, health, and diagnostics markets

• Reduce the time to result from days to hours or less

Sample Prep Detection/ID

Data Analysis/R lt

Overall Approach 8.7x104 cfu/ml + DEP2.3x105 cfu/ml + DEP2.3x105 cfu/ml + no DEP2.3x105 cfu/ml + no DEP Sterile HLBSterile HLB

130%140%150%160%170%

00H

z

107%108%109%110%111%

5.76

Hz

1 h Electrical detection ofStartingSample

Concentration ID Results

30%40%50%60%70%80%90%

100%110%120%130%

Rel

ativ

e Ad

mitt

ance

at 1

0

96%97%98%99%100%101%102%103%104%105%106%107%

Rel

ativ

e Ad

mitt

ance

at 9

35~1 hr

~7.5 hrs

Electrical detection of growth 1 cfu/ml from 100ml

0 2 4 6 8 10 12Time [hours]

3

4

5

cenc

e V

alue

s T

109% increase

339% increase

220% increase

PCR based detection

cells

/ml

pre

PCR

cells

/ml

ost P

CR

cells

/ml

pre

PCR

cells

/ml

ost P

CR

cells

/ml

pre

PCR

cells

/ml

ost P

CR

0

1

2

3

Nor

mal

ized

Flu

ores

cfr

om P

MT PCR based detection

of 104 cells/ml, 0.5ul/min for 12min,

60 cells !

66Gomez, et al, IEEE/ASME JMEMS, Vol. 14, No. 4, 829-838, 2005.Yang, et al., Lab Chip, 6, 896-905, 2006. Bhattacharya, et al, Lab. Chip., 8, 1130 – 1136, 2008

105 p

105

c po

with

DEP

105 p

with

DEP

105 po

with

DEP

104 p

with

DEP

104 po

Integrated Devices for Electrical Detection of CD4+ Cells from Blood

• Urgent need for rapid, cheap, easy to use sensors for blood analysis for global health applications

Mehmet Toner, William Rodriguez (Harvard/MGH)Rashid Bashir (UIUC)

35

40

45 People With HIV/AIDSCumulative Total (Millions) 45

40 35 30 analysis for global health applications

• Detection of CD4+ cells (T-lymphocytes) from whole blood for detection of HIV

• Normal patient has ~ 600cells – 1500cells/ul• When count < 200cells/ul, therapy is initiated 5

10

15

20

25

3030 25 20 15 10 5

0

5

1986 1988 1990 1992 1994 1995 1998 2000 2002 2004

Sub-Saharan Africa Asia Latin AmericaEurope & N. America* Eastern Europe & Central AsiaNorth Africa & Middle ECaribbean

0

1988 1992 1996 2000 2004

Micro-fluidicchannels

Biochips

Capture of pure cell population

from whole blood

7Cheng, Liu, Irimia, Dimirci, Zamir, Rodriguez, Toner, Bashir, Lab Chip, 2007

Electrical Counting of CD4+ Cells for Global Health2D

3D

Outlet

Sample2D3D

Outlet

Sample(a) (c)2D

Sample

2D

Sample

g

26 mm8 m

m

Outlet26 mm

8 mm

Outlet

(b) (d)

2D2D

Concentration Comparisons1000

ls p

er u

L)

Flow Cytometer vs. Chip Comparison (Quantitative)

10

100

ctric

al C

ount

er C

hip

(cel

l

11 10 100 1000

BD LSR II Flow Cytometer (cells per uL)

Elec

Integrated Field Effect Sensor Array for Monitoring of Breast Cancer

1 2ligand

Anti-ErbB (HER1-2) receptor monoclonal antibodies(trastuzumab, 2C4,cetuximab.

Anti-ErbB (HER1-2) receptor monoclonal antibodies(trastuzumab, 2C4,cetuximab.

Selected Targeted Therapies

Anti-HER1; HER2, HER 4 TKIs

Clinical Need/Grand Challenges

On-Chip Sample

Monitoring of Breast Cancer Therapy from

Aspirate (Clare)

On-Chip Lysing of

R. Bashir (UIUC), M. A. Alam (Purdue), D. Bergstrom (Purdue), S. Clare (IUSOM), L. Lee (Berkeley)

KKShc

PI3K

Shc

Grb2

Grb2Ras

Sos

Sos

Raf

MEK1/2

AktAkt

MAPK

PTEN

GSK-3GSK-3mTORmTOR FKHR

Bad

p27

( , ,EMD 7200, Abx=EGF)( , ,EMD 7200, Abx=EGF)

RAS farnesyltransferase inhibitors(BMS-214662, R115777)

RAF inhibitors(BAY 43-9006)

MEK inhibitors(CI-1040)

mTOR inhibitors(CCI-779, RAD)

(ZD1839, OSI-774, EKB-569, GW-2016, CI-1033)

On-Chip SamplePreparation

On Chip Lysing of Cells from Breast

Aspirate (Lee)

Commercial Antibodies/Proteins

(Clare)ReceptorsAttachment Thermal Power/Volume =

Cell cycleprogression

Survival Proliferation

Cyclin D1

p27

Some of the signaling pathway inhibitors currently in the clinic or in clinical

development

Surface Attachment/ Biofouling Avoidance (Bergstrom, Bashir)

SiNP Design and Fabrication (Bashir, Alam)

Microfluidic

Thermal Power/Volume (1/2)ωε”

rε0 |E|2

Biochip SensorAnd System Packaging, System

Integration and Testing(All)

Functionalized Nanosensor Array

Source

Drain

Elibol, et al. Applied Physics Letters. 83, 22, 4613-4615, 2003Elibol, et al. Applied Physics Letters, 93, 13, 2008.Elibol, et al., Applied Physics Letters, 92, 193904, 2008.

Nanomechanical Sensors for Viral DetectionObjectives: To develop technology for the rapid detection of virus particles in fluid and air using N h i l C til S

Frequency Shift, ∆f = 60 kHz ⇒ Mass change, ∆m = 9 fg

Nanomechanical Cantilever Sensors

g g⇒ This corresponds 1 vaccinia virus.

f0 = 1.27 f1 = 1.21 MHz

∆f=60kHz0

MHzQ ~ 5

k = 0.006 N/m

Courtesy of Seyet, LLC

A. Gupta, P. Nair, D. Akin, S. Broyles, M. Ladisch, A. Alam, R. Bashir, "Anamolous Resonance in a Nanomechanical Biosensor", Proceedings of National Academy of Sciences, USA. August 28, 2006, 103: 13362-13367.

Living Cantilever ArraysLiving Cantilever Arrays• Characterizing the physical properties of single cells can open new

areas of research in biological sciences and medicine. • Enabling integration of cellular components and MEMS structures.g g p

36.68KHz

Direction of flow

33.95KHz

Park, et al. 2008, Lab Chip

Volume: 2349 um3

Density3: 1.055g/cc Estimated mass :

2 48 ngp 2.48 ng

11

Solid State Nanopore Channels with DNA Selectivity

• Frontiers in biology Single molecule detection (and sequencing)

• Biological pores and channels can perform sensing for genomics proteomics and Systems Biologyfor genomics, proteomics, and Systems-Biology research

• Nanotechnology-based (top-down/bottoms up) are needed for making these approaches usable, and robust and form arrays of addressable pores.

12Samir Iqbal, Demir Akin, Rashid Bashir, "Solid State Nanopores with DNA Selectivity", Nature Nanotechnology, 2, 243 - 248, 01 Apr 2007.

Micro and Nano Mediated Cardiac Tissue Engineering

Stem Cell Biology(Schook)

Overview of Approach Our Interdisciplinary Team Extraction and MobilizationOf Stem CellsPI:

Rashid Bashir

SLA & 3‐D Fabrication(Bashir)

Polymer and Hydrogels(Kong)

Micro/Nano‐Medicated 

Cardiac Tissue Engineering

Nanoscale Optical Characterization(Cunningham)

Mechano‐Biology of Cardiac Cells

(Saif)

Consultants

Dr. M. Gibb,Head of Cardiology, 

Carle Hospital 

Dr. Sherrie Clark,  UIUC swine species 

veterinarian

Use of Novel Matrix Biomaterials 3-D fabrication Methods DFB Laser Biosensor

Laser

Elevator

Shaft

Mini-PlatformVat

Pre‐polymer solution• Macromer (PEG, Alginate)• Photoinitiator (Irgacure 2959)• Living Cells

Stereolithography