interfacing electrochemistry and dna interfacing … · 2011. 7. 12. · (chip substrate) n ss-dna...

19
1 Lièges 2004 -1- Groupe CREAB (Chimie de la Reconnaissance et Groupe CREAB (Chimie de la Reconnaissance et Etude Etude des Assemblages Biologiques) des Assemblages Biologiques) DRFMC/SI3M, CEA de Grenoble, 17 Rue des Martyrs 38054 Grenoble DRFMC/SI3M, CEA de Grenoble, 17 Rue des Martyrs 38054 Grenoble cedex 9, France cedex 9, France Pascal Pascal MAILLEY MAILLEY : [email protected] , [email protected] +33.(0)4.38.78.44.38 Interfacing electrochemistry and DNA for the design of genosensors Interfacing electrochemistry and DNA Interfacing electrochemistry and DNA for the design of genosensors for the design of genosensors Lièges 2004 Electrochemical genosensors Electrochemical genosensors -2- DNA Biochips Principle DNA Biochips Principle ODN probes ODN probes Transduction Transduction t V Hz I... Signal Hybridisation t V Hz I... Signal Hybridisation Immobilisation Immobilisation Adsorption Adsorption Chemisorption Chemisorption Covalent Grafting Covalent Grafting Entrapment… Entrapment… Localisation Localisation Microfluidic Microfluidic Hybridisation Hybridisation t V Hz I... Signal Hybridisation Detection Detection Main goals Immobilisation Immobilisation Transduction Transduction hn hnFluorophore streptavidin conjugate Biotynilated target hn hnReference method : Fluorescence detection Fluorophore streptavidin conjugate Biotynilated target F F n A - n F F n A - n F F n A - n Fluorescence response in a grey level scale

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Page 1: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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Groupe CREAB (Chimie de la Reconnaissance et Groupe CREAB (Chimie de la Reconnaissance et EtudeEtude des Assemblages Biologiques)des Assemblages Biologiques)DRFMC/SI3M, CEA de Grenoble, 17 Rue des Martyrs 38054 Grenoble DRFMC/SI3M, CEA de Grenoble, 17 Rue des Martyrs 38054 Grenoble cedex 9, Francecedex 9, France

PascalPascal MAILLEYMAILLEY:: [email protected] , [email protected]

℡℡ +33.(0)4.38.78.44.38

Interfacing electrochemistry and DNA for the design of genosensors

Interfacing electrochemistry and DNA Interfacing electrochemistry and DNA for the design of genosensorsfor the design of genosensors

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DNA Biochips PrincipleDNA Biochips Principle

ODN probesODN probes TransductionTransductiont

VHzI...

Signal

Hybridisation

t

VHzI...

Signal

Hybridisation

ImmobilisationImmobilisationAdsorptionAdsorptionChemisorptionChemisorptionCovalent GraftingCovalent GraftingEntrapment…Entrapment…

LocalisationLocalisationMicrofluidicMicrofluidic

HybridisationHybridisation

t

VHzI...

Signal

Hybridisation

DetectionDetection

Main goalsImmobilisationImmobilisation

TransductionTransductionhν hν’

Reference method : Fluorescence detection

Fluorophore streptavidinconjugate

Biotynilated target

hν hν’

Reference method : Fluorescence detection

Fluorophore streptavidinconjugate

Biotynilated target

F

F

n A-

n

F

F

n A-

n

F

F

n A-

n

Fluorescence response in a grey level scale

Page 2: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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1-Electrochemical Immobilisation

Using Polypyrrole Matrices

1-Electrochemical ImmobilisationElectrochemical Immobilisation

Using Polypyrrole MatricesUsing Polypyrrole Matrices

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ImmobilisationImmobilisation

DNA probe accessibility

Probe Integrity

Recognition properties

Recognition specificity/selectivity

Suitable with detection/transduction

11-- Electrochemical DNA Immobilisation using pyrrole and derivativeElectrochemical DNA Immobilisation using pyrrole and derivatives s

-n (2+δ) e -

-2nH+

+ nδA-n

,n A-

+

+06-0.8V vs. SCE

F

F

n A-

n

Mild conditions of immobilisation

Adressable

Routes of functionnalisation

Control of the polymer film coating

Physico-chemical activity of the matrixOther conducting polymers: PANIPANI, , PEDOTPEDOT, , PThPTh, , PJUGPJUG

Page 3: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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Electrode

NH

NH

NH

+

Charge p-

Electropolymérisation

-n x (2.3 e-, -2H+)

n

1.11.1-- DNA Immobilisation through electrostatic interactions with PPyDNA Immobilisation through electrostatic interactions with PPy

Polypyrrole doppingPolypyrrole dopping J . Wang et al, Langmuir 16 (2000) 2269G.G. Wallace et al, Synth. Met. 123 (2001) 279A. kumar et al, Chem. Commun (2004) 820 [PEDOT]

DNADNA CounterionCounterion

Electrostatic interactionsElectrostatic interactions D.S. Minehan et al, J. Macromol. Sci. A (Pure Appl. Chem.) 38 (2001) 1245

EEpp EEoxox

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1.21.2-- Immobilisation by postImmobilisation by post--functionnalisation of PPy matricesfunctionnalisation of PPy matricesBy covalent graftingBy covalent grafting H. Korri-Youssoufi et al, J. Am. Chem. Soc. 119 (1997) 7388

T.-Y Lee et al, Anal. Chem. 73 (2004) 5629 [PTh]

NH

OOH

NH

OO N

O

O

0,6 0,4

n

NH

OOH

NH

OO N

0,6 0,4

n

HCCT-AAG-AGG-GAG-TG

NH

OOH

NH

OO N

O

O

0,6 + 0,4

Electropolymerisation DNA grafting

By complexationBy complexationJ. Janata et al, J. Am. Chem. Soc. 125 (2003) 324

EEpp

By biological anchoringBy biological anchoringA. Dupont et al, Anal. Chim. Acta. 515 (2004) 271

Page 4: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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pyrrole : intelligent glue for biological applications

ELECTROCHEMISTRY BIOLOGY OPTICS

(applications) (detection)

CHEMITRY (chip substrate)

N

ssss--DNADNA

PeptideBiotinBiotin--pyrrolepyrrole

StreptavidinStreptavidin--pyrrolepyrrole

pyrrolepyrrole tooltool--boxboxds- DNA

1.31.3-- Electrodeposition and biochips : the PPy toolElectrodeposition and biochips : the PPy tool--boxbox

Protein

Sugars

Microorganism

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1.3.11.3.1-- DNA direct grafting on functionnal substrates: MICAMDNA direct grafting on functionnal substrates: MICAM™™

Livache al., Nucleic Acid Res., 22 (1994) 2915

O

O

P O-

O

O

ODN

HO O

NH

N

N

NH

(CH 2 )2

N

CH3

H

N

H

N

O

O

P O-

O

O

ODN

HO O

NH

N

N

NH

(CH 2 )2

N

CH3

H

N

H

N

H

N

1.1. ODNODN--derivatized pyrrolederivatized pyrrole

2.2. Multiplexed electrodes arrayMultiplexed electrodes array

3.3. ODN immobilisation ODN immobilisation viavia electrochemical addressingelectrochemical addressing

4.4. Fluorescence detectionFluorescence detection

Electrode 1 Electrode 2 Electrode 3

Electrode 1 Electrode 2 Electrode 3

EpEp

EpEp

Puce ADN ∼ MICAM® 128 dots (diam. = 50µm)Puce ADN ∼ MICAM®Puce ADN ∼ MICAM® 128 dots (diam. = 50µm)128 dots (diam. = 50µm)

Hepatitis C Virus genotyping”Livache et al., Anal.Biochem.,

255 (1998) 188

24 mM

2 to 40 µM

MMultiplexed IIntegrated CChip for AAdvanced MMicroanalysis

Page 5: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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1.3.21.3.2-- Wafer levelWafer level MICAMMICAM™™ processprocess

CMOS MUX CHIP 1 CMOS MUX CHIP 2 CMOS MUX CHIP N

Counter / Reference Electrode

Electrolyte

Oligo-Pyrrole Pyrrole

Active CMOS 100 mm wafer

Electronic boardPotentiostatComputer

From P. From P. CaillatCaillat, CEA/LETI, CEA/LETI

Electro-copolymerisation onultra thin electrolyte layer

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1.3.31.3.3-- DNA direct immobilisation on bulk substratesDNA direct immobilisation on bulk substrates

µ-Counter Electrode

EpEpBioactive PPyBioactive PPy SpotSpot

µ-Counter Electrode

EpEpBioactive PPyBioactive PPy SpotSpot

Localisation of the electrical field

SECMSECM

Miniaturised electrochemical cell

ElectrospottingElectrospotting

z

D

A

B

C

plat inum counter electrode

pipette t ippo lypy rrole spots

x

y

CECE WEWEPotentiostat

z

D

A

B

C

plat inum counter electrodeplat inum counter electrode

pipette t ippo lypy rrole spots

x

y

CECE WEWEPotentiostat

How to fabricate a multiparametric sensor ?

How to structurate the bulk and/or optical surfaces ?

Guedon et al, Anal. Chem., 72 (2000) 6003

Evans et al, Submited to Electrochem. Commun.Fortin et al, Electroanalysis in press

240 µm

teflon

Cavity of Inox needle

240 µm240 µm

teflon

Cavity of Inox needle

Page 6: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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1.3.31.3.3-- Electrospotting : Principle and films characteristicsElectrospotting : Principle and films characteristics

-2

-1.5

-1

-0.5

0

0.5

1

1.5

2

-2 -1 0 1 2 3 4

Voltage pulse (V)

Wor

kin

g E

lect

rod

e

Pot

enti

al (

V/S

CE

)

t1 t1+xInput voltage-impulsion

t1 t1+xTime(msec)

Up= Ui+∆U

U(V)

Ui - Uf

∆tUp= Ui+∆U

U(V)

Ui - Uf

∆t

Time(msec)

Up= Ui+∆U

U(V)

Ui - Uf

∆tUp= Ui+∆U

U(V)

Ui - Uf

∆t

Input voltage-impulsion

Generation of nm thick Ppy films

2D like biological structures

Compatibility Compatibility with SPRi with SPRi transductiontransduction

Reproducibility of the fabrication process

Homogeneity of the probes repartition

Specificity of the recognition event

Spot size (800 µm 250 µm)

Robustness-reusability of the multisensor

49

50

51

52

53

Arb

itrar

y un

its

2200 2400 2600 2800 3000 3200 3400 3600 3800

Time (s)

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1.3.31.3.3-- SubstrateSubstrate structuration structuration using using SECMSECM

N-(CH2)3-(O-CH2-CH 2)2-O-(CH 2)3-NH-CO-(CH2)5-NH-CO-(CH 2)4S

HN NH

O

Biotinylated-pyrrole monomer

-0.04

-0.02

0

0.02

0.04

0.06

0.08

0 2 4 6 8

Temps (s)

Co

ura

nt

(µA

)

0

0.2

0.4

0.6

0.8

Po

tentiel (V

/EC

S)

G O x E

GlucoseH2O2O2

e-

xy

z

G O x E

GlucoseH2O2O2

e-

xy

z

µ-Counter Electrode

EpEpBioactive PPyBioactive PPy SpotSpot

µ-Counter Electrode

EpEpBioactive PPyBioactive PPy SpotSpot

Detection of the biologically active spot using the

generation /collection mode

0 50 100 150 2000

50

100

150

200 i / nA

0.400.440.480.520.560.600.640.680.720.760.800.840.880.920.961.001.041.081.121.161.20

X Axis / µm

Y A

xis

/ µm

0 2 0 0 4 0 0 6 0 0 8 0 0 1 0 0 0

0 . 2

0 . 3

0 . 4

0 . 5

0 . 6

0 . 7

i / n

A

Y Ax is d isp lacement / µm

PBS 0.1 M pH 7[glucose] 10 mMEtip = 0.6 V/SCESpeed 7.5 µm s- 1

Validity of the conceptSSpot size reduction compared to spotting

Application to DNA spots generation

SECM detection ?

200 µmParameters:Tip diameter and shapeDistance tip-substrateDeposition time (100-500 ms)Deposition potentialMonomers concentrations

Page 7: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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2-Hybridization detection General considerations

2-Hybridization detection Hybridization detection General considerationsGeneral considerations

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2.12.1-- What’s the signal ? What’s the signal ?

Substrat

Couche biosensible

Substrat

Couche biosensible

Molecular recognition

No metabolic activity

What has changedWhat has changed

How to labell the recognition eventHow to labell the recognition event

Matrix

or

Labell

QCM

SPR

Photocurrent…

Real time Real time TransductionTransduction

Fluorescence

Redox intercalators

Microparticles

Enzymes

DNA electroactivity

Impedance

Conductivity

End point End point detectiondetection

IndirectIndirectDirectDirectSignal

t

Signal

t

Signal

t

Signal

LabellingLabellingAccumulationAccumulationAmplificationAmplification

e-?

∆∆E, i, Z, Y, σσ

Page 8: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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2.22.2-- Properties of the recognition signals Properties of the recognition signals

Direct or labelled reading

Detection or transduction (kinetic approach)

Positive or negative signal (dynamic range)

Parrallel or one-point (imaging)

Amplification (limit of detection)

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3-Electrochemical detection

of DNA hybridization:The conducting polymer approach

3-Electrochemical detection Electrochemical detection

of DNA hybridization:of DNA hybridization:The conducting polymer approachThe conducting polymer approach

Page 9: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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3.13.1-- PhysicoPhysico--chemical behaviour of PPy and other conducting polymerschemical behaviour of PPy and other conducting polymers

-0,16 0 0,16 0,32 0,48

-0,16

-0,12

-0,08

-0,04

0

0,04

0,08

0,12

0,16

0,2

0,24

I (m

A c

m-2

)

E (V/ECS)

1

2nnδδ AA--nnδδ AA-- --nnδδee----nnδδee--

, δ, δ AA--, δ, δ AA--

RedRed OxOx

nnN

H nnN

H nn

δδ++N

H nn

δδ++N

H

δδ++N

H

Semi-condutor (p) Conductive (bipolaron)

BC

BV

Eg

BC

BV

σσ S cm-1

- 106

-104

-102

-1

-10-2

-10-4

-10-6

-10-8

-10-10

-10-12

-10-14

-10-16

Métaux

Semi-conducteur

Isolant

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3.23.2-- Chronoamperometric hybridization detection at ODNChronoamperometric hybridization detection at ODN--doped Ppy filmsdoped Ppy films

Probe : (dG) 20

J . Wang et al, Anal. Chim. Acta 402 (1997) 7

Comp (dC)20

Non-comp

(dA)20 or (dT)20

dA20dT20

dC20 dC20dC20

(dG) 20 probe

(dA) 20 probe

-

+

SignalSignalReversible transient signalChange in film capacitance or conductivityCurrent until charge compensation

Comp : volume effectNon-Comp: adsorption

+0.15 V vs. Ag/AgCl

Page 10: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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A. kumar et al, Chem. Commun (2004) 820

3.33.3-- PEDOT conductivity as probing toolPEDOT conductivity as probing tool

Probe

Comp

Non-comp

Nanopore membraneGold thin film

ss-DNA doped PEDOT

∆∆∆∆R/RR/R00

SignalSignalDecrease of the PEDOT intrinsec conductivityHindrance of ionic transferEnhanced resistance variation with the duplex lenghtNo dependance of σ on the electrolyteDynamic range : 10-8 to 10-5 g mL-1

Potential (V)

n

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NH

OOH

NH

OO N

0,6 0,4n

HCCT-AAG-AGG- GAG-TG

H. Korri-Youssoufi et alJ. Am. Chem. Soc. 119 1997 7388

3.43.4-- PPy electroactivity as transduction vectorPPy electroactivity as transduction vector

Comp

Non-comp

a)a) NativeNativeb), Nonb), Non--complementarycomplementary

c) to e) Complementaryc) to e) Complementary10µM to 0.1 10µM to 0.1 mMmM

nnδδ AA --nnδδ AA -- --nnδδee----nnδδee--

, δ, δ AA --, δ, δ AA --

RedRed OxOx

nnN

H nnN

H nn

δδ++N

H nn

δδ++N

H

δδ++N

H

AA--

AA--

J. Janata et al,J. Am. Chem. Soc. 125 (2003) 324

Hindrance of the doping (ion exchange) processHindrance of the doping (ion exchange) process DNA hybridisation transistor

Page 11: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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3.53.5-- Redox probe functionnalised polymer as transduction vectorRedox probe functionnalised polymer as transduction vector

ODNODNprobeprobe

Detection limit 10 Detection limit 10 nMnM

H. Korri-Youssoufi et alAnal. Chim. Acta 469 (200)2 85

M.C. Pham et al, Anal. Chem. 75 (2003) 2478

Comp

Non-comp SignalSignalAccessibility of the redox sitesEnhanced cation exchange

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3.63.6-- Impedance spectroscopy of polymerImpedance spectroscopy of polymer--DNA filmsDNA films

Tae-Young Lee et al, Anal. Chem. 73 (2001) 5629

Hybridization

Comp

∆∆∆∆ZZ

SignalSignalDecrease of the electrochemical impedanceDependance on film thickness (and morphology)Discrimination of point-mutations

OCPOCP

Page 12: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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Photocurrent

3.73.7-- Photoelectrochemical behaviour of PPy as tansduction mediatorPhotoelectrochemical behaviour of PPy as tansduction mediator

O

O

P O-

O

O

ODN

HO O

NH

N

N

NH

(CH 2 ) 2

N

CH 3

n

H

N

m

H

N

O

O

P O-

O

O

ODN

HO O

NH

N

N

NH

(CH 2 ) 2

N

CH 3

n

H

N

m

H

N

H

N

VB

CBe-

Lumière

Noir

PPyPPy Semiconductor in the neutral reduced stateSemiconductor in the neutral reduced state

Lassalle et al, J. Electroanal. Chem.509 (2001) 48

0,04

0,08

0,12

0,16

0,2

1 2 3 4 5Energie(eV)

0

Copol+ODNc

3,65

Copol

Copol+ODNnc

0,04

0,08

0,12

0,16

0,2

1 2 3 4 5

Energie (eV)

0

Copol+ODNc

3,65

Copol

Copol+ODNnc

0 2 4 6 8 10 12 14 16 18 20

0,68

0,72

0,76

0,8

0,84

0,88

0,92

0,96

1

Temps (min)

iph

(t)

/ ip

h(0

)

0 2 4 6 8 10 12 14 16 18 20

0,68

0,72

0,76

0,8

0,84

0,88

0,92

0,96

1

Temps (min)

iph

(t)

/ ip

h(0

)

i (m

A W

-1)

Dark

Light

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4-Electrochemical detection

of DNA hybridization at PPy-DNA films using

Redox labells

4-Electrochemical detection Electrochemical detection

of DNA hybridization at of DNA hybridization at PPyPPy--DNA films usingDNA films using

Redox labellsRedox labells

Page 13: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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4.14.1-- Redox molecules in interaction with dsRedox molecules in interaction with ds--DNADNA

Minor groove Minor groove bindersbinders

InteractionsInteractions

IntercalatorIntercalatorππππ StackingStacking

Threading Threading agentagent

Hoecsht 33258

Daunomycin

S. Takenaka, DNA and RNA binders, M. Demeunynck et al Eds, Wiley-VCH (2002) 225-246

Metal complexMetal complex

ElectrostaticIntercalation

Minor Groove

S Takenaka et al , Anal Chem72 (2000) 1334

J. Barton et al, Nucl.Acid Res 27 (2000) 4830

Methylene blue

M. Mascini et al, Fresenius J.. Anal. Chem. 367 (2000) 364.

Wang et al, Anal. Chem., 68 (1996) 2629

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N

N

O

A B C

D

1

2

3

4

56

7

8

9

1011

8H-8oxo-pyrido[4,3,2-mn]acridine

N

N

Cl

O

SOH

COB 137COB 137

N

N

Cl

O

HN

NHH2N

COB 142COB 142

-3.5

-2.5

-1.5

-0.5

0.5

1.5

2.5

-600 -300 0 300

E (mV)

i ( µµ

A)

-15-10-505

101520

-700 -400 -100 200

E (mV)

i (µµ

A)

-30

-20

-10

0

10

20

30

-600 -300 0 300

E/V vs. Ag/AgCl

I/µA

R2 = 0.9974

0

10

20

30

4 8 12 16

n1/2

/v1/2

s-1/2

I/µ

A

N

N

Cl

O

HN N

COB 136COB 136

4.1.14.1.1-- PyridoPyrido--acridones : a new family of redox intercalatorsacridones : a new family of redox intercalators

Page 14: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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Elaboration du capteur

Film Polypyrrole

Adsorption d’ADN(SS ou DS

Interaction avec Intercalant

EEDétection

Elaboration du capteur

Film Polypyrrole

Adsorption d’ADN(SS ou DS

Interaction avec Intercalant

EEDétection

Electrochemical detection of ds-DNA adsorbed at PPy

0

1

2

3

4

5

-400 -300 -200 -100 0

E/V vs. Ag/AgCl

I/nACOB 136 in solution

With ss Calf Thymus DNAWith ds Salmon DNA

0

0.5

1

1.5

2

2.5

0 50 100 150

Time/min

I/µA

0

1

2

3

4

-350 -250 -150

E/V vs. Ag/AgCl

I/µA

Slow kinetic of the intercalation processSelectivity of the recognition signal

Strong interaction with ds-DNANon-specific interactions with ss-DNA

DNA/COB 136 interactions in solution

4.1.24.1.2-- Electrochemical approach of COB136/DNA interactionsElectrochemical approach of COB136/DNA interactions

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ProbeProbePyr T5 5’AG AGT GCC TTG ACG ATA

CAG CTA ATT CAG AAT CAT TTT GT 3’

TargetsTargets10c10c 5’-bio-AA GGC ACT CT3’

20c20c 5’-bio-CTG TAT CGT CAA GGC ACT CT3’

40c40c 5’-bio-AC AAA ATG ATT CTG AAT TAG CTG TAT CGT CAA GGC ACT CT3’

25nc25nc 5'-bio- GGG CAG GAC CGG GCA GGA CC 3'

2.5

3.5

4.5

5.5

6.5

-400 -300 -200 -100 0

E/V vs. Ag/AgCl

I/µA

Elaboration du capteur

Glassy carbon electrode

Film Polypyrrole-ODN

1. Adsorption 2. Interactionnon-specific

3. Hybridation

Elaboration du capteur

Glassy carbon electrode

Film Polypyrrole-ODN

1. Adsorption 2. Interactionnon-specific

3. Hybridation

11 PyrPyr--ODn4500 ODn4500 PyrPyr

Selectivity of the responseSignal intensityReusable

Specificity of the response

ODN probes density

4.1.24.1.2-- Electrochemical biosensor for DNA hybridization detectionElectrochemical biosensor for DNA hybridization detection

Page 15: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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4.24.2-- Electrochemiluminescence for DNA hybridization detectionElectrochemiluminescence for DNA hybridization detection

e-

FluorescenceElectrochemiluminescence

MICAM twin potentialitiesImplementation and Detection

Time and spatial controlCan be quantified

Key point is theConductivity of the supportE

hυe-

Au

7 x 10 -2 cm 2 Avidin

Pyr-ODN/Pyr =1/20000 ABEI-biotin

Tampon borate pH=10, 50 µM H2O2

hυhυe-

AuAu

7 x 10 -2 cm 2 Avidin

Pyr-ODN/Pyr =1/20000 ABEI-biotin

Tampon borate pH=10, 50 µM H2O2

NN--(4(4--aminobutylaminobutyl))--NN--ethylIsoethylIso--luminolluminol

biotinbiotin

NHHN

S

O

NH

NH

NH

NH(CH2)4-CO-NH-(CH2)4 -N

O

O

O

O

C2H5

NN--(4(4--aminobutylaminobutyl))--NN--ethylIsoethylIso--luminolluminol

biotinbiotin

NHHN

S

O

NH

NH

NH

NH(CH2)4-CO-NH-(CH2)4 -N

O

O

O

O

C2H5

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ApiT8ApiT8

4.24.2-- Electrochemiluminescence on a chipElectrochemiluminescence on a chip

6

7

8

9 1

2

3

4

Pyr-ODN/Pyr = 1/4000

Pyrrole

0

500

1000

1500

2000

2500

0 2 4 6 8 10 12temps (s)

sign

al (

nb c

oups

/50m

s)

ECL plot 1

0

50

100

150

200

250

300

350

400

450

500

0 2 4 6 8 10 12 14

temps (s)

sig

na

l (n

bs

co

up

s/5

0m

s)

ECL plot 9

hυe-

Pyr-ODN/Pyr =1/4000

Page 16: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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5-Electrochemical detection

of DNA hybridization:The SECM approach

5-Electrochemical detection Electrochemical detection

of DNA hybridization:of DNA hybridization:The SECM approachThe SECM approach

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-32-

Sample or substrate

XYZActuator

xy

z

xy

z

Bipotentiostat

POT 2mA

POT 1nA

Reference

Counter electrode

Working 2-substrate

Working 1 - µelectrode

5.15.1-- SECM: working principlesSECM: working principles

MedR MedO

a

MedR MedO

a

MedR MedO dMedR MedOMedR MedO d

d

MedR MedOMedR MedO

Stationnary modeHemispheric diffusionShort time constantLateral resolution

i T > i T, ∞∞i T > i T, ∞∞

i T > i T, ∞∞i T > i T, ∞∞

i T,∞∞ = 4nFDCa

L=d/a

Positive feedback (F+)(recycling)

Negative feedback (F-) (diffusion hindrance)

GC mode(Collection of

generated species)

µelectrode

Page 17: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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5.25.2-- DNA hybridization modulate the SECM feedback modeDNA hybridization modulate the SECM feedback mode

Single strand spotSingle strand spot

Positive feedback modePositive feedback mode

Decrease of the apparent substrate reactivity toward Fe(CN)63-/4-

No change for in feedback current for Ru(NH)33+/2+

DNA hybridization detection due to reppelant electrostatic forcereppelant electrostatic force

3’ thiol modified ODN (20 mers) spotsAnionic redox mediator

W. Schuhmann et al, Angew. Chem. Intl. Ed43 (2004) 3482

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5.35.3-- DNA detection through guanosine oxydationDNA detection through guanosine oxydation

Xanthon CorpRaleigh-DurhamUSAH.H. Thorp et al,Anal Chem 72 (2000) 3764

SequenceSequence dependantdependant

Biochips imaging using SECMBiochips imaging using SECM

F. Zhou et al, J. Electroanal. Chem. 537 (2002) 95

a c

Ru2+ Ru3+ Ru2+ Ru3+

Ru2+ Ru2+

a c

Ru2+ Ru3+ Ru2+ Ru3+

Ru2+ Ru2+

(Inosine modified)

F+ F-

Positive feedback modePositive feedback mode

Page 18: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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Amplification through substrate recyclingAmplification through substrate recycling

InfineonGermany

5.45.4-- Enzyme labelling for localised hybridization detectionEnzyme labelling for localised hybridization detection

GOxGOx

e-

GC mode GOx labellingH2O2 localised detection

Glucose

O2 H2O2

Gluconolactone

Glucose

APPAPPAPPAPP

e-

p-APP

p-AP

p-APP

p-AP

C. Toth et al, Bioelectrochem.63 (2004) 207

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DRFMCDRFMCCEACEA

SynchrotronSynchrotronILLILL

Some pictures of Grenoble and CEASome pictures of Grenoble and CEA

Page 19: Interfacing electrochemistry and DNA Interfacing … · 2011. 7. 12. · (chip substrate) N ss-DNA Biotin-pyrrole Peptide Streptavidin-pyrrole pyrrole tool-box ds- DNA 1.3- Electrodeposition

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AknowlegmentsAknowlegments

B. Corso

G. Bidan

E. Fortin

A. Roget

T. Livache

M. Billon

H. Kim

L. GrosjeanC. BrakhaN. Lassalle

L. Blum C. Marquette

M.-L. Calvo-MuñozE. Dunot

S. Szunerits

A. Thaumoux

J.P. CorreiaL.M. Abrantes

J. Chane-TuneE.Vieil

J.P. Petit

M. DemeunynckL. Bouffier

B. Wang E. Descamps Y. Defontaine

G. Denuault, S. Evans