2 3 4 accepted article - university of east anglia2, Ángel maq ötzen4, jaime 6022 valenci...

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Accepted Article Expe sen Ángela Ruiz Wheele 1 Nano 2 IDM, Ins 3 Key 1. Introdu The develop and RNA s several appli 2], pathogen detection of biomedical f to personal forensic in treatments, systems ba An experi conformatio probes -upo oligonucleot reported. To on silicon p where the termination. their 3’ term molecule to obtained tow the streptav not, demons MB upon hy the streptav photonic sen erimen nsors re z-Tórtola 1 , Fr r 3 , Tamas Da ophotonics Tech stituto Interuniv School of biolo y words: silicon uction pment of new strands has b ication fields n detection [3, f DNA/RNA field, due to th lized medici nvestigation among other ased on th imental study onal change suf on the biorec tides over evan o this end, high photonic bandg MB probes . Those MBs in mination in orde o them. The dif wards the targe vidin molecule strate the confo ybridization, wh vidin molecule nsing structure. * Correspond ntal stu espons co rancisco Prats lmay 3 , Amade hnology Center versitario de Inv Química, U ogical Sciences 4 microTEC G n photonics, ph w strategies fo become highl such as food 4] or biologic A strands is he close link o ne, early d or assessme rs [6-13]. Nu e hybridizat y of the i ffered by mole cognition of n nescent wave p sensitivity pho gap (PBG) stru were immobil ncorporate a bio er to selectively fferent photonic et oligonucleoti was bound to ormational chan hich promotes t e away from t ding author: e-m dy of t se in p nforma s-Quílez 1 , Dan eu Griol 1 , Juan r, Universitat Po vestigación de R Universitat Polit , University of Gesellschaft für hotonic biosenso or detecting D ly interesting quality contro cal safety [5]. also key in of these molec disease detec ent of me umerous detec tion between nfluence of ecular beacon (M nucleic acid ta photonic sensor otonic sensors b uctures were u lized via their otin moiety clo y bind a streptav c sensing respo ide detection, w the MB probe nge suffered by the displacemen the surface of mail: j.garcia@n the eva resenc ational niel Gónzalez- n Hurtado 1 , H Rupérez 1,* olitècnica de Va Reconocimiento tècnica de Valè East Anglia, N Mikrotechnolo or, photonic ban DNA g for ol [1, . The n the cules ction, dical ction n a DNA been stran 15]. G DNA rese have the u a ste stran itsel the MB) arget rs- is based used, r 5’ se to vidin onses when es or y the nt of f the Schem strepta ntc.upv.es, Phon anesce ce of m chang -Lucas 2 , Marí Helge Bohlman alència, Camino o Molecular y D ncia, 46022 Va Norwich Researc ogie mbH, Duisb ndgap, molecul A/RNA targe n reported up nded DNA pr . Given the r A/RNA targ earch, alterna e been invest use of MB pr em-loop struc nd produces lf [16]. The matic diagram o avidin-labeled M ne: +34 96 387 nt-wav molecul ges ía-José Bañuls nn 4 , Reiner G o de Vera s/n, 4 Desarrollo Tecn alencia, Spain. ch Park, Norwic burg, Germany lar beacon, conf et and its co to date, in wh robes are used relevance of gets for bioa ative approach tigated. Amon obes: a specia cture where th a conformati use of fluo of the PBG sens MB probes were 00 00, Fax: +3 ve phot lar bea s 2 , Ángel Maq ötzen 4 , Jaime 46022 Valencia nológico, Depar ch, NR4 7TJ, U y formational cha omplementary hich typically d in microarray the detectio analysis and hes for their ng them, we al type of nucl he recognition onal change orophore-labe sing structure o e immobilized. 34 96 387 78 27 tonic acon quieira 2 , Guy García- a, Spain. rtamento de UK ange. strand have linear single- y formats [14 on of these d biomedical r recognition can highlight leic acid with n of the target of the probe eled MBs in on which the 7 , t t This article is protected by copyright. All rights reserved. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jbio.201800030

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Page 1: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

Acc

epte

d A

rticl

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Expesen

Ángela RuizWheele

1 Nano2 IDM, Ins

3

Key

1. Introdu

The developand RNA sseveral appli2], pathogendetection ofbiomedical fto personalforensic intreatments, systems ba

An expericonformatioprobes -upooligonucleotreported. Toon silicon pwhere the termination.their 3’ termmolecule toobtained towthe streptavnot, demonsMB upon hythe streptavphotonic sen

erimennsors re

z-Tórtola 1, Frr3, Tamas Da

ophotonics Techstituto Interuniv

School of biolo

y words: silicon

uction

pment of newstrands has bication fields

n detection [3, f DNA/RNAfield, due to thlized medicinvestigation among other

ased on th

imental studyonal change sufon the biorectides over evan

o this end, high photonic bandgMB probes

. Those MBs inmination in ordeo them. The difwards the targe

vidin molecule strate the confoybridization, whvidin moleculensing structure.

* Correspond

ntal stuespons

corancisco Pratslmay3, Amade

hnology Centerversitario de Inv

Química, Uogical Sciences

4 microTEC G

n photonics, ph

w strategies fobecome highlsuch as food 4] or biologic

A strands is he close link one, early dor assessme

rs [6-13]. Nue hybridizat

y of the iffered by mole

cognition of nnescent wave psensitivity pho

gap (PBG) struwere immobil

ncorporate a bioer to selectivelyfferent photonicet oligonucleotiwas bound to

ormational chanhich promotes t

e away from t

ding author: e-m

dy of tse in pnformas-Quílez1, Daneu Griol1, Juan

r, Universitat Povestigación de R

Universitat Polit, University of

Gesellschaft für

hotonic biosenso

or detecting Dly interestingquality controcal safety [5].also key in

of these molecdisease detecent of me

umerous detection between

nfluence of ecular beacon (Mnucleic acid taphotonic sensorotonic sensors buctures were ulized via theirotin moiety cloy bind a streptavc sensing respoide detection, wthe MB probe

nge suffered bythe displacementhe surface of

mail: j.garcia@n

the evaresencationalniel Gónzalez-n Hurtado1, H

Rupérez1,*

olitècnica de VaReconocimientotècnica de ValèEast Anglia, NMikrotechnolo

or, photonic ban

DNA g for ol [1, . The

n the cules ction, dical ction n a

DNAbeenstran15]. GDNAresehavethe ua stestranitsel

the MB) arget rs- is based used, r 5’ se to vidin onseswhen es or y the nt of

f the

Schemstrepta

ntc.upv.es, Phon

anescece of m chang-Lucas2, Marí

Helge Bohlman

alència, Caminoo Molecular y Dncia, 46022 Va

Norwich Researcogie mbH, Duisb

ndgap, molecul

A/RNA targen reported up nded DNA pr. Given the rA/RNA targ

earch, alternae been investuse of MB prem-loop strucnd produces lf [16]. The

matic diagram oavidin-labeled M

ne: +34 96 387

nt-wavmoleculges ía-José Bañulsnn4, Reiner G

o de Vera s/n, 4Desarrollo Tecnalencia, Spain.ch Park, Norwicburg, Germany

lar beacon, conf

et and its coto date, in wh

robes are used

relevance of gets for bioaative approachtigated. Amonobes: a specia

cture where tha conformati

use of fluo

of the PBG sensMB probes were

00 00, Fax: +3

ve photlar bea

s2, Ángel Maqötzen4, Jaime

46022 Valencianológico, Depar

ch, NR4 7TJ, Uy

formational cha

omplementary hich typically d in microarray

the detectioanalysis andhes for theirng them, we al type of nuclhe recognitiononal change orophore-labe

sing structure oe immobilized.

34 96 387 78 27

tonic acon

quieira2, Guy García-

a, Spain. rtamento de

UK

ange.

strand have linear single-y formats [14

on of these d biomedical r recognition can highlight leic acid with

n of the target of the probe

eled MBs in

on which the

7

,

t

t

This article is protected by copyright. All rights reserved.

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jbio.201800030

Page 2: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

Acc

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d A

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solution hasdetection ofcalled oligonan extraordihigher specilinear single- Some exMBs are immfound using surface ennanotweezerHowever, wconformationinteraction othose works,electrochemiso that a vaproduced whthe conforma[28-31]. Thoexploiting thupon hybridmolecule/paropen the doMB-based bi Within tdemonstratiochange of evanescent wmechanism transduction to our knowobserved for

2. Molecu

When a MB undergoes aand adopting33]. The mconsists of a(reporter) ahybridizationaway from depicted in Fthe describeoligonucleotits performathe small foligonucleot In the prorder to provany potentialmodified MB5’ end, for tstructure, an

s proven to f short sequennucleotides [1inary stabilityificity than si-stranded prob

xamples of hemobilized onta range of opnhanced Rrs [26]) and elwe can find nal change ofover a transd, a particle/moical transduceariation in thehen that particational changose works demhe hairpin co

dization changrticle with a or to the deviosensing devthis context, on of the inf

molecule-labwave photonichas been demapproaches,

wledge the r evanescent w

ular Beacon

hybridizes wa conformatiog the typical d

most commona hairpin proband a quenchn promotes ththe reporter,

Figure 1 [16]. ed fluorescenctide detection ance is limitedfluorescence tide concentraresent work, vide a simple l labeled MB B design incluthe immobiliznd a biotin

have high nce nucleic a17-19]. Moreoy, a better imilar assaysbes [20]. eterogeneous to a solid sub

ptical (e.g. fluoRaman speclectronic [27]

some few wf the MB is uduction elemolecule, able ter, is attached e measured ecle/molecule ie of the MB amonstrate the

onformational ging the intertransduction

velopment of vices.

we report fluence of thbeled MB c sensing strucmonstrated foas previouslyfirst time th

wave photonic

n detection

with its compleonal change odouble helix n exploitationbe structure wher on each he separationrestoring the Despite the

ce-based MB in homogeno

d by the diffichanges pro

ations. the MB desand versatile to a given phoudes a thiol tzation on the moiety close

potential foracid strands, over, MBs exselectivity an performed u

assays, wherestrate, can alsorescence [21ctroscopy sensing platfo

works whereused to chang

ment. Typicallto interact witto the MB pr

electrical signis displaced duafter hybridizae high potenti

changes of Mraction of a gelement, thathigh perform

an experimhe conformatiprobes overcture. Despite

or electrochemy indicated, thhat this effecc sensors.

scheme

ementary stranopening theconfigurationn of MB prwith a fluorop

end. Then, n of the quene fluorescencewidespread uconfiguration

ous assays [21iculty of detecoduced by s

ign is adapteway of ancho

otonic sensor.termination on

photonic sene to the 3’

r the also

xhibit nd a using

e the so be -24], [25],

forms. e the ge its ly in th an robe,

nal is ue to ation al of MBs

given t can

mance

ental ional r an e this mical his is ct is

nd, it stem [32,

robes phore

the ncher e, as se of n for -24], cting small

ed in oring . The n the nsing end,

allowmolbiorstrepthe bothMBawaThalabestrepdetemol

Figufluor

Figustrepimm

Cdistawerpolaknowconfand whiof n

3.

wing the inlecule to the recognition optavidin-labelresponse of

h the hybridiz probe, which

ay from the suat response of eled MB probeptavidin-free ermine the inlecule on the o

ure 1 Schematirescence-based

ure 2 Schemeptavidin-free an

mobilized on the

Conformationances of strepe previously arization interwledge the firformational chexploited usinch will be of g

novel label-fre

Materials a

ncorporation MB [34], as

of the targetled MB probethe photonic

zation and conh will displaceurface of the pthe photonic ses will be com

MB probesnfluence of optical sensing

ic explanation od MB probe for

e of the hybnd the streptavie surface of a ph

nal changesptavidin-labele

reported by rferometry [35rst report whehanges upon hng an evanescgreat interest

ee biosensors.

and method

of a streps shown in Ft oligonucleoe will induce sensing stru

nformational ce the streptaviphotonic senssensor havingmpared with ths are used the displacem

g response.

of the workingoligonucleotide

bridization evidin-labeled MBhotonic structur

s and pred MB upon our group ba

5]. However, ere the potentihybridization cent-wave phofor the future

ds

ptavidin (St) Figure 2. The otide by the e a change in ucture due to change of the idin molecule sing structure. g streptavidin-he case when in order to ment of the

g principle of a e detection.

vents for the B probes being re.

rotein-surface hybridization ased on dual this is to our

ial use of MB are observed

otonic sensor, development

r

d

t

This article is protected by copyright. All rights reserved.

Page 3: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

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3.1 Photon

For the demeffects on euse of planartheir multipland high intedetection, uswith CMSemiconductParticularly, created by prefractive itransduction their responsthe surroundof the target surface will in turn to aspectral rangallowed owishown in Foptical fieldwave effect make PBG refractive-inmultiplexed

Figure 3 SchPBG edge whby the MB tak Figure 4structure usemode wavegnm, where wi=140 nm aperiodicity atop of a silicthe PBG seobtain a PBGnm when a was this is theequipment aelements tap

nic sensing s

onstration of evanescent war integrated nle advantagesegration levelse of very lowMOS (Comtor) technolo

we developperiodically inindex of th

principle is se to changesding medium

oligonucleotilead to a vari

a shift in the ge where the ing to the p

Figure 3. Thed with the tar

[42, 43], ansensing stru

dex-sensitive biomolecular

hematic explanhen a biorecognkes place.

4 schematicaled in this workguide of heigh

50 silicon tand length we=a=380 nm; thecon oxide lowensing structuG edge locatewater upper cle wavelengthavailable at oper, where t

structures

the MB confoave photonic anophotonic t: high sensitil, short time to

w sample volummplementary ogy fabricatioped PBG sntroducing a mhe photonic

based on ths in the refrac[39-41]. So, tide by the MBiation in the R

position of propagation oeriodicity of e enhanced irget analytes, nd their extreuctures an em

structures sensing appli

nation of the snition of the tar

lly depicts tk. It consists oht h=220 nm transversal el=1500 nm aree silicon struc

wer cladding. Ture were seleed at a waveleladding surrou

h range whereour laboratorythe length o

ormational chsensor, we m

technology, duvity, compacto result, labelmes, compatib

Metal-Oxon, etc. [36ensing structmodulation in

structure. The dependenctive index (Rthe biorecognB occurring onRI distributionthe PBG, i.eof the light isthe structure

interaction ofdue to the s

emely smallmerging clas

for labelications.

spectral shift orget oligonucle

the PBG senon a silicon siand width w=

lements of we introduced wcture is placeThe dimensionected in ordeength around unds the struce the interrogary operates. Aof the transv

hange made ue to tness l-free bility xide--38]. tures n the Their ce of

RI) of nition n the n and , the s not e, as f the slow-size,

ss of l-free

of the eotide

nsing ingle =460 width with a ed on ns of er to 1550 cture, ation A 5-

versal

elemand impwav

Figustructop acce Tperfby mvoltetchmicrstrustruperfsensstrepwasshal

Figu

3.2

Thehas

ments is lineathe output of

prove the lighveguide.

ure 4 Schematicture. The perioof a silicon o

ess taper is not i

The fabricatioformed in a stmeans of e-btage of 100 hing of the troscope (SEMcture is showctures were iform multiplesing responseptavidin-free

s accessed at tllow etch 1D g

ure 5 SEM ima

Functional

e immobilizatito be robust a

rly varied, is f the PBG senht coupling

c representationodic silicon ph

oxide lower claincluded in the

on of the PBtandard siliconbeam lithograkeV and indop silicon la

M) image of wn in Figurincluded in a

exed detectione for the strMB probes a

the input and grating couple

ge of a fabricat

lization

ion of MBs oand biocompa

also includednsing structurfrom/to the

n of the selectehotonic structuradding. Note tscheme.

BG sensing stn-on-insulatoraphy with anductively couayer. A scanna fabricated

re 5. Four Pa single photn in order to eptavidin-labe

at the same timthe output viaers.

ted PBG sensing

on the photonatible. In this

d at the input re in order to single mode

d PBG sensing re is placed on that the linear

tructures wasr (SOI) wafer

n acceleration upled plasma ning electron PBG sensing PBG sensing tonic chip to compare the

eled and the me. The chip a 70 nm-deep

g structure.

nic structuresregard, thiol-

t

r

r

This article is protected by copyright. All rights reserved.

Page 4: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

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ene couplinhomogeneoumild conditiothiolated MCCT ATC Adenotes a mEurofins Scipreviously structures foTo introducethe photonicimmediately(50 mW·cmimmersed in(Sigma-Aldrthe photonicFinally, a wmeasured aftdemonstratin Then, thvinyl-functiochemistry. Tin ultrapure dry at room 254 nm (5photoimmobthe photonic(phosphate bwater and air StreptaviPBG structu(5 µL, 20 structures anthe streptavithe chip wasto remove anMBs. The targexperiments the MB seqGUG AUA diluted in sconcentration

3.3 Experi

The biofunassembled wbottom holda top fluidic 7.5 mm-longplaced on anin Figure 6, aspectrum of spectral shif81980A), cen

ng (TEC) us biofunctionons [35, 44, 4Bs (5’-3’ seACG ATT A

modified T toientific, Luxevinyl-derivatllowing a preve alkene grou

c chip was riny activated witm-2) for 10 n a 2% sorich, Germany chip was wasater contact a

fter curing theng functionalizhe MB probeonalized PBGThiolated MB

water) were dtemperature. 0 mW·cm-2)

bilization. Oncc chip was thbuffer saline wr dried. idin was attacures by depos

ppm in PBnd incubated iidin-biotin lins intensively ny streptavidi

get oligonuclhad the seq

quence (AUC GGG GUG

saline-sodium n.

imental setu

nctionalized with a microfer, where the lid having a 5

g rubber chann automated oable to continthe PBG sen

fting. A waventered at 1550

chemistry pnalization of 45]. To achievquence: SH-A

AGC ATT AAo incorporate embourg) wertized surfaceviously optimups on the phsed with ethath UV-vis irraminutes. Thelution of vi

y) in toluene shed with acetangle (WCA) e chip for 30 zation.

es were immG sensing str

probe solutiodrop casted onThe chip was for 30 secce the MBs whoroughly wawith a 0.5 % tw

ched to the Miting a solutio

BS-T) over tin a humid chnk at room tewashed with n unspecifica

leotide used quence fully c

GAC UUA UCG AU 5citrate (SSC

up

photonic senfluidic flow cphotonic chip

500 µm-wide,nnel. The assoptical readounuously acquirsing structureelength-tunabl0 nm, was cou

provides a the surface u

ve immobilizaATC GAC AAG *TCG A

a biotin more coupled toe of the

mized protocolhotonic structanol and wateradiation at 254e chip was inyltriethoxysfor 2 hours. Ttone and air dof 76.7±0.1°minutes at 90

obilized ontoructures by

ons (30 nL, 10n them and les then irradiatconds to achwere immobilashed with PBween 20), dist

MBs of two oon of streptavthe desired P

hamber to promemperature. APBS-T and wlly attached to

for the sencomplementarAUG CUA A’ to 3’) and

C) 5× at 0.5

nsing chip cell comprisinp was placed,, 500 µm-highsembled chip ut setup, as shre the transmises to monitor le laser (Keyupled to the ac

fast, under ation, ACC

AT; * oiety, o the PBG [35].

tures, r and 4 nm then ilane Then dried. was

0 °C,

o the TEC

0 µM eft to ed at hieve ized,

BS-T tilled

f the vidin PBG mote

After, water o the

nsing ry to AUC

was µM

was ng a , and h and

was hown ssion their sight ccess

grat(Thooutp(20XusinTheimpcontof thwermod

Figuon tcell

4.

An 7 foon t156

Figubiofu

ting couplersorlabs CFS2put grating coX Olympus Png an infrarede interrogationplemented in tinuous sweephe IR camera e flown usingde and set to a

ure 6 Picture ofthe interrogatiohaving the micr

Experimen

example of tror one of the bthe photonic c0 nm.

ure 7 Examplefunctionalized P

s using a f-1550-APC)

ouplers was cPlan Achromad (IR) camern platform wa

LabVIEWp of the laser via a trigger s

g a syringe pua constant flow

f the assembledon platform androfluidic chann

ntal results

ansmission spiofunctionaliz

chip, whose PB

e of transmissiPBG sensing str

fiber aspheriand the lig

collected with at, 0.4 NA) ara (Xenics Xas controlled bable to synwith the imagsignal. The tarump working

w rate of 20 µl

d photonic sensid detailed imagnel on its bottom

pectrum is shozed PBG sensiBG edge is lo

ion spectrum fructures.

c collimator ght from the

an objective and measured eva-1.7-320). by a software chronize the ge acquisition rget solutions

g in withdraw l/min.

ing chip placed ge of the flow

m side.

own in Figure ing structures

ocated around

for one of the

r

This article is protected by copyright. All rights reserved.

Page 5: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

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Figure 8 evolution ooligonucleotPBG sensingwas obtaineemployed asin the experioligonucleotrecognition bPBG edgesadditional cyin order to rpresent in thunchanged, oligonucleotexperiment wwas stable Unfortunatelbiofunctionadamaged and

Figure 8 Temsensing structflown over thstructure beinprobes is depithe PBG senswith the strept2) are depicted From Firemarkable Pfor target oleven ~1000sensing rebiofunctionathe experimelabeled MB these differebiorecognitiodifferences oadditional RInormalize ththe PBG edg

shows the senof the PBGtide hybridizag structures oed flowing s carrier buffeiments. At t=tide was flowby the MB pr

s of the senycle of SSC 5remove any n

he medium; thindicating th

tide strand wwas carried oand constan

ly, one alized with d no output sig

mporal evolutiontures when thehe sensors. Thg biofunctionalicted with red dsing structures btavidin-labeled d with green an

igure 8, it PBG edge shligonucleotide

0 pm). Howesponse was

alized PBG seents, even betw

probes. So, ent responses on process byof the PBG seI calibration c

he sensing respge shift produc

nsing responsG edge, towation for the on the chip. T

SSC 5× buer for the targ14 min, a soluwn over therobes producensing structu× buffer was non-hybridizee PBG edge p

hat hybridizatwas successfuout at room tnt during the

PBG senstreptavidin-

gnal was mea

n of the PBG ee target oligonhe sensing resplized with the sdots, while the being identical MB probes (M

nd blue solid lin

can be obshifts were obte detection (fever, a signis obtained ensing structuween those hain order to dwere due to the MB prob

ensing structurcycle was carrponses. In thiced by the cha

e, i.e., the spewards the ta

biofunctionaThe initial basuffer, which get oligonucleoution of the tae sensors, wed the shift oures. Finally,flown at t=24

ed oligonucleopositions remation of the taul. Note thatemperature ane whole pronsing struc-free MBs sured.

edge position onucleotide stranponse for the streptavidin-freesensing responly biofunctiona

MB+St 1 and Mnes.

served that tained in all cfrom ~350 pmificantly diffe

for the tures considereaving streptavdetermine whedifferences ines or to sensitres themselveried out in ords calibration cange from SSC

ectral arget lized eline was

otide arget

whose f the , an

4 min otide ained arget t the nd it cess. cture was

of the nd is PBG

e MB nse of alized

MB+St

very cases m to

ferent three ed in

vidin-ether n the tivity es, an der to cycle, C 5×

buffthe oligcaliboligstrucalibedgeincluothebiofand expeoverPBGstrep Taboligocoluoligo

resu

Figupositrespstrepsensbiofudepi

MB+MB+MB MB MB

fer to ultrapurspectral sh

gonucleotide bration cycle,

gonucleotide dctures when bration cycle e shifts are audes additioner two idfunctionalizedMB 2*) obta

eriment [46]. rcome the proG sensing sptavidin-free M

le 1 Measured onucleotide stra

umn indicates thonucleotide det

lts obtained in a

ure 9 Normaliztion of the seonse for the PBptavidin-free Ming response

functionalized wicted with green

Oligondete

(p+St 1 3+St 2 6 11* 92* 1

re water was hifts measure

detection e, while Figurdetection respthat absolute was consider

also indicated nal oligonucledentical PBd with streptaained using a d

These resultoblem of havstructure bioMB in the ori

spectral shifts and and for the he normalized Ptection experim

another experim

zed temporal ensing structurBG structure bei

MB probes is depof the PBG

with the streptan and blue solid

nucleotide ection pm)

RI

345 620 020 920 120

measured. Taed for bothexperiment ae 9 shows th

ponse of the value of the

red (normalizein Table 1).

eotide detectioBG sensingavidin-free Mdifferent chip s are include

ving only a sinofunctionalizeginal experim

for the detectioRI calibration

PBG edge shiftment. The * ma

ment using anot

evolution of tres. The norming biofunctionpicted with red

G sensing stravidin-labeled Md lines.

calibration (pm)

ol

-1890 -3230 -1560 -1390 -1804

able 1 shows h the target and the RI he normalized PBG sensing e shift in the ed final PBG Table 1 also

on results for g structures MBs (MB 1*

in a different d in order to ngle working

ed with thement.

on of the target cycle. The last

ts for the target ark denotes the

ther chip.

the PBG edge alized sensing

nalized with the dots, while the

ructures being MB probes are

Normalized ligonucleotide

detection 0.183 0.192 0.654 0.662 0.621

r

t

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On one handtwo PBG senstreptavidin-different shiattributed tosensing strucfabrication pdifferent shstructures befree MB printeraction othe photonistreptavidin. In the experiments,streptavidin a significant of the PBG susing streptaorder to disrecognition probe and fluorophore-the experimecompared fosimilar resulobserved in by the additstreptavidin-explained inwas displaceMB, matterphotonic senbackshift of magnitude significantlydetection ostreptavidin-shift was obMB probes d

Figure 10 a) the streptavidwhen the MB with the targethe photonic

d, the normaliznsing structur-labeled MB ifts previousl

o the differenctures, probabprocess. On

hifts were obeing biofunctirobes (~0.65

of the MB proic sensing s light of the, it can be obmolecule attadecrease of th

sensing structuavidin-free MBscard that the

of the targelead to a

-labeled oligonents; the fluoror both MB prlts. Thus, wethe photonic

tional displac-labeled MBn Figure 10. Wed, due to ther was removnsing structurf the PBG edof that back

y large positivof the targ-free MB probbtained when due to the com

Schematic repin from the surchanges its con

et oligonucleotisensor respon

zed shifts werres being biofuprobes (~0.19

ly observed inces in sensitbly because of

the other hbtained for tionalized with), thus indic

obe with the estructure wh

e results obbserved that thached to the Mhe normalizedures, compareB probes (by ae streptavidin et oligonucleoa lower hybnucleotide tar

rescence after robes configu

e concluded thmeasurement

cement effect B probes, aWhen the strepe conformatioved from there, what was dge. Howeverkshift was s

ve shift measuget oligonucbes. So, a smusing the st

mbination of b

presentation of rface of the PBnformation dueide. b) Schemat

nse when strep

re identical founctionalized 9). Thereforein Figure 8 wtivity of the Pf deviations onand, significathe PBG senh the streptavcating a diffeevanescent fiehen incorpora

btained fromhe presence o

MB probe prodd sensing resped with the caa ~3.6× factormay hamper

otide by the bridization yrgets were usehybridization

urations, provihat the differts was determproduced for

as schematiptavidin mole

onal change oe surface of

translated inr, in this casesmaller than ured for the dcleotide by maller positivetreptavidin-labboth effects.

the displacemeBG sensing stru to the hybridiztic representatiotavidin-labeled

or the with , the were PBG n the antly nsing vidin-ferent ld of ating

the f the

duces ponse se of r). In r the MB

yield, ed in

n was iding rence

mined r the cally ecule f the

f the nto a e the

the direct

the e net beled

ent of ucture zation on of

d MB

probcomof ththe s

5.

In tinfluoveris, trepo Bto obothdispconfexpecomthe the usedthe biggthat migphot Aimpmolantiblowprodmolnegatargoligreplconfspec Fpropto hfieldthe disp

AckfundthroSAPMIN

Ref

bes are used. mbination of the he target oligonstreptavidin disp

Conclusion

this work, wuence of the r evanescent to our knowlorted for this tBy labeling Mobtain a sensih the direct oplacement offormational cerimental stu

mbination of tsensing respotarget oligon

d), a proper sMB (e.g., a

ger size molesignificantly

ght lead to antonic sensing Another pote

prove the sensilecular weighbiotics, whose

spectral shduced by tlecule/particleative shift sig

get detection.gonucleotide-blaced by anformational ccific target. Finally, this eper design of have several od profiles, wh

hybridized placed molecu

knowledgemeding receiveough the HoPHELY projecNECO (CTQ/2

ferences

The final net positive shift g

nucleotide and oplacement.

n

we have expconformationwave photoniledge, the firtype of optical

MB probes witing response oligonucleotidf that molechange of thudy, the netthese two effeonse comparednucleotide (i.election of thhigh refractiv

ecule) mightdominates th

n amplificatiostructure.

ential applicaitivity toward

ht targets, as e direct detect

hift. In that the displace

e will dominagnificantly hi. Note that based targets, n aptamer, change upon

effect might the photonic

optical modeshich can intera

target oligonule/nanoparticl

ents The d from the

orizon 2020 ct). This work2016/75749-R

response is agiven by the dirof the negative

perimentally onal changes oic sensing strst time that l sensors. th a molecule,being the co

de detection eecule produche MB. Dest shift obtai

fects means a d to the directe., when no

he matter beinve index nanoinduce a highhe detection pon of the res

ation of this s the detectionfor example tion provides case, the n

ement of tate, thus proigher to that

for the cathe MB probwhich also

n the recogn

be further exsensing struc with differenact in a differnucleotide anle [47].

authors ackne European

programme k has been parR BIHOLOG p

a result of the ect recognition shift given by

observed the f MB probes

ructures. This this effect is

, it is possible ombination of event and the ced by the spite, in this ined by the reduction of

t detection of molecule is

ng attached to oparticle or a her backshift process, what ponse of the

effect is to n of very low pesticides or an extremely egative shift the attached oviding a net

of the direct ase of non-be should be o suffers a nition of its

xploited by a cture in order nt evanescent rent way with nd with the

nowledge the Commission (ICT-644242

rtly funded by project).

f

f f

r

d t t

rt

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Page 7: 2 3 4 Accepted Article - University of East Anglia2, Ángel Maq ötzen4, Jaime 6022 Valenci ológico, Depar h, NR4 7TJ, U ormational cha mplementary ich typically in microarray the

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d A

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