Detection of various thrombin concentrations using etched fiber Bragg gratings functionalized with DNA aptamer

1. detection of various thrombin concentrations using etched fiber Bragg gratings functionalized with DNA aptamer

DETECTION OF VARIOUS THROMBIN
CONCENTRATIONS USING ETCHED
FIBER BRAGG GRATINGS
FUNCTIONALIZED WITH DNA
APTAMER
Madina Shaimerdenovaa, Aliya Bekmurzayevaa,b, Takhmina
Ayupovaa, Marzhan Sypabekovaa,b, Sanzhar Korganbayeva, Kanat
Dukenbayev a,b, Carlo Molardib, Daniele Tosia,b
aLaboratory
of biosensors and bioinstruments; National Laboratory
Astana, Astana, Kazakhstan
bSchool of engineering, Nazarbayev University, Astana,
Kazakhstan

2. Outline

OUTLINE
Background:
Optical fibers
Fiber Bragg grating (FBG) sensors
Thrombin
Thrombin aptamers
Etched FBG biosensor for thrombin detection

3. thrombin

THROMBIN
Thrombin is important during blood
coagulation
Thrombin levels can be elevated during
extra- and intravascular activation of
blood coagulation by tumor cells
Thrombin is involved in diseases:
atherosclerosis, thromboembolic disease,
cancer and inflammatory disease
Detecting and quantification of thrombin
in a complex medium (serum or plasma)
is important both for research and clinic
applications
Due to its clinical importance there is a
wide range of works aimed to detect
thrombin and most of them are based on
aptamers

4. aptamers

APTAMERS
-
Aptamers – oligonucleotides (DNA or RNA) or
peptides that bind to their target with high
affinity and specificity
Various targets: from ions to whole organisms
Selected in vitro by SELEX method
Advantages over antibodies:
In vitro selection
Non-immunogenic targets
No batch-to-batch variation
Longer shelf-life
Source of figures: Wu et al 2016

5. thrombin binding aptamer (tba)

THROMBIN BINDING APTAMER (TBA)
Two frequently used TBA: 15-mer and 29-mer
Thrombin and its 15-mer TBA were selected as a ligandanalyte pair because it is a well-characterized system widely
used in the development of different biosensors

6. why fiber optic sensors (fos) for thrombin sensing

WHY FIBER OPTIC SENSORS (FOS) FOR
THROMBIN SENSING
Miniaturized
dimension
In-vivo
insertion
Cat
hete
riza
tion
High
sensi
tivity
Biocompa
tible
4
Multiplexing and
distributed
sensing
Immunity to
electromagnet
ic interference
Stability in
harsh
environments

7. fiber Bragg grating (fbg) → etched fbg

FIBER
BRAGG GRATING (FBG) → ETCHED FBG
• Etching the cladding in hydrofluoric acid (HF)→ confers sensitivity
to outer RI
• When the cladding is removed→ RI of the cladding is replaced by the
RI of the surrounding medium
• The interaction between an analyte of interest and ligand changes
the refractive index on the surface and thus Bragg wavelength is
shifted and grating reflectivity is changed
Source of figures: Chiavaioli et al 2017

8. objectives

OBJECTIVES
We used a well-established pair of ligand-analyte system
to build a biosensor based on functionalized EFBG

9. setup and fabrication

SETUP AND FABRICATION

10. functionalization of efbg

FUNCTIONALIZATION OF EFBG

11. before and after etching

BEFORE AND AFTER ETCHING
-15
-2.1 nm
Original FBG
-20
Etched FBG
Spectrum (dB)
-25
11.6 dB
-30
-35
-40
-45
-50
-55
-60
1540
1542
1544
1546
1548
1550
1552
Wavelength (nm)
1554
1556
1558
1560

12. fabrication of biosensor

FABRICATION OF BIOSENSOR
1 - Original FBG (1549.979 nm)
2 - Etched FBG (1547.886 nm)
3 - Piranha, 10 min (1548.617 nm)
4 - Piranha, 30 min (1548.373 nm)
5 - APTES, 15 min (1547.910 nm)
6 - APTES, 30 min (1547.910 nm)
7 - GA (1547.730 nm)
8 - Aptamer (1547.921 nm)
9 - BSA (1548.284 nm)
Bragg wavelength (nm)
1550
1549.5
1549
1548.5
1548
1547.5
1
2
3
4
5
6
Fabrication step
7
8
9

13. thrombin concentrations

THROMBIN CONCENTRATIONS
10
Wavelength shift (pm)
8
6
4
2
0
10 nM
20 nM
40 nM
80 nM
-2
-4
0
10
20
30
40
Time (min)
50
60
70

14. conclusion

CONCLUSION
The sensitivity of the EFBG biosensor to refractive index
of 17.4 nm/RIU is reported
Biosensor has been functionalized to selective thrombin
detection
Thrombin binding aptamers have been immobilized on
the sensor surface using a silanization process
We observed a different shift of the Bragg wavelength for
each concentration value, reaching a final value of 0.5 (10
nM), 2 (20 nM), 4 (40 nM), 7 pm (80 nM) with standard
deviation of 0.3 pm

15. future work

FUTURE WORK
Future work will be addressed to improve the
fabrication process to a large batch of sensors, and
functionalizing other aptamers for use in other
biosensing applications such as for detection of
biomarkers implicated in cancer or infectious diseases

16. acknowledgement

ACKNOWLEDGEMENT
Research supported by ORAU project “LIFESTART:
Lab-in-a-fiber for smart thermo-haptic treatment of
tumors” and was funded by the autonomous
organization of education “Nazarbayev University
within its Development Program of the Research
University 2016-2020”.