Carbon nanodots based biosensors for gene mutation detection

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Sensors and Actuators, B: Chemical 256 (2018): 226-233 DOI: https://doi.org/10.1016/j.snb.2017.10.105 Copyright: © 2017 Elsevier B.V. All rights reserved.

1

Supporting Information

Carbon nanodots based biosensors for gene mutation detection

Tania García-Mendiola^a,b,c, Iria Bravo^a,b, José María López-Moreno^a, Félix Pariente^a,b,c, Reinhold Wannemacher^b, Karina Weber^d,e, Jürgen Popp^d,e and Encarnación Lorenzo^a,b,c

a Departamento Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Spain

b Instituto Madrileño de Estudios Avanzados (IMDEA) Nanociencia, Faraday, 9, Campus UAM, Cantoblanco, 28049 Madrid, Spain

c Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain

d Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany

e Institute for Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.

2 Materials and methods

Table 1SI. Oligonucleotides and PCR samples used in this work.

SYNTHETIC OLIGONUCLEOTIDES (25bp)

PROBE 5'- GCGTTCCAAAGGGCAGGATCATTGA HP1

COMPLEMENTARY 5'-TCAATGATCCTGCCCTTTGGAACGC HP2C

5'-TCAATGATCCTACCCTTTGGAAGCG HPSM

NON-COMPLEMENTARY 5'-GACCGTCGAAGTAAAGGGTTCCATA HP2NC

SYNTHETIC OLIGONUCLEOTIDES (100bp)

PROBE ^5'-CTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAA

ATATCATCTTTGGTGTTTCCTATGATGAATATAGATACAGAAGCGTC ATCAAA GCATGCC

WT

PCR SAMPLES

WILD TYPE 5´_ AACCGATTGAATATGGAGCCAAATATATAATTTGGGTAGTGTGAAGGGTTCATATGCA TAATCAAAAAGTTTTCACATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTG TATCTATATTCATCATAGGAAACACCAAAGATGATATTTTCTTTAATGGTGCCAGGCATAATC CAGGAAAACTGAGAACAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCTCTGAAGGCTCC AGTTCTCCCATAATCACCATTAGAAGTGAAGTCTGGAAATAAAACCCATCATTATTAGGTCAT TATCAAATCACGCTCAGGATTCACTTGCCTCCAATTATCATCCTAAGCAGAAGTGTATATTC

WT

MUTATED 5´_AACCGATTGAATATGGAGCCAAATATATAATTTGGGTAGTGTGAAGGGTTCATATGCATAA TCAAAAAGTTTTCACATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATC TATATTCATCATAGGAAACACCA___ATGATATTTTCTTTAATGGTGCCAGGCATAATCCAGGAA AACTGAGAACAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCTCTGAAGGCTCCAGTTCTCC CATAATCACCATTAGAAGTGAAGTCTGGAAATAAAACCCATCATTATTAGGTCATTATCAAATC ACGCTCAGGATTCACTTGCCTCCAATTATCATCCTAAGCAGAAGTGTATATTC

F508del

NON COMPLEMENTARY

5´ACAGCTGAGTGCCCTGTCCTCAGATGGGGAGGGACAGGGTCGGCCTGTACCCCGGAGGCACCTG AGGTGACAGAGGCGAAGGCAGATGGGGCACTGACCCAGGAGGAGAAAGCAGCCATTGGCACT NC

3 Figure 1SI. A) Size distribution obtained for the synthesized CDs after analysing by DLS more than 100 particles. B) FTIR, C) Absorption and D) Fluorescence emission spectra of the 0.56 µM CDs in 0.1 M PB pH 7.0 solution.

A B

C D

4 Figure 2SI. (A, B) TEM images of the synthesized CDs. The red lines show the spacing of the planes. (C) FFT analysis of the images.

A

2.1 Å

B C

2 nm

5 Figure 3SI. Normalized Raman spectrum of the synthesized CDs. Excitation at 632.8 nm, 50x objective lens.

Figure 4SI. SEM image of a gold substrate at 50000x magnification.

500 1000 1500 2000 2500 3000

G (1602 cm

)

Ram an i nt ens ity / a rb. u .

Wavenumber / cm

D (1330 cm

)

6 Figure 5SI. Cyclic voltammograms in 0.1 M PB pH 7.0 solution containing A) 1.0 mM SAF or B) 5.0 mM [Fe(CN)6]^3- for a bare AuSPE (blue curve) and a CDs/AuSPE electrode (red curve). Cyclic voltammograms in 0.1 M PB pH 7.0 solution of a CDs/AuSPE electrode (black curve). Scan rate 100 mV/s.

-0.3 0.0 0.3 0.6

-150 0 150

I / µ A

E / V

B

-0.8 -0.6

-40 -20 0 20

I / µA

E / V

A

7 Figure 6SI. A) Absorption spectra of 60 µM dsDNA in 0.1 M PB pH 7.0 solution in absence (black curve) and presence of increasing amounts (from 0.5 to 5.5 µM) of CDs (colored curves). B) Emission spectra of 1.3 µM CDs in 0.1 M PB pH 7.0 solution, in absence (black curve) and presence of increasing amounts (from 0.5 to 750 µM) of DNA (colored curves).

225 250 275 300 325

0.00 0.25 0.50 0.75

5.5 µM

Absorbance

λ / nm

0 µM

A B

8 Figure 7SI. Cyclic voltammograms of CDs/AuSPE (black curve), dsDNA/CDs/AuSPE (blue curve) and ssDNA/CDs/AuSPE (red curve) in 0.1M PB pH 7.0, after accumulation of SAF by consecutive potential cycling,

-0.8 -0.6

-20 -10 0

I / µA

E / V

9 Figure 8SI. DPVs response of HP1/AuSPE (A) and HP1/CSPE (B) in 0.1M PB pH 7.0 solution, before (red curve) and after hybridization with a fully complementary sequence, HP2C (black curve), after accumulation of SAF by consecutive potential cycling.

-0.9 -0.8 -0.7 -0.6 0

2 4 6

I / µA

E / V

A

-0.9 -0.8 -0.7 -0.6 0

20 40

60 B

I / µA

E / V

10 Table 2SI. Analytical parameters of electrochemical DNA biosensors.

Probe Redox indicator DL Target (bp) Reference

aminated Daumicine 0.1nM 24 [41]

aminated Methylene blue 0.1nM 24 [56]

thiolated RuL complex 4.6µM 25 [51]

thiolated Safranine 22nM 373 [43]

aminated MnL 0.14nM 24 [57]

aminated FCA 40 [58]

unmodified Meldola´s blue 109nM 247 [59]

unmodified Safranine 0.16nM 373 Present work