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82. Wang, C., Dong, X., Liu, Q., & Wang, K. (2015). Label-free colorimetric aptasensor for
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83. Roday, S., Sturm, M. B., Blakaj, D., & Schramm, V. L. (2008). Detection of an abasic site in
RNA with stem-loop DNA beacons: Application to an activity assay for Ricin Toxin
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84. Long, F., Zhu, A., & Wang, H. (2014). Optofluidics-based DNA structure-competitive
aptasensor for rapid on-site detection of lead(II) in an aquatic environment. Analytica Chimica
Acta, 7(849), 43–49.
85. Xing, Y. P., Liu, C., Zhou, X. H., & Shi, H. C. (2015). Label-free detection of kanamycin
based on a G-quadruplex DNA aptamer-based fluorescent intercalator displacement assay.
Scientific Reports, 30(5), 8125.
230
P. Arrigo and D. Baroni
docking approach based on biochemical or biophysical information. Journal of the American
Chemical Society, 125(7), 1731–1737.
69. Ruiz-Carmona, S., Alvarez-Garcia, D., Foloppe, N., Garmendia-Doval, A. B., Juhos, S.,
Schmidtke, P., et al. (2014). rDock: A fast, versatile and open source program for docking
ligands to proteins and nucleic acids. PLoS Computational Biology, 10(4), e1003571.
70. Ghobadi, A. F., & Jayaraman, A. (2016). Effects of polymer conjugation on hybridization
thermodynamics of oligonucleic acids. The Journal of Physical Chemistry B, 120(36), 9788–
9799.
71. Solov’yov, I. A., Yakubovich, A. V., Nikolaev, P. V., Volkovets, I., & Solov’yov, A. V.
(2012). MesoBioNano Explorer–a universal program for multiscale computer simulations of
complex molecular structure and dynamics. Journal of Computational Chemistry, 33(30),
2412–2439.
72. Douglas, S. M., Marblestone, A. H., Teerapittayanon, S., Vazquez, A., Church, G. M., &
Shih, W. M. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic
Acids Research, 37(15), 5001–5006.
73. Castro, C. E., Kilchherr, F., Kim, D. N., Shiao, E. L., Wauer, T., Wortmann, P., et al. (2011).
A primer to scaffolded DNA origami. Nature Methods, 8(3), 221–229.
74. Bindewald, E., Grunewald, C., Boyle, B., O’Connor, M., & Shapiro, B. A. (2008).
Computational strategies for the automated design of RNA nanoscale structures from building
blocks using NanoTiler. Journal of Molecular Graphics and Modelling, 27(3), 299–308.
75. Massire, C., & Westhof, E. (1998). MANIP: An interactive tool for modelling RNA. Journal
of Molecular Graphics and Modelling, 16(4–6), 197–205, 255–257.
76. Justino, C. I. L., Duarte, A. C., & Rocha-Santos, T. A. P. (2017). Recent progress in
biosensors for environmental monitoring: A review. Sensors (Basel), 17(12).
77. Wu, L., Qi, P., Fu, X., Liu, H., Li, J., Wang, Q., et al. (2016). A novel electrochemical
PCB77-binding DNA aptamer biosensor for selective detection of PCB77. Journal of
Electroanalytical Chemistry, 771, 45–49.
78. Wang, X., Yang, C., Zhu, S., Yan, M., Ge, S., & Yu, J. (2017). 3D origami electrochemical
device for sensitive Pb
2+ testing based on DNA functionalized iron-porphyrinic metal-organic
framework. Biosensors & Bioelectronics, 87, 108–115.
79. Liu, X., Song, M., & Li, F. (2017). Triplex DNA-based bioanalytical platform for highly
sensitive homogeneous electrochemical detection of melamine. Scientific Reports, 7(1), 4490.
80. Tortolini, C., Bollella, P., Antonelli, M. L., Antiochia, R., Mazzei, F., & Favero, G. (2015).
DNA-based biosensors for Hg
2+ determination by polythymine–methylene blue modified
electrodes. Biosensors and Bioelectronics, 67, 524–531.
81. Reinemann, C., von Fritsch, U. F., Rudolph, S., & Strehlitz, B. (2016). Generation and
characterization of quinolone-specific DNA aptamers suitable for water monitoring.
Biosensors and Bioelectronics, 77, 1039–1047.
82. Wang, C., Dong, X., Liu, Q., & Wang, K. (2015). Label-free colorimetric aptasensor for
sensitive detection of ochratoxin A utilizing hybridization chain reaction. Analytica Chimica
Acta, 20(860), 83–88.
83. Roday, S., Sturm, M. B., Blakaj, D., & Schramm, V. L. (2008). Detection of an abasic site in
RNA with stem-loop DNA beacons: Application to an activity assay for Ricin Toxin
A-Chain. Journal of Biochemical and Biophysical Methods, 70(6), 945–953.
84. Long, F., Zhu, A., & Wang, H. (2014). Optofluidics-based DNA structure-competitive
aptasensor for rapid on-site detection of lead(II) in an aquatic environment. Analytica Chimica
Acta, 7(849), 43–49.
85. Xing, Y. P., Liu, C., Zhou, X. H., & Shi, H. C. (2015). Label-free detection of kanamycin
based on a G-quadruplex DNA aptamer-based fluorescent intercalator displacement assay.
Scientific Reports, 30(5), 8125.
230
P. Arrigo and D. Baroni