1 Introduction of Aptamer, SELEX, and Different SELEX Variants
29
57. Misono TS, Kumar PKR (2005) Selection of RNA aptamers against human influenza virus
hemagglutinin using surface plasmon resonance. Anal Biochem 342:312–317
58. Hobbs K, Cathcart N, Kitaev V (2016) Gold-plated silver nanoparticles engineered for sensitive
plasmonic detection amplified by morphological changes. Chem Commun 52:9785–9788
59. Gao C, Lu Z, Liu Y, Zhang Q, Chi M, Cheng Q, Yin Y (2012) Highly stable silver nanoplates for
surface plasmon resonance biosensing. Angewandte Chemie—International Edition 51:5629–
5633
60. Jia W, Li H, Wilkop T, Liu X, Yu X, Cheng Q, Xu D, Chen H-Y (2018) Silver decahedral
nanoparticles empowered SPR imaging-SELEX for high throughput screening of aptamers
with real-time assessment. Biosens Bioelectron 109:206–213
61. Hong SL, Wan YT, Tang M, Pang DW, Zhang ZL (2017) Multifunctional screening platform
for the highly efficient discovery of aptamers with high affinity and specificity. Anal Chem
89:6535–6542
62. Damase TR, Miura TA, Parent CE, Allen PB (2018) Application of the open qPCR instrument for the in vitro selection of DNA aptamers against epidermal growth factor receptor and
Drosophila C virus. ACS Combinatorial Sci 20:45–54
63. Fang X, Tan W (2010) Aptamers generated from cell-SELEX for molecular medicine: a
chemical biology approach. Acc Chem Res 43:48–57
64. Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W (2010) Development of DNA
aptamers using Cell-SELEX. Nat Protoc 5:1169–1185
65. Ara MN, Hyodo M, Ohga N, Hida K, Harashima H (2012) Development of a novel DNA
aptamer ligand targeting to primary cultured tumor endothelial cells by a cell-based SELEX
method. PLoS One 7:e50174
66. Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L (2003) A tenascin-C aptamer identified
by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl
Acad Sci USA 100:15416–15421
67. Cerchia L, Duconge F, Pestourie C, Boulay J, Aissouni Y, Gombert K, Tavitian B, de Franciscis
V, Libri D (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor
tyrosine kinase. PLoS Biol 3:e123
68. Shamah SM, Healy JM, Cload ST (2008) Complex target SELEX. Acc Chem Res 41:130–138
69. Blank M, Weinschenk T, Priemer M, Schluesener H (2001) Systematic evolution of a DNA
aptamer binding to rat brain tumor microvessels. selective targeting of endothelial regulatory
protein pigpen. J Biol Chem 276:16464–16468
70. Zhuo Z, Yu Y, Wang M, Li J, Zhang Z, Liu J, Wu X, Lu A, Zhang G, Zhang B (2017) Recent
advances in SELEX technology and aptamer applications in biomedicine. Int J Mol Sci 18:2142
71. Hori SI, Herrera A, Rossi JJ, Zhou J (2018) Current advances in aptamers for cancer diagnosis
and therapy. Cancers (Basel) 10:9
72. Cho M, Xiao Y, Nie J, Stewart R, Csordas AT, Oh SS, Thomson JA, Soh HT (2010) Quantitative
selection of DNA aptamers through microfluidic selection and high-throughput sequencing.
Proc Natl Acad Sci USA 107:15373–15378
73. Riley KR, Gagliano J, Xiao JJ, Libby K, Saito S, Yu G, Cubicciotti R, Macosko J, Colyer
CL, Guthold M, Bonin K (2015) Combining capillary electrophoresis and next-generation
sequencing for aptamer selection. Anal Bioanal Chem 407:1527–1532
74. Scoville DJ, Uhm TK, Shallcross JA, Whelan RJ (2017) Selection of DNA aptamers for ovarian
cancer biomarker CA125 using one-pot SELEX and high-throughput sequencing. J Nucleic
Acids 2017:9879135
75. Chushak Y, Stone MO (2009) In silico selection of RNA aptamers. Nucleic Acids Res 37:e87
76. Wondergem JAJ, Schiessel H, Tompitak M (2017) Performing SELEX experiments in silico.
J Chem Phys 147
77. Ahirwar R, Nahar S, Aggarwal S, Ramachandran S, Maiti S, Nahar P (2016) In silico selection
of an aptamer to estrogen receptor alpha using computational docking employing estrogen
response elements as aptamer-alike molecules. Sci. Rep. 6
78. Obeid S, Baccaro A, Welte W, Diederichs K, Marx A (2010) Structural basis for the synthesis
of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc Nat Acad Sci USA
107:21327–21331
29
57. Misono TS, Kumar PKR (2005) Selection of RNA aptamers against human influenza virus
hemagglutinin using surface plasmon resonance. Anal Biochem 342:312–317
58. Hobbs K, Cathcart N, Kitaev V (2016) Gold-plated silver nanoparticles engineered for sensitive
plasmonic detection amplified by morphological changes. Chem Commun 52:9785–9788
59. Gao C, Lu Z, Liu Y, Zhang Q, Chi M, Cheng Q, Yin Y (2012) Highly stable silver nanoplates for
surface plasmon resonance biosensing. Angewandte Chemie—International Edition 51:5629–
5633
60. Jia W, Li H, Wilkop T, Liu X, Yu X, Cheng Q, Xu D, Chen H-Y (2018) Silver decahedral
nanoparticles empowered SPR imaging-SELEX for high throughput screening of aptamers
with real-time assessment. Biosens Bioelectron 109:206–213
61. Hong SL, Wan YT, Tang M, Pang DW, Zhang ZL (2017) Multifunctional screening platform
for the highly efficient discovery of aptamers with high affinity and specificity. Anal Chem
89:6535–6542
62. Damase TR, Miura TA, Parent CE, Allen PB (2018) Application of the open qPCR instrument for the in vitro selection of DNA aptamers against epidermal growth factor receptor and
Drosophila C virus. ACS Combinatorial Sci 20:45–54
63. Fang X, Tan W (2010) Aptamers generated from cell-SELEX for molecular medicine: a
chemical biology approach. Acc Chem Res 43:48–57
64. Sefah K, Shangguan D, Xiong X, O’Donoghue MB, Tan W (2010) Development of DNA
aptamers using Cell-SELEX. Nat Protoc 5:1169–1185
65. Ara MN, Hyodo M, Ohga N, Hida K, Harashima H (2012) Development of a novel DNA
aptamer ligand targeting to primary cultured tumor endothelial cells by a cell-based SELEX
method. PLoS One 7:e50174
66. Daniels DA, Chen H, Hicke BJ, Swiderek KM, Gold L (2003) A tenascin-C aptamer identified
by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl
Acad Sci USA 100:15416–15421
67. Cerchia L, Duconge F, Pestourie C, Boulay J, Aissouni Y, Gombert K, Tavitian B, de Franciscis
V, Libri D (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor
tyrosine kinase. PLoS Biol 3:e123
68. Shamah SM, Healy JM, Cload ST (2008) Complex target SELEX. Acc Chem Res 41:130–138
69. Blank M, Weinschenk T, Priemer M, Schluesener H (2001) Systematic evolution of a DNA
aptamer binding to rat brain tumor microvessels. selective targeting of endothelial regulatory
protein pigpen. J Biol Chem 276:16464–16468
70. Zhuo Z, Yu Y, Wang M, Li J, Zhang Z, Liu J, Wu X, Lu A, Zhang G, Zhang B (2017) Recent
advances in SELEX technology and aptamer applications in biomedicine. Int J Mol Sci 18:2142
71. Hori SI, Herrera A, Rossi JJ, Zhou J (2018) Current advances in aptamers for cancer diagnosis
and therapy. Cancers (Basel) 10:9
72. Cho M, Xiao Y, Nie J, Stewart R, Csordas AT, Oh SS, Thomson JA, Soh HT (2010) Quantitative
selection of DNA aptamers through microfluidic selection and high-throughput sequencing.
Proc Natl Acad Sci USA 107:15373–15378
73. Riley KR, Gagliano J, Xiao JJ, Libby K, Saito S, Yu G, Cubicciotti R, Macosko J, Colyer
CL, Guthold M, Bonin K (2015) Combining capillary electrophoresis and next-generation
sequencing for aptamer selection. Anal Bioanal Chem 407:1527–1532
74. Scoville DJ, Uhm TK, Shallcross JA, Whelan RJ (2017) Selection of DNA aptamers for ovarian
cancer biomarker CA125 using one-pot SELEX and high-throughput sequencing. J Nucleic
Acids 2017:9879135
75. Chushak Y, Stone MO (2009) In silico selection of RNA aptamers. Nucleic Acids Res 37:e87
76. Wondergem JAJ, Schiessel H, Tompitak M (2017) Performing SELEX experiments in silico.
J Chem Phys 147
77. Ahirwar R, Nahar S, Aggarwal S, Ramachandran S, Maiti S, Nahar P (2016) In silico selection
of an aptamer to estrogen receptor alpha using computational docking employing estrogen
response elements as aptamer-alike molecules. Sci. Rep. 6
78. Obeid S, Baccaro A, Welte W, Diederichs K, Marx A (2010) Structural basis for the synthesis
of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc Nat Acad Sci USA
107:21327–21331