title: New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.
abstract: Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
authors.forename: Abdullah
authors.initials: A
authors.lastname: Ozer
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Pagano
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
authors.forename: John T
authors.initials: JT
authors.lastname: Lis
references.citation: J Clin Invest. 2008 Jan;118(1):376-86
references.pmid: 18060045
references.citation: Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5428-32
references.pmid: 8516284
references.citation: Methods Mol Biol. 2011;703:247-63
references.pmid: 21125495
references.citation: Biosens Bioelectron. 2014 Jan 15;51:324-9
references.pmid: 23994614
references.citation: BMC Biotechnol. 2007 Aug 15;7:48
references.pmid: 17697378
references.citation: Nucleic Acids Res. 1996 Feb 15;24(4):702-6
references.pmid: 8604313
references.citation: Nat Genet. 2003 Feb;33(2):155-61
references.pmid: 12524544
references.citation: Angew Chem Int Ed Engl. 2014 May 5;53(19):4796-801
references.pmid: 24644057
references.citation: Microsc Res Tech. 2007 Apr;70(4):372-81
references.pmid: 17262788
references.citation: Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7158-63
references.pmid: 11404456
references.citation: Proteomics Clin Appl. 2012 Dec;6(11-12):563-73
references.pmid: 23090891
references.citation: Molecules. 2010 Jan 07;15(1):215-25
references.pmid: 20110884
references.citation: Biomol Eng. 2007 Oct;24(4):381-403
references.pmid: 17627883
references.citation: PLoS One. 2012;7(8):e43940
references.pmid: 22952815
references.citation: Nat Biotechnol. 2009 Sep;27(9):839-49
references.pmid: 19701187
references.citation: Anal Chim Acta. 2009 Jan 5;631(1):102-7
references.pmid: 19046686
references.citation: Anal Bioanal Chem. 2012 Aug;404(3):835-42
references.pmid: 22733247
references.citation: Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1449-54
references.pmid: 24379378
references.citation: Biochemistry. 1995 Apr 25;34(16):5651-9
references.pmid: 7537093
references.citation: Chem Biol. 2012 Oct 26;19(10):1247-54
references.pmid: 23102219
references.citation: Mol Ther. 2012 Jun;20(6):1242-50
references.pmid: 22434135
references.citation: Anal Biochem. 2009 Jul 15;390(2):203-5
references.pmid: 19374883
references.citation: J Am Chem Soc. 2009 May 13;131(18):6330-1
references.pmid: 19385619
references.citation: Nucleic Acids Res. 2010 Mar;38(4):e21
references.pmid: 19955232
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11838-43
references.pmid: 16873550
references.citation: Biol Chem. 2012 Apr;393(5):343-53
references.pmid: 22505517
references.citation: Trends Biotechnol. 2010 Oct;28(10):517-25
references.pmid: 20719399
references.citation: Biochimie. 2012 Sep;94(9):1900-9
references.pmid: 22609015
references.citation: Nat Protoc. 2009;4(3):393-411
references.pmid: 19265799
references.citation: Nat Commun. 2014 Mar 11;5:3364
references.pmid: 24618921
references.citation: PLoS One. 2011;6(9):e24910
references.pmid: 21949784
references.citation: Mol Cell Biol. 1989 Jul;9(7):2944-9
references.pmid: 2674675
references.citation: Methods Mol Biol. 2009;535:59-78
references.pmid: 19377980
references.citation: J Virol. 2014 Feb;88(4):1870-80
references.pmid: 24335293
references.citation: Biosens Bioelectron. 2010 Mar 15;25(7):1761-6
references.pmid: 20061133
references.citation: PLoS One. 2014 Jan 29;9(1):e87002
references.pmid: 24489826
references.citation: Nucleic Acids Res. 2013 Aug;41(14):7167-75
references.pmid: 23737446
references.citation: J Anal Methods Chem. 2012;2012:415697
references.pmid: 23326761
references.citation: Acc Chem Res. 2008 Jan;41(1):130-8
references.pmid: 18193823
references.citation: PLoS One. 2011;6(11):e27051
references.pmid: 22110600
references.citation: Methods Mol Biol. 2011;714:387-406
references.pmid: 21431754
references.citation: Annu Rev Anal Chem (Palo Alto Calif). 2009;2:241-64
references.pmid: 20636061
references.citation: RNA. 2009 Dec;15(12):2105-11
references.pmid: 19846574
references.citation: J Virol. 2009 Jan;83(2):802-10
references.pmid: 18971263
references.citation: Anal Chem. 2012 Jan 3;84(1):350-5
references.pmid: 22103644
references.citation: PLoS One. 2008 Jul 16;3(7):e2720
references.pmid: 18628955
references.citation: Anal Chem. 2013 Mar 19;85(6):3417-24
references.pmid: 23398198
references.citation: RNA. 2007 Apr;13(4):614-22
references.pmid: 17283213
references.citation: Nucleic Acids Res. 2009 Jan;37(1):e6
references.pmid: 19029139
references.citation: Nat Biotechnol. 1996 Aug;14(8):1021-5
references.pmid: 9631044
references.citation: Biochemistry. 2012 Oct 23;51(42):8321-3
references.pmid: 23057694
references.citation: Expert Opin Ther Pat. 2009 Aug;19(8):1073-82
references.pmid: 19514954
references.citation: PLoS Genet. 2014 Jan;10(1):e1004090
references.pmid: 24453987
references.citation: Lab Chip. 2011 Nov 7;11(21):3703-9
references.pmid: 21947169
references.citation: Nat Biotechnol. 2014 Jun;32(6):562-8
references.pmid: 24727714
references.citation: Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18460-5
references.pmid: 24167271
references.citation: Nucleic Acids Res. 2005 Sep 25;33(17):e141
references.pmid: 16186128
references.citation: Mol Ther Nucleic Acids. 2013 Jan 08;2:e67
references.pmid: 23299833
references.citation: Lab Chip. 2009 May 7;9(9):1206-12
references.pmid: 19370238
references.citation: Nucleic Acids Res. 2008 May;36(9):3118-27
references.pmid: 18403417
references.citation: PLoS One. 2013 Aug 13;8(8):e71798
references.pmid: 23967247
references.citation: Oligonucleotides. 2006 Winter;16(4):323-35
references.pmid: 17155908
references.citation: J Proteomics. 2010 Jan 3;73(3):649-66
references.pmid: 19755178
references.citation: Angew Chem Int Ed Engl. 2014 Jun 2;53(23):5821-6
references.pmid: 24753303
references.citation: Anal Biochem. 2011 Jul 15;414(2):246-53
references.pmid: 21420926
references.citation: Recent Pat DNA Gene Seq. 2008;2(3):172-86
references.pmid: 19075955
references.citation: PLoS One. 2012;7(7):e41702
references.pmid: 22860007
references.citation: Oligonucleotides. 2010 Dec;20(6):317-23
references.pmid: 21133818
references.citation: Anal Chem. 2010 Dec 1;82(23):9736-42
references.pmid: 21038863
references.citation: Anal Chem. 2011 Sep 1;83(17):6883-9
references.pmid: 21774453
references.citation: RNA. 2009 Dec;15(12):2385-97
references.pmid: 19861426
references.citation: Anal Chem. 2009 Mar 1;81(5):1747-54
references.pmid: 19193102
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):2989-94
references.pmid: 19202068
references.citation: Mol Cell Biol. 1998 Nov;18(11):6447-56
references.pmid: 9774661
references.citation: Chem Commun (Camb). 2008 Apr 28;(16):1883-5
references.pmid: 18401506
references.citation: Expert Rev Mol Diagn. 2014 Mar;14(2):143-51
references.pmid: 24400930
references.citation: Science. 1990 Aug 3;249(4968):505-10
references.pmid: 2200121
references.citation: Mol Cell Biol. 1997 May;17(5):2649-57
references.pmid: 9111335
references.citation: Angew Chem Int Ed Engl. 2010;49(2):355-8
references.pmid: 19967683
references.citation: Science. 2011 Jul 29;333(6042):642-6
references.pmid: 21798953
references.citation: Mol Cell Proteomics. 2014 Apr;13(4):1050-64
references.pmid: 24505114
references.citation: Nucleic Acids Res. 2010 Jul;38(13):e139
references.pmid: 20448026
references.citation: Nat Methods. 2014 Jun;11(6):683-8
references.pmid: 24809628
references.citation: Oligonucleotides. 2009 Sep;19(3):209-22
references.pmid: 19653880
references.citation: Proc Natl Acad Sci U S A. 1999 May 25;96(11):6131-6
references.pmid: 10339553
references.citation: Nature. 2013 Jul 11;499(7457):172-7
references.pmid: 23846655
references.citation: PLoS One. 2013 Dec 20;8(12):e82667
references.pmid: 24376564
references.citation: Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3900-5
references.pmid: 21368158
references.citation: Anal Bioanal Chem. 2007 Jan;387(1):171-82
references.pmid: 17072603
references.citation: J Pharm Biomed Anal. 2013 Jul-Aug;81-82:210-7
references.pmid: 23666257
references.citation: Methods Mol Biol. 2014;1103:241-65
references.pmid: 24318899
references.citation: J Pharm Biomed Anal. 2014 Mar;91:151-9
references.pmid: 24463043
references.citation: Anal Chem. 2013 May 7;85(9):4705-12
references.pmid: 23541235
references.citation: J Am Chem Soc. 2006 Feb 8;128(5):1410-1
references.pmid: 16448086
references.citation: PLoS One. 2010 Dec 07;5(12):e15004
references.pmid: 21165148
references.citation: Nucleic Acid Ther. 2013 Jun;23(3):238-42
references.pmid: 23550551
references.citation: PLoS Genet. 2012;8(3):e1002610
references.pmid: 22479205
references.citation: Methods Mol Biol. 2014;1111:1-15
references.pmid: 24549608
references.citation: Bioinformatics. 2012 Jun 15;28(12):i215-23
references.pmid: 22689764
references.citation: Nat Biotechnol. 2013 May;31(5):453-7
references.pmid: 23563318
references.citation: Protein Expr Purif. 2010 Jan;69(1):21-8
references.pmid: 19500672
references.citation: Nucleic Acid Ther. 2013 Dec;23(6):443-9
references.pmid: 24256293
references.citation: RNA. 2010 Nov;16(11):2252-62
references.pmid: 20870801
references.citation: Nucleic Acids Res. 2009 Jul;37(12):e87
references.pmid: 19465396
references.citation: Cell. 2013 Jan 17;152(1-2):327-39
references.pmid: 23332764
references.citation: RNA. 2002 Nov;8(11):1461-70
references.pmid: 12458799
references.citation: Nucleic Acids Res. 2014 Apr;42(8):e63
references.pmid: 24500199
references.citation: Nucleic Acids Res. 2012 Jul;40(13):6319-37
references.pmid: 22467215
references.citation: PLoS One. 2012;7(9):e43836
references.pmid: 22962591
references.citation: J Histochem Cytochem. 2003 Jun;51(6):797-808
references.pmid: 12754291
references.citation: Nat Rev Drug Discov. 2010 Jul;9(7):537-50
references.pmid: 20592747
references.citation: Nature. 1990 Aug 30;346(6287):818-22
references.pmid: 1697402
references.citation: Anal Biochem. 2012 Feb 15;421(2):362-7
references.pmid: 22033290
references.citation: Biochimie. 2006 Jul;88(7):897-904
references.pmid: 16540230
references.citation: J Nucleic Acids. 2012;2012:748913
references.pmid: 23150810
references.citation: RNA. 2005 Jun;11(6):853-63
references.pmid: 15923372
references.citation: Oligonucleotides. 2007 Spring;17(1):1-11
references.pmid: 17461758
references.citation: Molecules. 2009 Dec 24;15(1):1-11
references.pmid: 20110867
references.citation: Methods Mol Biol. 2012;905:177-200
references.pmid: 22736004
references.citation: Clin Chem. 1999 Sep;45(9):1628-50
references.pmid: 10471678
references.citation: PLoS One. 2011;6(12):e29604
references.pmid: 22242135
references.citation: Nucleic Acids Res. 2012 Mar;40(5):e39
references.pmid: 22189104
references.citation: Eur J Pharm Sci. 2013 Jan 23;48(1-2):259-71
references.pmid: 23142634
references.citation: Biotechniques. 2008 Mar;44(3):351-60
references.pmid: 18361789
references.citation: Curr Top Med Chem. 2009;9(12):1144-57
references.pmid: 19860714
references.citation: J Biol Chem. 2013 Jul 19;288(29):21136-21147
references.pmid: 23744070
references.citation: J Am Chem Soc. 2008 Jul 16;130(28):9137-43
references.pmid: 18558676
references.citation: Biochem Soc Trans. 2008 Jun;36(Pt 3):546-7
references.pmid: 18482004
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3742-6
references.pmid: 17360423
references.citation: Anal Chem. 2009 Jul 1;81(13):5490-5
references.pmid: 19480397
references.citation: Science. 2012 Feb 17;335(6070):831-4
references.pmid: 22344439
references.citation: Methods Mol Biol. 1999;118:105-14
references.pmid: 10549518
references.citation: Nucleic Acids Res. 2010 Mar;38(4):e23
references.pmid: 19965765
references.citation: Nucleic Acids Res. 2002 Dec 15;30(24):e138
references.pmid: 12490729
references.citation: J Nucl Med. 2014 Mar;55(3):353-6
references.pmid: 24525205
references.citation: Genome Res. 2010 Jun;20(6):861-73
references.pmid: 20378718
references.citation: Nucleosides Nucleotides Nucleic Acids. 2008 Aug;27(8):949-66
references.pmid: 18696364
references.citation: Anal Bioanal Chem. 2014 Apr;406(11):2727-32
references.pmid: 24553662
references.citation: J Am Chem Soc. 2004 Jan 14;126(1):20-1
references.pmid: 14709039
references.citation: Oligonucleotides. 2011 Mar-Apr;21(2):93-100
references.pmid: 21413890
references.citation: Analyst. 2012 Mar 21;137(6):1307-15
references.pmid: 22314701
references.citation: Biomed Res Int. 2014;2014:849743
references.pmid: 24779017
references.citation: Nucleic Acids Res. 2007;35(22):7626-35
references.pmid: 17981839
references.citation: Analyst. 2014 Feb 7;139(3):589-95
references.pmid: 24325000
references.citation: Nucleic Acids Res. 2008 Dec;36(21):6739-51
references.pmid: 18948292
references.citation: Nat Biotechnol. 1996 Sep;14(9):1112-5
references.pmid: 9631061
references.citation: Nat Methods. 2012 Oct;9(10):938-9
references.pmid: 23018995
references.citation: Expert Opin Med Diagn. 2010 Nov;4(6):511-8
references.pmid: 23496229
references.citation: Anal Chem. 2012 Sep 18;84(18):7603-6
references.pmid: 22931544
references.citation: Nat Biotechnol. 2011 Jun 26;29(7):659-64
references.pmid: 21706015
references.citation: Nat Biotechnol. 1999 Jun;17(6):573-7
references.pmid: 10385322
references.citation: EMBO J. 2012 Oct 3;31(19):3935-48
references.pmid: 23032188
references.citation: Nucleic Acid Ther. 2011 Aug;21(4):253-63
references.pmid: 21793789
references.citation: Biotechniques. 2014 Mar 01;56(3):125-8, 130, 132-3
references.pmid: 24641476
references.citation: Nucleic Acids Res. 2012 Dec;40(22):11777-83
references.pmid: 23042245
references.citation: Oligonucleotides. 2007 Spring;17(1):12-21
references.pmid: 17461759
references.citation: J Nanobiotechnology. 2011 Jun 03;9:25
references.pmid: 21639912
references.citation: Cytometry A. 2009 Sep;75(9):727-33
references.pmid: 19565638
references.citation: Nucleic Acids Res. 2013 Feb 1;41(3):1873-84
references.pmid: 23241386
references.citation: Chem Commun (Camb). 2012 Nov 4;48(85):10472-80
references.pmid: 22951893
references.citation: PLoS One. 2010 Dec 07;5(12):e15003
references.pmid: 21170350
references.citation: Molecules. 2009 Mar 27;14(4):1353-69
references.pmid: 19384268
references.citation: RNA. 2008 Dec;14(12):2504-12
references.pmid: 18971322
references.citation: Oligonucleotides. 2009 Sep;19(3):243-54
references.pmid: 19732022
references.citation: Nat Biotechnol. 2006 Aug;24(8):1005-15
references.pmid: 16823371
references.citation: Langmuir. 2012 Jun 5;28(22):8281-5
references.pmid: 22458258
references.citation: PLoS One. 2012;7(4):e35990
references.pmid: 22558297
references.citation: Molecules. 2010 Aug 09;15(8):5423-44
references.pmid: 20714306
references.citation: Curr Opin Pharmacol. 2009 Oct;9(5):602-7
references.pmid: 19717337
references.citation: Nucleic Acids Res. 1999 May 1;27(9):2006-14
references.pmid: 10198434
references.citation: Anal Chem. 2012 Jun 19;84(12):5365-71
references.pmid: 22624874
references.citation: Nat Chem Biol. 2010 Jan;6(1):22-4
references.pmid: 19946274
references.citation: Biochem Biophys Res Commun. 2009 Aug 14;386(1):223-6
references.pmid: 19520057
references.citation: PLoS One. 2010 Feb 11;5(2):e9169
references.pmid: 20161784
references.citation: J Cell Biochem. 2013 Feb;114(2):250-5
references.pmid: 22949372
references.citation: Angew Chem Int Ed Engl. 2008;47(28):5190-3
references.pmid: 18512861
references.citation: Science. 2012 Apr 20;336(6079):341-4
references.pmid: 22517858
references.citation: Anal Chem. 2008 Oct 1;80(19):7372-8
references.pmid: 18729475
references.citation: Electrophoresis. 2012 Sep;33(17):2783-9
references.pmid: 22965726
references.citation: Oligonucleotides. 2011 Mar-Apr;21(2):85-91
references.pmid: 21413891
references.citation: Curr Opin Chem Biol. 2008 Aug;12(4):448-56
references.pmid: 18644461
references.citation: Chem Biol. 2002 Mar;9(3):351-9
references.pmid: 11927260
references.citation: Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2902-7
references.pmid: 9501188
references.citation: PLoS One. 2009 Nov 24;4(11):e7971
references.pmid: 19956692
references.citation: Nat Med. 2009 Oct;15(10):1224-8
references.pmid: 19801990
references.citation: Anal Chem. 2013 May 21;85(10):4961-7
references.pmid: 23662585
references.citation: Biotechniques. 2011 Dec;51(6):413-6
references.pmid: 22150332
references.citation: J Mol Evol. 2008 Jul;67(1):95-102
references.pmid: 18594898
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13174-9
references.pmid: 15329412
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15373-8
references.pmid: 20705898
references.citation: Biotechniques. 2007 May;42(5):578, 580, 582
references.pmid: 17515195
references.citation: J Am Chem Soc. 2010 Jul 14;132(27):9453-64
references.pmid: 20565094
references.citation: Anal Bioanal Chem. 2008 Feb;390(4):1033-7
references.pmid: 17994225
references.citation: RNA. 2001 Apr;7(4):632-41
references.pmid: 11345441