title: Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents.
abstract: BACKGROUND
  DNA aptamers generated by cell-SELEX offer an attractive alternative to antibodies, but generating aptamers to specific, known membrane protein targets has proven challenging, and has severely limited the use of aptamers as affinity reagents for cell identification and purification.
  
  
  METHODS
  We modified the BJAB lymphoblastoma cell line to over-express the murine c-kit cell surface receptor. After six rounds of cell-SELEX, high-throughput sequencing and bioinformatics analysis, we identified aptamers that bound BJAB cells expressing c-kit but not wild-type BJAB controls. One of these aptamers also recognizes c-kit endogenously expressed by a mast cell line or hematopoietic progenitor cells, and specifically blocks binding of the c-kit ligand stem cell factor (SCF). This aptamer enables better separation by fluorescence-activated cell sorting (FACS) of c-kit(+) hematopoietic progenitor cells from mixed bone marrow populations than a commercially available antibody, suggesting that this approach may be broadly useful for rapid isolation of affinity reagents suitable for purification of other specific cell types.
  
  
  CONCLUSIONS
  Here we describe a novel procedure for the efficient generation of DNA aptamers that bind to specific cell membrane proteins and can be used as high affinity reagents. We have named the procedure STACS (Specific TArget Cell-SELEX).
authors: Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA.
authors: Susanne
authors: S
authors: Meyer
authors: John P
authors: JP
authors: Maufort
authors: Jeff
authors: J
authors: Nie
authors: Ron
authors: R
authors: Stewart
authors: Brian E
authors: BE
authors: McIntosh
authors: Lisa R
authors: LR
authors: Conti
authors: Kareem M
authors: KM
authors: Ahmad
authors: H Tom
authors: HT
authors: Soh
authors: James A
authors: JA
authors: Thomson
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000235:genetics / Q000378:metabolism; D001854:Bone Marrow Cells / Q000378:metabolism; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D005434:Flow Cytometry; D015870:Gene Expression; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D051379:Mice; D011485:Protein Binding; D019009:Proto-Oncogene Proteins c-kit / Q000235:genetics / Q000378:metabolism; D052156:SELEX Aptamer Technique; D019089:Stem Cell Factor / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D019089:Stem Cell Factor; D019009:Proto-Oncogene Proteins c-kit
references: Proc Natl Acad Sci U S A. 1975 Sep;72(9):3518-20
references: 171663
references: Biol Chem. 2009 Feb;390(2):137-44
references: 19040357
references: Science. 1995 Jan 6;267(5194):104-8
references: 7528940
references: PLoS One. 2010 Dec 10;5(12):e14269
references: 21170319
references: Cell. 2005 Aug 12;122(3):473-83
references: 16096065
references: Analyst. 2011 Apr 7;136(7):1310-2
references: 21321690
references: J Biol Chem. 2001 May 11;276(19):16464-8
references: 11279054
references: Mol Ther. 2012 Jun;20(6):1242-50
references: 22434135
references: Anal Chem. 2007 Jul 1;79(13):4900-7
references: 17530817
references: Mol Syst Biol. 2011 Oct 11;7:539
references: 21988835
references: PLoS One. 2011;6(6):e20299
references: 21687663
references: Oligonucleotides. 2006 Winter;16(4):323-35
references: 17155908
references: Cell. 1997 Nov 28;91(5):661-72
references: 9393859
references: Science. 1990 Aug 3;249(4968):505-10
references: 2200121
references: Int J Mol Sci. 2008 Apr;9(4):668-78
references: 19325777
references: PLoS One. 2012;7(9):e43836
references: 22962591
references: Nucleic Acids Res. 2012 Jul;40(13):6319-37
references: 22467215
references: Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15416-21
references: 14676325
references: Nature. 1990 Aug 30;346(6287):818-22
references: 1697402
references: Nat Protoc. 2010 Jun;5(6):1169-85
references: 20539292
references: Nat Protoc. 2010 Dec;5(12):1993-2004
references: 21127492
references: Molecules. 2009 Dec 24;15(1):1-11
references: 20110867
references: J Mol Recognit. 2009 Mar-Apr;22(2):57-64
references: 18546091
references: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9
references: 20439314
references: J Nucleic Acids. 2011;2011:904750
references: 21904667
references: Nature. 2004 Dec 16;432(7019):838-45
references: 15602549
references: PLoS One. 2009 Nov 24;4(11):e7971
references: 19956692
references: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15373-8
references: 20705898
references: PLoS Biol. 2005 Apr;3(4):e123
references: 15769183
references: ChemMedChem. 2008 Jun;3(6):991-1001
references: 18338423