title: Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments.
abstract: We have investigated the time-dependent strand displacement activity of several targets with double-stranded DNA probes (dsProbes) of varying affinity. Here, the relative affinity of various dsProbes is altered through choices in hybridization length (11-15 bases) and the selective inclusion of center mismatches in the duplexes. While the dsProbes are immobilized on microspheres, the soluble, 15 base-long complementary sequence is presented either alone as a short target strand or as a recognition segment embedded within a longer target strand. Compared to the short target, strand displacement activity of the longer targets is slower, but still successful. Additionally, the longer targets exhibit modest differences in the observed displacement rates, depending on the location of recognition segment within the long target. Overall, our study demonstrates that the kinetics of strand displacement activity can be tuned through dsProbe sequence design parameters and is only modestly affected by the location of the complementary segment within a longer target strand.
authors: School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
authors: Bryan A
authors: BA
authors: Baker
authors: Valeria T
authors: VT
authors: Milam
references: Langmuir. 2006 Dec 19;22(26):11290-304
references: 17154618
references: Nature. 2002 Jan 3;415(6867):62-5
references: 11780115
references: Appl Environ Microbiol. 2003 May;69(5):2848-56
references: 12732557
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
references: 15980540
references: Anal Chem. 2009 Mar 15;81(6):2150-8
references: 19215066
references: J Mol Biol. 1971 Dec 14;62(2):361-81
references: 5138337
references: Nat Mater. 2003 Dec;2(12):815-20
references: 14634643
references: Nat Biotechnol. 1998 Jan;16(1):40-4
references: 9447591
references: Nucleic Acids Res. 2001 Dec 15;29(24):5163-8
references: 11812850
references: J Am Chem Soc. 2009 Dec 2;131(47):17303-14
references: 19894722
references: Nucleic Acids Res. 2002 Aug 15;30(16):e86
references: 12177314
references: Nucleic Acids Res. 2004 Apr 14;32(6):e57
references: 15084672
references: J Am Chem Soc. 2011 Feb 23;133(7):2177-82
references: 21268641
references: Nano Lett. 2011 Mar 9;11(3):1032-5
references: 21323380
references: Proc Natl Acad Sci U S A. 1994 May 24;91(11):5022-6
references: 8197176
references: Nucleic Acids Res. 2009 Jun;37(11):3756-65
references: 19380378
references: J Mol Biol. 2000 Mar 24;297(2):511-20
references: 10715217
references: Nucleic Acids Res. 2002 Jan 15;30(2):E5
references: 11788731
references: Clin Chem. 1986 Sep;32(9):1696-701
references: 2427259
references: Nano Lett. 2008 Jul;8(7):1803-8
references: 18540653
references: Methods Cell Sci. 2002;24(1-3):1-9
references: 12815284
references: Trends Biotechnol. 2002 Apr;20(4):167-73
references: 11906749
references: Anal Chem. 1998 Apr 1;70(7):1288-96
references: 15779144
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Apr;63(4 Pt 1):041913
references: 11308883
references: Clin Chem. 1986 Sep;32(9):1631-6
references: 3742791
references: Langmuir. 2007 Sep 11;23(19):9728-36
references: 17696456
references: J Microbiol Methods. 2003 May;53(2):235-43
references: 12654494
references: Nat Nanotechnol. 2010 Feb;5(2):116-20
references: 20023646
references: Science. 1995 Oct 20;270(5235):467-70
references: 7569999
references: Biophys J. 2005 Nov;89(5):2950-9
references: 16126833
references: Nucleic Acids Res. 1981 Apr 24;9(8):1905-18
references: 6264399
references: J Am Chem Soc. 2007 Dec 19;129(50):15477-9
references: 18034495
references: Nano Lett. 2009 Jul;9(7):2641-7
references: 19496602
references: Clin Chem. 1997 Sep;43(9):1749-56
references: 9299971
references: Clin Chim Acta. 2006 Jan;363(1-2):71-82
references: 16102740
references: Nucleic Acids Res. 2007;35(21):7197-208
references: 17947320
references: Nat Genet. 1996 Dec;14(4):441-7
references: 8944024
references: Nature. 2005 Jun 9;435(7043):834-8
references: 15944708
references: Biosens Bioelectron. 2005 Aug 15;21(2):322-9
references: 16023959
references: Langmuir. 2010 Jun 15;26(12):9818-26
references: 20349914
references: Nature. 2000 Aug 10;406(6796):605-8
references: 10949296
references: Phys Rev Lett. 2003 Mar 21;90(11):118102
references: 12688969
references: Nucleic Acids Res. 1987 Sep 11;15(17):6883-97
references: 3309890
references: Anal Biochem. 2006 Nov 15;358(2):225-38
references: 16982029
references: Nucleic Acids Res. 1996 Nov 15;24(22):4395-400
references: 8948629
references: J Am Chem Soc. 2002 Dec 11;124(49):14601-7
references: 12465970
references: J Microbiol Methods. 2003 May;53(2):245-52
references: 12654495
references: Nucleic Acids Res. 1987 Apr 10;15(7):2911-26
references: 2951654
references: Nucleic Acids Res. 1999 Apr 1;27(7):1719-27
references: 10076004
references: Angew Chem Int Ed Engl. 2004 Dec 3;43(47):6469-71
references: 15578785
references: Biomacromolecules. 2009 Jun 8;10(6):1619-26
references: 19425572
references: Nat Genet. 1999 Jan;21(1 Suppl):20-4
references: 9915496