title: DNA branch migration reactions through photocontrollable toehold formation.
abstract: Strand displacement cascades are commonly used to make dynamically assembled structures. Particularly, the concept of "toehold-mediated DNA branch migration reactions" has attracted considerable attention in relation to dynamic DNA nanostructures. However, it is a challenge to obtain and control the formation of pure 1:1 ratio DNA duplexes with toehold structures. Here, for the first time, we report a photocontrolled toehold formation method, which is based on the photocleavage of 2-nitrobenzyl linker-embedded DNA hairpin precursor structures. UV light irradiation (λ ≈ 365 nm) of solutions containing these DNA hairpin structures causes the complete cleavage of the nitrobenzyl linker, and pure 1:1 DNA duplexes with toehold structures are easily formed. Our experimental results indicate that the amount of toehold can be controlled by simply changing the dose of UV irradiation and that the resulting toehold structures can be used for subsequent toehold-mediated DNA branch migration reactions, e.g., DNA hybridization chain reactions. This newly established method will find broad application in the construction of light-powered, controllable, and dynamic DNA nanostructures or large-scale DNA circuits.
authors: Department of Chemistry, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA.
authors: Fujian
authors: F
authors: Huang
authors: Mingxu
authors: M
authors: You
authors: Da
authors: D
authors: Han
authors: Xiangling
authors: X
authors: Xiong
authors: Haojun
authors: H
authors: Liang
authors: Weihong
authors: W
authors: Tan
mesh_terms: D004247:DNA / Q000737:chemistry*; D055668:Photochemical Processes; D014466:Ultraviolet Rays
chemical_list: D004247:DNA
references: Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):5932-7
references: 15829589
references: Nature. 2002 Jan 3;415(6867):62-5
references: 11780115
references: Nat Nanotechnol. 2007 Aug;2(8):490-4
references: 18654346
references: Nat Biotechnol. 2001 Apr;19(4):342-7
references: 11283592
references: J Am Chem Soc. 2012 Jul 4;134(26):10803-6
references: 22703552
references: Angew Chem Int Ed Engl. 2004 Sep 20;43(37):4906-11
references: 15372637
references: Science. 2011 Jun 3;332(6034):1196-201
references: 21636773
references: Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5488-93
references: 15064393
references: Angew Chem Int Ed Engl. 2011 Jan 10;50(2):401-4
references: 21154791
references: J Mol Biol. 1970 Feb 28;48(1):1-22
references: 4915293
references: Annu Rev Biomed Eng. 2002;4:129-53
references: 12117754
references: J Am Chem Soc. 2012 Aug 29;134(34):13918-21
references: 22894754
references: Angew Chem Int Ed Engl. 2012 Mar 5;51(10):2457-60
references: 22298502
references: J Am Chem Soc. 2011 Feb 23;133(7):2177-82
references: 21268641
references: Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5393-8
references: 20203007
references: J Am Chem Soc. 2012 Feb 29;134(8):3810-5
references: 22239155
references: Angew Chem Int Ed Engl. 2005 Jul 11;44(28):4358-61
references: 15959864
references: Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16777-82
references: 20823260
references: Nature. 2011 Jul 20;475(7356):368-72
references: 21776082
references: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15275-8
references: 15492210
references: Chem Commun (Camb). 2009 May 21;(19):2625-36
references: 19532904
references: J Am Chem Soc. 2011 Feb 2;133(4):1077-86
references: 21166410
references: J Am Chem Soc. 2004 Sep 22;126(37):11410-1
references: 15366866
references: Science. 2007 Nov 16;318(5853):1121-5
references: 18006742
references: Nat Biotechnol. 2010 Nov;28(11):1208-12
references: 21037591
references: Anal Chem. 2012 Oct 2;84(19):8277-83
references: 22950631
references: J Am Chem Soc. 2006 Sep 20;128(37):12211-20
references: 16967972
references: J Am Chem Soc. 2008 Oct 22;130(42):13921-6
references: 18823118
references: Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):409-13
references: 12515854
references: Science. 2006 Dec 8;314(5805):1585-8
references: 17158324
references: Nature. 2003 Jan 23;421(6921):427-31
references: 12540916
references: Nature. 2000 Aug 10;406(6796):605-8
references: 10949296
references: Nature. 2008 Jan 17;451(7176):318-22
references: 18202654
references: Nat Nanotechnol. 2007 May;2(5):275-84
references: 18654284
references: Angew Chem Int Ed Engl. 2011 Mar 28;50(14):3124-56
references: 21432950
references: J Am Chem Soc. 2012 Jan 11;134(1):263-71
references: 22129141
references: Biosens Bioelectron. 2012 Oct-Dec;38(1):258-63
references: 22739472
references: Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):5926-31
references: 15829588
references: Angew Chem Int Ed Engl. 2011 Dec 9;50(50):11934-6
references: 22012587
references: Angew Chem Int Ed Engl. 1998 Dec 17;37(23):3220-3238
references: 29711407