title: An intercalation-locked parallel-stranded DNA tetraplex.
abstract: DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. (1)H-(1)H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
authors: Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA.
authors: Shailesh
authors: S
authors: Tripathi
authors: Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA.
authors: Daoning
authors: D
authors: Zhang
authors: Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA paukstel@umd.edu.
authors: Paul J
authors: PJ
authors: Paukstelis
mesh_terms: D004247:DNA / Q000737:chemistry*; D006219:Halogens / Q000737:chemistry; D007364:Intercalating Agents / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation
chemical_list: D006219:Halogens; D007364:Intercalating Agents; D004247:DNA
references: Nucleic Acids Res. 2003 Feb 1;31(3):844-9
references: 12560479
references: Structure. 1999 Jul 15;7(7):803-15
references: 10425682
references: Nano Lett. 2005 Dec;5(12):2586-92
references: 16351220
references: Biosens Bioelectron. 2013 May 15;43:372-8
references: 23356995
references: Science. 2005 Dec 9;310(5754):1661-5
references: 16339440
references: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references: 20383002
references: Nucleic Acids Res. 2002 Dec 1;30(23):5253-60
references: 12466550
references: Acc Chem Res. 2014 Jun 17;47(6):1853-60
references: 24845472
references: Nature. 2006 Mar 16;440(7082):297-302
references: 16541064
references: J Am Chem Soc. 2010 Mar 17;132(10):3248-9
references: 20163139
references: Science. 1982 Apr 30;216(4545):475-85
references: 7071593
references: Acc Chem Res. 2014 Aug 19;47(8):2514-24
references: 25134974
references: Chem Biol. 2004 Aug;11(8):1119-26
references: 15324813
references: Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6188-93
references: 17379665
references: Nature. 1991 Apr 18;350(6319):631-3
references: 2017259
references: Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
references: 22505256
references: Science. 2008 Aug 8;321(5890):824-6
references: 18687961
references: J Mol Biol. 1994 Sep 30;242(4):508-26
references: 7932707
references: Nucleic Acids Res. 2012 Dec;40(22):11737-47
references: 23042679
references: Science. 2006 Dec 8;314(5805):1585-8
references: 17158324
references: Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16789-94
references: 15557000
references: Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5224-8
references: 8506370
references: Nature. 1998 Aug 6;394(6693):539-44
references: 9707114
references: Bioorg Med Chem. 2014 Aug 15;22(16):4407-18
references: 24957878
references: Nucleic Acids Res. 2014 Dec 1;42(21):13422-9
references: 25389267
references: Science. 2011 Apr 15;332(6027):342-6
references: 21493857
references: Angew Chem Int Ed Engl. 2006 Jan 23;45(5):730-5
references: 16365843
references: Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):422-9
references: 10089350
references: J Am Chem Soc. 2006 May 31;128(21):6794-5
references: 16719452
references: EMBO J. 1992 Oct;11(10):3777-86
references: 1396571
references: Science. 2003 Sep 26;301(5641):1882-4
references: 14512621
references: J Am Chem Soc. 2012 Aug 1;134(30):12557-64
references: 22768973
references: Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3130-4
references: 16492787
references: Bioconjug Chem. 2012 Mar 21;23(3):382-91
references: 22239558
references: Nucleic Acids Res. 1998 Oct 15;26(20):4696-705
references: 9753739
references: Nucleic Acids Res. 2009 May;37(9):2810-7
references: 19279188
references: Nature. 1993 Jun 10;363(6429):561-5
references: 8389423
references: Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):717-22
references: 14709674
references: J Am Chem Soc. 2005 May 18;127(19):6914-5
references: 15884910
references: Nature. 2001 Nov 22;414(6862):430-4
references: 11719800
references: J Theor Biol. 1982 Nov 21;99(2):237-47
references: 6188926
references: Nature. 2009 Sep 3;461(7260):74-7
references: 19727196
references: Nucleic Acids Res Suppl. 2002;(2):179-80
references: 12903164
references: IUCrJ. 2014 May 30;1(Pt 4):213-20
references: 25075342
references: Biochim Biophys Acta. 2001 Jul 2;1527(1-2):73-80
references: 11420145
references: Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12577-82
references: 12232051
references: Science. 2009 Aug 7;325(5941):725-30
references: 19661424