title: Methods for assessing DNA hybridization of peptide nucleic acid-titanium dioxide nanoconjugates.
abstract: We describe the synthesis of peptide nucleic acid (PNA)-titanium dioxide (TiO(2)) nanoconjugates and several novel methods developed to investigate the DNA hybridization behaviors of these constructs. PNAs are synthetic DNA analogs resistant to degradation by cellular enzymes that hybridize to single-stranded DNA (ssDNA) with higher affinity than DNA oligonucleotides, invade double-stranded DNA (dsDNA), and form different PNA/DNA complexes. Previously, we developed a DNA-TiO(2) nanoconjugate capable of hybridizing to target DNA intracellularly in a sequence-specific manner with the ability to cleave DNA when excited by electromagnetic radiation but susceptible to degradation that may lower its intracellular targeting efficiency and retention time. PNA-TiO(2) nanoconjugates described in the current article hybridize to target ssDNA, oligonucleotide dsDNA, and supercoiled plasmid DNA under physiological-like ionic and temperature conditions, enabling rapid, inexpensive, sequence-specific concentration of nucleic acids in vitro. When modified by the addition of imaging agents or peptides, hybridization capabilities of PNA-TiO(2) nanoconjugates are enhanced, providing essential benefits for numerous in vitro and in vivo applications. The series of experiments shown here could not be done with either TiO(2)-DNA nanoconjugates or PNAs alone, and the novel methods developed will benefit studies of numerous other nanoconjugate systems.
authors.affiliation: Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Avenue, Ward-13-002, Chicago, IL 60611, USA.
authors.forename: Eric M B
authors.initials: EM
authors.lastname: Brown
authors.forename: Tatjana
authors.initials: T
authors.lastname: Paunesku
authors.forename: AiGuo
authors.initials: A
authors.lastname: Wu
authors.forename: K Ted
authors.initials: KT
authors.lastname: Thurn
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haley
authors.forename: Jimmy
authors.initials: J
authors.lastname: Clark
authors.forename: Taisa
authors.initials: T
authors.lastname: Priester
authors.forename: Gayle E
authors.initials: GE
authors.lastname: Woloschak
mesh_terms: D000042:Absorption; D001483:Base Sequence; D053758:Nanoparticles / Q000032:analysis / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D020135:Peptide Nucleic Acids / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D010455:Peptides / Q000378:metabolism; D010957:Plasmids / Q000235:genetics; D013499:Surface Properties; D013696:Temperature; D014025:Titanium / Q000032:analysis / Q000737:chemistry*
chemical_list: D020135:Peptide Nucleic Acids; D010455:Peptides; C009495:titanium dioxide; D014025:Titanium
references.citation: Nucleic Acids Res. 2005 Oct 04;33(17):e146
references.pmid: 16204449
references.citation: Science. 1991 Dec 6;254(5037):1497-500
references.pmid: 1962210
references.citation: Chem Biol. 2004 Jun;11(6):749-58
references.pmid: 15217608
references.citation: Anal Biochem. 2006 May 15;352(2):169-75
references.pmid: 16579951
references.citation: Anal Chem. 2005 Nov 1;77(21):6976-84
references.pmid: 16255598
references.citation: Nanoscale Res Lett. 2007 Aug 15;2(9):430-41
references.pmid: 21794189
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1558-62
references.pmid: 11917016
references.citation: Nucleic Acids Res. 1993 Jan 25;21(2):197-200
references.pmid: 8382793
references.citation: Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10648-52
references.pmid: 8248156
references.citation: Nano Lett. 2007 Mar;7(3):596-601
references.pmid: 17274661
references.citation: Nat Mater. 2003 May;2(5):343-6
references.pmid: 12692534
references.citation: Methods. 2001 Feb;23(2):97-107
references.pmid: 11181029
references.citation: Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14276-81
references.pmid: 10588696
references.citation: Nucleic Acids Res. 1994 Dec 11;22(24):5371-7
references.pmid: 7816628
references.citation: Oncogene. 1999 Nov 4;18(46):6191-200
references.pmid: 10597217
references.citation: Science. 1995 Dec 15;270(5243):1838-41
references.pmid: 8525381
references.citation: Science. 1994 Aug 5;265(5173):777-80
references.pmid: 7519361
references.citation: Biochemistry. 2003 Dec 2;42(47):13996-4003
references.pmid: 14636068
references.citation: Proc Natl Acad Sci U S A. 1997 Nov 11;94(23):12320-5
references.pmid: 9356447
references.citation: Biochem Pharmacol. 1994 Sep 15;48(6):1310-3
references.pmid: 7945427
references.citation: Biochemistry. 1977 Jan 11;16(1):25-9
references.pmid: 188445
references.citation: Nanomedicine. 2008 Sep;4(3):201-7
references.pmid: 18567541
references.citation: J Am Chem Soc. 2007 Dec 26;129(51):15760-1
references.pmid: 18047347
references.citation: J Am Chem Soc. 2003 Feb 12;125(6):1643-54
references.pmid: 12568626
references.citation: J Am Chem Soc. 2004 Sep 8;126(35):10832-3
references.pmid: 15339154
references.citation: Science. 2000 Sep 8;289(5485):1757-60
references.pmid: 10976070
references.citation: Pharmacol Ther. 2007 Apr;114(1):34-55
references.pmid: 17316816
references.citation: J Am Chem Soc. 2005 Sep 21;127(37):12754-5
references.pmid: 16159241
references.citation: Curr Opin Mol Ther. 2007 Jun;9(3):242-7
references.pmid: 17608022
references.citation: Anal Biochem. 1999 Mar 15;268(2):401-4
references.pmid: 10075832
references.citation: Nat Struct Biol. 1996 May;3(5):410-3
references.pmid: 8612069
references.citation: Chemistry. 2008;14(5):1492-8
references.pmid: 18046680
references.citation: Antisense Nucleic Acid Drug Dev. 2002 Apr;12(2):65-70
references.pmid: 12074366
references.citation: Nat Struct Biol. 1997 Feb;4(2):98-101
references.pmid: 9033585
references.citation: Anal Biochem. 2008 Apr 15;375(2):299-305
references.pmid: 18211817
references.citation: Nucleic Acids Res. 1997 Nov 15;25(22):4674-8
references.pmid: 9358181
references.citation: J Mol Biol. 2002 Apr 26;318(2):237-43
references.pmid: 12051833
references.citation: Nucleic Acids Res. 2005 Oct 27;33(19):e168
references.pmid: 16257979
references.citation: Gene Ther. 2007 Jul;14(14):1057-64
references.pmid: 17607313
references.citation: Biochemistry. 2001 Jul 3;40(26):7853-9
references.pmid: 11425312
references.citation: Nucleic Acids Res. 2007;35(17):e111
references.pmid: 17720714