title: C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes.
abstract: Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
authors.affiliation: Department of Chemistry, University of Idaho, Moscow, Idaho 83844, United States.
authors.forename: Sujay P
authors.initials: SP
authors.lastname: Sau
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Hrdlicka
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry*; D011721:Pyrenes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D015347:RNA Probes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D014230:Triazoles / Q000737:chemistry*
chemical_list: D015342:DNA Probes; D009841:Oligonucleotides; D011721:Pyrenes; D015347:RNA Probes; D014230:Triazoles; D012313:RNA; D004247:DNA; C030984:pyrene
references.citation: Bioorg Med Chem. 2011 Jan 1;19(1):249-55
references.pmid: 21146995
references.citation: Nucleic Acids Res. 1995 Jul 11;23(13):2361-6
references.pmid: 7630712
references.citation: Bioconjug Chem. 2009 Mar 18;20(3):558-64
references.pmid: 19220008
references.citation: Bioorg Med Chem. 2008 Sep 15;16(18):8427-39
references.pmid: 18774721
references.citation: Org Biomol Chem. 2004 Jan 7;2(1):80-9
references.pmid: 14737663
references.citation: Nature. 1994 Jun 9;369(6480):492-3
references.pmid: 8202140
references.citation: Bioconjug Chem. 2008 Jan;19(1):211-24
references.pmid: 18020404
references.citation: Nucleic Acids Res. 2005 Dec 15;33(22):7111-9
references.pmid: 16361269
references.citation: J Org Chem. 2009 Feb 6;74(3):1070-81
references.pmid: 19108636
references.citation: J Am Chem Soc. 2004 Apr 21;126(15):4820-7
references.pmid: 15080686
references.citation: Org Lett. 2008 Sep 4;10(17):3729-32
references.pmid: 18656947
references.citation: Org Biomol Chem. 2010 May 7;8(9):2028-36
references.pmid: 20401378
references.citation: J Org Chem. 2002 May 3;67(9):3057-64
references.pmid: 11975567
references.citation: Nucleic Acids Res. 1999 Jun 1;27(11):2387-92
references.pmid: 10325429
references.citation: Chem Soc Rev. 2010 Apr;39(4):1388-405
references.pmid: 20309492
references.citation: J Org Chem. 2008 Sep 19;73(18):7060-6
references.pmid: 18710289
references.citation: Int J Biochem. 1984;16(12):1179-92
references.pmid: 6397369
references.citation: Org Lett. 2001 Jun 28;3(13):1977-80
references.pmid: 11418028
references.citation: Org Lett. 2006 Aug 17;8(17):3639-42
references.pmid: 16898780
references.citation: Chem Commun (Camb). 2010 Jul 21;46(27):4929-31
references.pmid: 20526503
references.citation: Org Biomol Chem. 2011 Mar 7;9(5):1381-8
references.pmid: 21210043
references.citation: Bioconjug Chem. 2011 Jan 19;22(1):108-14
references.pmid: 21174402
references.citation: Nucleic Acids Res. 2001 Jun 15;29(12):2522-34
references.pmid: 11410660
references.citation: J Am Chem Soc. 2010 Oct 13;132(40):14221-8
references.pmid: 20845923
references.citation: J Org Chem. 2011 Sep 2;76(17):7119-31
references.pmid: 21827174
references.citation: Nucleic Acids Res. 2005 Oct 19;33(18):5887-95
references.pmid: 16237124
references.citation: Nucleic Acids Res. 1993 Jul 11;21(14):3197-203
references.pmid: 8393563
references.citation: J Org Chem. 2008 Jan 4;73(1):287-90
references.pmid: 18052191
references.citation: Nucleic Acids Res. 1984 Oct 11;12(19):7435-53
references.pmid: 6548562
references.citation: Nucleic Acids Res. 1995 Jul 11;23(13):2499-505
references.pmid: 7630728
references.citation: Chemistry. 2011 Mar 7;17(11):3157-65
references.pmid: 21328492
references.citation: Chem Commun (Camb). 2011 May 7;47(17):5004-6
references.pmid: 21431191
references.citation: J Biol Chem. 2001 Nov 9;276(45):42347-54
references.pmid: 11551943
references.citation: Chem Rev. 2009 Sep;109(9):4207-20
references.pmid: 19737023
references.citation: Chembiochem. 2007 Jul 9;8(10):1122-5
references.pmid: 17551917
references.citation: Chembiochem. 2005 May;6(5):848-51
references.pmid: 15776408
references.citation: J Am Chem Soc. 2007 May 30;129(21):6859-64
references.pmid: 17488075
references.citation: Chembiochem. 2005 Jan;6(1):69-77
references.pmid: 15584015
references.citation: J Org Chem. 2003 Jan 24;68(2):609-12
references.pmid: 12530893
references.citation: Org Lett. 2005 Oct 27;7(22):4931-3
references.pmid: 16235925
references.citation: J Am Chem Soc. 2010 Aug 4;132(30):10424-8
references.pmid: 20617829
references.citation: J Org Chem. 2010 Jan 15;75(2):284-95
references.pmid: 20000692
references.citation: Bioorg Khim. 2010 Jul-Aug;36(4):437-81
references.pmid: 20823915
references.citation: J Am Chem Soc. 2009 Sep 9;131(35):12671-81
references.pmid: 19722718
references.citation: Angew Chem Int Ed Engl. 2002 Jul 15;41(14):2596-9
references.pmid: 12203546
references.citation: J Am Chem Soc. 1998;120(24):6191-6192
references.pmid: 20852721
references.citation: Bioconjug Chem. 2011 Jun 15;22(6):1249-55
references.pmid: 21539388
references.citation: Nucleic Acids Res. 2000 Sep 1;28(17):3224-32
references.pmid: 10954589
references.citation: Bioorg Med Chem Lett. 2009 Jun 15;19(12):3316-9
references.pmid: 19419865
references.citation: Chemistry. 2010 Dec 27;16(48):14385-96
references.pmid: 21117098
references.citation: J Clin Microbiol. 2002 Jul;40(7):2398-407
references.pmid: 12089254
references.citation: Nucleic Acids Res. 2010 May;38(9):3133-46
references.pmid: 20081201
references.citation: Nucleic Acids Res. 2000 Aug 1;28(15):2911-4
references.pmid: 10908353
references.citation: J Med Chem. 1993 Nov 12;36(23):3533-41
references.pmid: 8246221
references.citation: Bioorg Med Chem Lett. 2011 Jun 1;21(11):3420-2
references.pmid: 21524577
references.citation: Org Biomol Chem. 2004 Oct 21;2(20):2885-7
references.pmid: 15480448
references.citation: Nucleic Acids Res. 1994 Oct 11;22(20):4039-43
references.pmid: 7937128
references.citation: Nucleic Acids Res. 1990 May 25;18(10):3080
references.pmid: 2190190
references.citation: J Org Chem. 2011 Jul 15;76(14):5584-97
references.pmid: 21591729
references.citation: Angew Chem Int Ed Engl. 2003 Aug 25;42(33):3958-60
references.pmid: 12949880
references.citation: Chem Commun (Camb). 2001 Oct 21;(20):2114-5
references.pmid: 12240189
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15329-34
references.pmid: 20713730
references.citation: J Am Chem Soc. 2006 Feb 8;128(5):1398-9
references.pmid: 16448080