title: Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation.
abstract: The incorporation of C5-amino-modified 2'-deoxyuridine analogues into DNA have found application in nucleic acid labelling, the stabilization of nucleic acid structures, functionalization of nucleic acid aptamers and catalysts, and the investigation of sequence-specific DNA bending. In this study, we describe the physicochemical properties of four different C5-amino-modified 2'-deoxyuridines in which the amino group is tethered to the base via a 3-carbon alkyl, Z- or E-alkenyl or alkynyl linker. Conformational parameters of the nucleosides and their pK(a) values were deduced using 1H NMR. All of them display the expected anti-conformation of the nucleoside with 2'-endo sugar puckers for the deoxyribose ring. A preference for the cisoid conformation for the Z-alkenyl analogue is found, while the E-alkenyl analogue exists exclusively as its transoid conformation. The pK(a) values range from 10.0 for the analogue with an aliphatic propyl linker to 8.5 for the propargylamino analogue. The analogues have been used for the synthesis of triple-helix forming oligonucleotides (TFOs) in which they replace thymidine in the natural sequence. Oligonucleotides containing the propargylamino analogue display the highest stability especially at low pH, while those containing analogues with propyl and especially Z-alkenyl linkers are destabilized to a great extent. TFOs containing the analogue with the E-alkenyl linker have stability similar to the unmodified structures. The chemical synthesis of TFOs containing the analogue, 5-(3-hydroxyprop-1-ynyl)-2'-deoxyuridine that possesses a neutral but polar side chain show a remarkable stability, which is higher than that of all TFOs containing the alkylamino or alkenylamino analogues and only slightly lower than that of TFOs containing the propargylamino analogue. Both the hydroxyl and propargylamino substitutions impart enhanced triple-helix stability relative to the analogous sequences containing C5-propynyl-2'-deoxyuridine. Furthermore, a similar dependence of stability on pH is found between TFOs containing the hydroxypropynyl modifications and those containing the propargylamino side chains. This suggests that the major factor responsible for stabilizing such triple helices is due to the presence of the alkyne with an attached electronegative group.
authors.affiliation: Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield Sheffield S3 7HF, UK.
authors.forename: John A
authors.initials: JA
authors.lastname: Brazier
authors.forename: Takayuki
authors.initials: T
authors.lastname: Shibata
authors.forename: John
authors.initials: J
authors.lastname: Townsley
authors.forename: Brian F
authors.initials: BF
authors.lastname: Taylor
authors.forename: Elaine
authors.initials: E
authors.lastname: Frary
authors.forename: Nicholas H
authors.initials: NH
authors.lastname: Williams
authors.forename: David M
authors.initials: DM
authors.lastname: Williams
mesh_terms: D000478:Alkylation; D000588:Amines / Q000737:chemistry*; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D003857:Deoxyuridine / Q000031:analogs & derivatives*; D006358:Hot Temperature; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry
chemical_list: D000588:Amines; D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA; D003857:Deoxyuridine
references.citation: Nucleic Acids Res. 1999 Apr 15;27(8):1802-9
references.pmid: 10101187
references.citation: Nucleosides Nucleotides. 1999 Mar;18(3):377-91
references.pmid: 10358942
references.citation: Bioorg Med Chem Lett. 2000 Jun 5;10(11):1299-302
references.pmid: 10866405
references.citation: Biochem Biophys Res Commun. 2000 May 27;272(1):64-74
references.pmid: 10872804
references.citation: Nucleic Acids Res. 2000 Sep 1;28(17):3316-22
references.pmid: 10954600
references.citation: Nucleic Acids Res. 2001 Apr 1;29(7):1565-73
references.pmid: 11266559
references.citation: J Am Chem Soc. 2001 Feb 28;123(8):1556-63
references.pmid: 11456753
references.citation: J Am Chem Soc. 1999;121(42):9781-9
references.pmid: 11543572
references.citation: Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):1113-5
references.pmid: 11562967
references.citation: Nucleosides Nucleotides Nucleic Acids. 2001 Apr-Jul;20(4-7):1421-4
references.pmid: 11563035
references.citation: Chem Biol. 2001 Oct;8(10):967-80
references.pmid: 11590021
references.citation: Org Lett. 2001 Dec 13;3(25):3983-6
references.pmid: 11735565
references.citation: Biochemistry. 2002 Jun 11;41(23):7224-31
references.pmid: 12044153
references.citation: J Am Chem Soc. 2002 Jul 24;124(29):8553-60
references.pmid: 12121096
references.citation: J Am Chem Soc. 2002 Aug 28;124(34):9960-1
references.pmid: 12188639
references.citation: Biopolymers. 2002 Nov 5;65(3):173-9
references.pmid: 12228922
references.citation: Bioconjug Chem. 2003 Sep-Oct;14(5):919-26
references.pmid: 13129394
references.citation: Org Lett. 2004 Feb 19;6(4):489-92
references.pmid: 14961605
references.citation: Bioorg Med Chem. 2004 Mar 1;12(5):1111-20
references.pmid: 14980623
references.citation: J Biomol Struct Dyn. 1987 Feb;4(4):621-49
references.pmid: 2856025
references.citation: Angew Chem Int Ed Engl. 1998 Nov 2;37(20):2872-2875
references.pmid: 29711104
references.citation: Nucleic Acids Res. 1988 May 11;16(9):4077-95
references.pmid: 3375076
references.citation: Nucleic Acids Res. 1994 Jul 25;22(14):2817-22
references.pmid: 7519769
references.citation: Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9515-20
references.pmid: 8790362
references.citation: Chem Biol. 1996 Aug;3(8):671-8
references.pmid: 8807901
references.citation: Biochemistry. 1997 May 20;36(20):6024-32
references.pmid: 9166773
references.citation: Biochemistry. 1998 Apr 28;37(17):5820-30
references.pmid: 9558315
references.citation: Nucleic Acids Res. 1998 Jul 1;26(13):3127-35
references.pmid: 9628909
references.citation: Biochemistry. 1998 Oct 27;37(43):15188-98
references.pmid: 9790683