title: Structural properties of g,t-parallel duplexes.
abstract: The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.
authors.affiliation: Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Elena
authors.initials: E
authors.lastname: Cubero
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
references.citation: Bioorg Med Chem Lett. 2001 Jul 9;11(13):1761-3
references.pmid: 11425555
references.citation: J Biol Chem. 1998 Sep 18;273(38):24640-8
references.pmid: 9733760
references.citation: Biochemistry. 1998 Sep 15;37(37):12962-70
references.pmid: 9737876
references.citation: Annu Rev Biophys Biomol Struct. 1994;23:703-30
references.pmid: 7919797
references.citation: Curr Opin Struct Biol. 1996 Jun;6(3):327-33
references.pmid: 8804836
references.citation: Science. 1991 Jun 21;252(5013):1711-4
references.pmid: 1675488
references.citation: J Am Chem Soc. 2001 Dec 5;123(48):12018-25
references.pmid: 11724610
references.citation: Nucleic Acids Res. 2002 Jun 15;30(12):2609-19
references.pmid: 12060677
references.citation: Anal Bioanal Chem. 2008 Feb;390(4):989-1007
references.pmid: 17581746
references.citation: EMBO J. 1986 Sep;5(9):2341-2347
references.pmid: 16453705
references.citation: Science. 1988 Jul 29;241(4865):551-7
references.pmid: 3399890
references.citation: Nucleic Acids Res. 1999 May 1;27(9):1991-8
references.pmid: 10198432
references.citation: Biochemistry. 1996 Aug 20;35(33):10985-94
references.pmid: 8718892
references.citation: Nucleic Acids Res. 1995 Oct 25;23(20):4116-21
references.pmid: 7479074
references.citation: Nucleic Acids Res. 2000 Sep 15;28(18):3511-6
references.pmid: 10982870
references.citation: Biochemistry. 1996 Dec 3;35(48):15332-9
references.pmid: 8952484
references.citation: Nucleic Acids Res. 2001 Jun 15;29(12):2522-34
references.pmid: 11410660
references.citation: Biochemistry. 1993 Nov 9;32(44):11802-9
references.pmid: 8218251
references.citation: J Biotechnol. 2000 Mar;74(1):5-13
references.pmid: 10943568
references.citation: Biophys J. 2007 Jun 1;92(11):3817-29
references.pmid: 17351000
references.citation: Methods Enzymol. 1992;211:199-220
references.pmid: 1383673
references.citation: J Biomol Struct Dyn. 1999 Feb;16(4):845-62
references.pmid: 10217454
references.citation: J Am Chem Soc. 2002 Mar 27;124(12):3133-42
references.pmid: 11902902
references.citation: J Theor Biol. 2000 Sep 21;206(2):317-22
references.pmid: 10966769
references.citation: J Am Chem Soc. 2003 Dec 24;125(51):16127-38
references.pmid: 14678005
references.citation: J Mol Med (Berl). 1997 Apr;75(4):267-82
references.pmid: 9151213
references.citation: Nucleic Acids Res. 2000 Nov 15;28(22):4531-9
references.pmid: 11071942
references.citation: FEBS Lett. 1992 Feb 10;297(3):233-6
references.pmid: 1544402