title: NMR solution structures of clustered abasic site lesions in DNA: structural differences between 3'-staggered (-3) and 5'-staggered (+3) bistranded lesions.
abstract: Ionizing radiation produces a distinctive pattern of bistranded clustered lesions in DNA. A relatively low number of clustered lesions may be lethal to cells when compared to a larger number of single lesions. Enzyme cleavage experiments suggest that the orientation of bistranded lesions causes differential recognition and removal of these lesions. Like that of a previous study of bistranded abasic site lesion [Hazel, R. D., Tian, K., and de los Santos, C. (2008) Biochemistry 47, 11909-11919], the aim of this investigation was to determine the structures of two DNA duplexes each containing two synthetic apurinic/apyrimidinic (AP) residues, positioned on opposite strands and separated by two base pairs. In the first duplex, the AP residues are staggered in the 3' orientation [-3 duplex, (AP)(2)-3 duplex], while in the second duplex, the AP residues are staggered in the 5' orientation [+3 duplex, (AP)(2)+3 duplex]. NOESY spectra recorded in 100 and 10% D(2)O buffer solutions allowed the assignment of the nonexchangeable and exchangeable protons, respectively, for each duplex. Cross-peak connectivity in the nonexchangeable proton spectra indicates that the duplex is a regular right-handed helix with the AP residues and orphan bases located inside the duplexes. The exchangeable proton spectra establish the formation of Watson-Crick G·C alignment for the two base pairs between the lesion sites in both duplexes. Distance-restrained molecular dynamics simulation confirmed the intrahelical orientations of the AP residues. The proximity of the AP residues across the minor groove of the -3 duplex and across the major groove in the +3 duplex is similar to their locations in the case of -1 and +1 clusters. This difference in structure may be a key factor in the differential recognition of bistranded AP lesions by human AP endonuclease.
authors.affiliation: Department of Physiology and Biophysics, Stony Brook University, School of Medicine, Stony Brook, NY 11794-8651, USA.
authors.forename: Raphael D
authors.initials: RD
authors.lastname: Hazel
authors.forename: Carlos
authors.initials: C
authors.lastname: de los Santos
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA; C085108:APEX1 protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase
references.citation: J Biol Chem. 1997 Jun 20;272(25):15650-5
references.pmid: 9188454
references.citation: J Biomol Struct Dyn. 1987 Feb;4(4):621-49
references.pmid: 2856025
references.citation: J Mol Biol. 1983 Dec 15;171(3):319-36
references.pmid: 6317867
references.citation: J Mol Biol. 2001 Apr 27;308(2):341-52
references.pmid: 11327771
references.citation: Eur J Biochem. 1988 Dec 1;178(1):1-38
references.pmid: 3060357
references.citation: Biochemistry. 1997 Sep 30;36(39):11629-39
references.pmid: 9305952
references.citation: Nucleic Acids Res. 2004 Oct 19;32(18):5609-20
references.pmid: 15494449
references.citation: Biochemistry. 2000 Jul 11;39(27):8026-31
references.pmid: 10891084
references.citation: Biochemistry. 2002 Jan 15;41(2):634-42
references.pmid: 11781104
references.citation: Radiat Res. 2001 Nov;156(5 Pt 2):584-9
references.pmid: 11604076
references.citation: Nucleic Acids Res. 1987 Oct 12;15(19):8003-22
references.pmid: 3671070
references.citation: Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):103-8
references.pmid: 10618378
references.citation: Nature. 2000 Jan 27;403(6768):451-6
references.pmid: 10667800
references.citation: Biochemistry. 1989 Jan 10;28(1):294-303
references.pmid: 2706253
references.citation: J Biomol Struct Dyn. 1988 Aug;6(1):63-91
references.pmid: 2482765
references.citation: J Biol Chem. 1987 Jul 25;262(21):10171-9
references.pmid: 2440861
references.citation: J Mol Biol. 2001 Apr 6;307(4):1023-34
references.pmid: 11286553
references.citation: FEBS Lett. 1991 Apr 9;281(1-2):9-19
references.pmid: 1849843
references.citation: Biochemistry. 1989 Apr 18;28(8):3373-83
references.pmid: 2545258
references.citation: EMBO J. 1997 Nov 3;16(21):6548-58
references.pmid: 9351835
references.citation: Biochemistry. 1988 Feb 9;27(3):924-31
references.pmid: 3259144
references.citation: Biochemistry. 2008 Nov 18;47(46):11909-19
references.pmid: 18950195
references.citation: J Biomol Struct Dyn. 1989 Feb;6(4):655-67
references.pmid: 2619933
references.citation: Prog Nucleic Acid Res Mol Biol. 1988;35:95-125
references.pmid: 3065826
references.citation: J Mol Biol. 1995 Jun 23;249(5):914-22
references.pmid: 7791217
references.citation: J Biol Chem. 1998 Jun 19;273(25):15565-73
references.pmid: 9624147
references.citation: J Mol Biol. 1999 Jul 16;290(3):667-84
references.pmid: 10395822