BACKGROUND: The breast and ovarian cancer susceptibility gene BRCA1 encodes a multifunctional tumor suppressor protein BRCA1, which is involved in regulating cellular processes such as cell cycle, transcription, DNA repair, DNA damage response and chromatin remodeling. BRCA1 protein, located primarily in cell nuclei, interacts with multiple proteins and various DNA targets. It has been demonstrated that BRCA1 protein binds to damaged DNA and plays a role in the transcriptional regulation of downstream target genes. As a key protein in the repair of DNA double-strand breaks, the BRCA1-DNA binding properties, however, have not been reported in detail. RESULTS: In this study, we provided detailed analyses of BRCA1 protein (DNA-binding domain, amino acid residues 444-1057) binding to topologically constrained non-B DNA structures (e.g. cruciform, triplex and quadruplex). Using electrophoretic retardation assay, atomic force microscopy and DNA binding competition assay, we showed the greatest preference of the BRCA1 DNA-binding domain to cruciform structure, followed by DNA quadruplex, with the weakest affinity to double stranded B-DNA and single stranded DNA. While preference of the BRCA1 protein to cruciform structures has been reported previously, our observations demonstrated for the first time a preferential binding of the BRCA1 protein also to triplex and quadruplex DNAs, including its visualization by atomic force microscopy. CONCLUSIONS: Our discovery highlights a direct BRCA1 protein interaction with DNA. When compared to double stranded DNA, such a strong preference of the BRCA1 protein to cruciform and quadruplex structures suggests its importance in biology and may thus shed insight into the role of these interactions in cell regulation and maintenance.

Institute of Biophysics Academy of Sciences of the Czech Republic v v i Královopolská 135 612 65 Brno Czech Republic

School of Medicine University of Queensland Brisbane 4006 Australia

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Rosen EM. BRCA1 in the DNA damage response and at telomeres. Front Genet. 2013;4:85. doi: 10.3389/fgene.2013.00085. PubMed DOI PMC

Tu Z, Aird KM, Zhang R. Chromatin remodeling, BRCA1, SAHF and cellular senescence. Cell Cycle. 2013;12(11):1653–1654. doi: 10.4161/cc.24986. PubMed DOI PMC

Xu Y, Price BD. Chromatin dynamics and the repair of DNA double strand breaks. Cell Cycle. 2011;10(2):261–267. doi: 10.4161/cc.10.2.14543. PubMed DOI PMC

Wu J, Lu LY, Yu X. The role of BRCA1 in DNA damage response. Protein Cell. 2010;1(2):117–123. doi: 10.1007/s13238-010-0010-5. PubMed DOI PMC

Mark WY, Liao JC, Lu Y, Ayed A, Laister R, Szymczyna B, Chakrabartty A, Arrowsmith CH. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? J Mol Biol. 2005;345(2):275–287. doi: 10.1016/j.jmb.2004.10.045. PubMed DOI

Kennedy RD, Gorski JJ, Quinn JE, Stewart GE, James CR, Moore S, Mulligan K, Emberley ED, Lioe TF, Morrison PJ, et al. BRCA1 and c-Myc associate to transcriptionally repress psoriasin, a DNA damage-inducible gene. Cancer Res. 2005;65(22):10265–10272. doi: 10.1158/0008-5472.CAN-05-1841. PubMed DOI

Paull TT, Cortez D, Bowers B, Elledge SJ, Gellert M. Direct DNA binding by Brca1. Proc Natl Acad Sci USA. 2001;98(11):6086–6091. doi: 10.1073/pnas.111125998. PubMed DOI PMC

Parvin JD. BRCA1 at a branch point. Proc Natl Acad Sci USA. 2001;98(11):5952–5954. doi: 10.1073/pnas.121184998. PubMed DOI PMC

Brazda V, Jagelska EB, Liao JC, Arrowsmith CH. The central region of BRCA1 binds preferentially to supercoiled DNA. J Biomol Struct Dyn. 2009;27(1):97–104. doi: 10.1080/07391102.2009.10507299. PubMed DOI

Smith GR. Meeting DNA palindromes head-to-head. Genes Dev. 2008;22(19):2612–2620. doi: 10.1101/gad.1724708. PubMed DOI PMC

Palecek E. Local supercoil-stabilized DNA structures. Crit Rev Biochem Mol Biol. 1991;26(2):151–226. doi: 10.3109/10409239109081126. PubMed DOI

van Holde K, Zlatanova J. Unusual DNA structures, chromatin and transcription. Bioessays. 1994;16(1):59–68. doi: 10.1002/bies.950160110. PubMed DOI

Zlatanova J, van Holde K. Binding to four-way junction DNA: a common property of architectural proteins? Faseb J. 1998;12(6):421–431. PubMed

Gonzalez V, Guo K, Hurley L, Sun D. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein. J Biol Chem. 2009;284(35):23622–23635. doi: 10.1074/jbc.M109.018028. PubMed DOI PMC

Compton SA, Tolun G, Kamath-Loeb AS, Loeb LA, Griffith JD. The Werner syndrome protein binds replication fork and holliday junction DNAs as an oligomer. J Biol Chem. 2008;283(36):24478–24483. doi: 10.1074/jbc.M803370200. PubMed DOI PMC

Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H. Escherichia coli RuvC protein is an endonuclease that resolves the holliday structure. EMBO J. 1991;10(13):4381–4389. PubMed PMC

Kim E, Deppert W. The complex interactions of p53 with target DNA: we learn as we go. Biochem Cell Biol. 2003;81(3):141–150. doi: 10.1139/o03-046. PubMed DOI

Zannis-Hadjopoulos M, Frappier L, Khoury M, Price GB. Effect of anti-cruciform DNA monoclonal antibodies on DNA replication. EMBO J. 1988;7(6):1837–1844. PubMed PMC

Zannis-Hadjopoulos M, Sibani S, Price GB. Eucaryotic replication origin binding proteins. Front Biosci. 2004;9:2133–2143. doi: 10.2741/1369. PubMed DOI

Brazda V, Laister RC, Jagelska EB, Arrowsmith C. Cruciform structures are a common DNA feature important for regulating biological processes. BMC Mol Biol. 2011;12:33. doi: 10.1186/1471-2199-12-33. PubMed DOI PMC

Jagelska EB, Pivonkova H, Fojta M, Brazda V. The potential of the cruciform structure formation as an important factor influencing p53 sequence-specific binding to natural DNA targets. Biochem Biophys Res Commun. 2010;391(3):1409–1414. doi: 10.1016/j.bbrc.2009.12.076. PubMed DOI

Coufal J, Jagelska EB, Liao JC, Brazda V. Preferential binding of p53 tumor suppressor to p21 promoter sites that contain inverted repeats capable of forming cruciform structure. Biochem Biophys Res Commun. 2013;441(1):83–88. doi: 10.1016/j.bbrc.2013.10.015. PubMed DOI

Naseem R, Webb M. Analysis of the DNA binding activity of BRCA1 and its modulation by the tumour suppressor p53. PLoS ONE. 2008;3(6):e2336. doi: 10.1371/journal.pone.0002336. PubMed DOI PMC

Klysik J. Cruciform extrusion facilitates intramolecular triplex formation between distal oligopurine.oligopyrimidine tracts: long range effects. J Biol Chem. 1992;267(24):17430–17437. PubMed

Frank-Kamenetskii M. DNA structure. The turn of the quadruplex? Nature. 1989;342(6251):737. doi: 10.1038/342737a0. PubMed DOI

Hershman SG, Chen Q, Lee JY, Kozak ML, Yue P, Wang LS, Johnson FB. Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Res. 2008;36(1):144–156. doi: 10.1093/nar/gkm986. PubMed DOI PMC

Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem. 2013;5(3):182–186. doi: 10.1038/nchem.1548. PubMed DOI PMC

Huppert JL. Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chem Soc Rev. 2008;37(7):1375–1384. doi: 10.1039/b702491f. PubMed DOI

Johnson JE, Smith JS, Kozak ML, Johnson FB. In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie. 2008;90(8):1250–1263. doi: 10.1016/j.biochi.2008.02.013. PubMed DOI PMC

Welcsh PL, Lee MK, Gonzalez-Hernandez RM, Black DJ, Mahadevappa M, Swisher EM, Warrington JA, King MC. BRCA1 transcriptionally regulates genes involved in breast tumorigenesis. Proc Natl Acad Sci USA. 2002;99(11):7560–7565. doi: 10.1073/pnas.062181799. PubMed DOI PMC

Naseem R, Sturdy A, Finch D, Jowitt T, Webb M. Mapping and conformational characterization of the DNA-binding region of the breast cancer susceptibility protein BRCA1. Biochem J. 2006;395(3):529–535. doi: 10.1042/BJ20051646. PubMed DOI PMC

Zhang N, Fan YH, Bi CF, Zuo J, Zhang PF, Zhang ZY, Zhu Z. Synthesis, crystal structure, and DNA interaction of magnesium(II) complexes with Schiff bases. J Coord Chem. 2013;66(11):1933–1944. doi: 10.1080/00958972.2013.796039. DOI

Kohwi Y, Kohwishigematsu T. Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc Natl Acad Sci USA. 1988;85(11):3781–3785. doi: 10.1073/pnas.85.11.3781. PubMed DOI PMC

Adhikari S, Toretsky JA, Yuan LS, Roy R. Magnesium, essential for base excision repair enzymes, inhibits substrate binding of N-methylpurine-DNA glycosylase. J Biol Chem. 2006;281(40):29525–29532. doi: 10.1074/jbc.M602673200. PubMed DOI

Frick DN, Banik S, Rypma RS. Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding. J Mol Biol. 2007;365(4):1017–1032. doi: 10.1016/j.jmb.2006.10.023. PubMed DOI PMC

Cameron IL, Smith NKR. Cellular concentration of magnesium and other ions in relation to protein-synthesis cell-proliferation and cancer. Magnesium. 1989;8(1):31–44. PubMed

Palecek E, Brazdova M, Cernocka H, Vlk D, Brazda V, Vojtesek B. Effect of transition metals on binding of p53 protein to supercoiled DNA and to consensus sequence in DNA fragments. Oncogene. 1999;18(24):3617–3625. doi: 10.1038/sj.onc.1202710. PubMed DOI

Coleman KA, Greenberg RA. The BRCA1-RAP80 complex regulates DNA repair mechanism utilization by restricting end resection. J Biol Chem. 2011;286(15):13669–13680. doi: 10.1074/jbc.M110.213728. PubMed DOI PMC

Moynahan ME, Chiu JW, Koller BH, Jasin M. Brca1 controls homology-directed DNA repair. Mol Cell. 1999;4(4):511–518. doi: 10.1016/S1097-2765(00)80202-6. PubMed DOI

Zhong Q, Chen CF, Chen PL, Lee WH. BRCA1 facilitates microhomology-mediated end joining of DNA double strand breaks. J Biol Chem. 2002;277(32):28641–28647. doi: 10.1074/jbc.M200748200. PubMed DOI

Cote AG, Lewis SM. Mus81-dependent double-strand DNA breaks at in vivo-generated cruciform structures in S. cerevisiae. Mol Cell. 2008;31(6):800–812. doi: 10.1016/j.molcel.2008.08.025. PubMed DOI

Balasubramanian S, Hurley LH, Neidle S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov. 2011;10(4):261–275. doi: 10.1038/nrd3428. PubMed DOI PMC

Brazda V, Haronikova L, Liao JC, Fojta M. DNA and RNA quadruplex-binding proteins. Int J Mol Sci. 2014;15(10):17493–17517. doi: 10.3390/ijms151017493. PubMed DOI PMC

Xiong J, Fan S, Meng Q, Schramm L, Wang C, Bouzahza B, Zhou J, Zafonte B, Goldberg ID, Haddad BR, et al. BRCA1 inhibition of telomerase activity in cultured cells. Mol Cell Biol. 2003;23(23):8668–8690. doi: 10.1128/MCB.23.23.8668-8690.2003. PubMed DOI PMC

Ballal RD, Saha T, Fan S, Haddad BR, Rosen EM. BRCA1 localization to the telomere and its loss from the telomere in response to DNA damage. J Biol Chem. 2009;284(52):36083–36098. doi: 10.1074/jbc.M109.025825. PubMed DOI PMC

Pooley KA, McGuffog L, Barrowdale D, Frost D, Ellis SD, Fineberg E, Platte R, Izatt L, Adlard J, Bardwell J, et al. Lymphocyte telomere length is long in BRCA1 and BRCA2 mutation carriers regardless of cancer-affected status. Cancer Epidemiol Biomarkers Prev. 2014;23(6):1018–1024. doi: 10.1158/1055-9965.EPI-13-0635-T. PubMed DOI PMC

Staff S, Isola J, Tanner M. Haplo-insufficiency of BRCA1 in sporadic breast cancer. Cancer Res. 2003;63(16):4978–4983. PubMed

Jagelska EB, Brazda V, Pecinka P, Palecek E, Fojta M. DNA topology influences p53 sequence-specific DNA binding through structural transitions within the target sites. Biochem J. 2008;412(1):57–63. doi: 10.1042/BJ20071648. PubMed DOI

Simonsson T, Pecinka P, Kubista M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 1998;26(5):1167–1172. doi: 10.1093/nar/26.5.1167. PubMed DOI PMC

Necas D, Klapetek P. Gwyddion: an open-source software for SPM data analysis. Cent Eur J Phys. 2012;10(1):181–188.

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids