Strong preference of BRCA1 protein to topologically constrained non-B DNA structures
© The Author(s) 2016
Received: 12 August 2015
Accepted: 30 May 2016
Published: 8 June 2016
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.
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.
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.
KeywordsBRCA1 protein DNA binding Protein-DNA complex
The BRCA1 protein is encoded by the tumor suppressor gene BRCA1, mutation in which occurs often in breast and ovarian cancer patients . This multifunctional protein plays critical roles in different cellular pathways including cell cycle, transcription, DNA repair, DNA damage response and chromatin remodeling [2–4]. BRCA1 is a large phosphoprotein of 1863 amino acid residues (aa) and it is located primarily in cell nuclei. One of the key functions of BRCA1 protein is its ability to modulate multiple protein–protein and protein-DNA interactions. Despite the enormous molecular weight of BRCA1 protein, only two small conserved domains have been identified: ring finger motif (RING) at the N-terminus and two tandem BRCT repeats at the C-terminus. The central region of BRCA1 protein is largely unfolded, but it has been demonstrated to act as a scaffold to interacts directly with proteins and DNA . It was determined that BRCA1 protein binds also to damaged DNA and regulates downstream target genes transcriptionally . Moreover, previous studies have shown preferential binding of BRCA1 to cruciform , branch point  and superhelical  DNAs, highlighting the important relationship of BRCA1 protein with non-B DNA structures.
Non-B DNA structures are present in all living organisms  and are constantly been remodeled during processes such as DNA replication, transcription and repair. Local nucleotide sequence-dependent conformational changes, which give rise to cruciform, left-handed DNA, triplex and quadruplex structures, could all be stabilized further by negative supercoiling [11–13]. These non-B DNA structures can be recognized and stabilized also by various proteins, resulting in modulation of transcription , replication , junction resolving  and chromatin remodeling . Cruciform structure, which originates from inverted repeats of variable length, plays key roles in replication and transcription [18, 19] and is a target for many essential proteins  including the human tumor suppressor proteins p53 [21, 22] and BRCA1 . Triplex DNA, consisting of Watson–Crick and Hoogsten base-pairing, is formed by mirror repeats of homupurine-homopyrimidine sequences . G-quadruplex DNA, as the name implies, arises from a G-rich sequence and forms a four-stranded structure through Hoogsteen base-pairing . G-quadruplex structures were first characterized in vitro, but have nowadays been shown to exist in vivo using G-quadruplex stabilizing compounds  and specific G-quadruplex antibody . The increased interest in G-quadruplexes stems from the high abundance of potential G-quadruplex-forming sequences in both eukaryotic and prokaryotic genomes (for reviews see ref: [28, 29]). In addition, the prevalence of G-quadruplexes in promoter regions and telomeres further reveals the significance of such structures in the genome.
It has been illustrated by microarray analysis that BRCA1 protein regulates the expression of a broad variety of genes . Although upregulation of BRCA1 protein leads to drastic changes in transcription of gene targets, the mechanism remains unclear. Several studies have shown that the central region of BRCA1 is capable of interacting with DNA including short double-stranded oligonucleotide and long supercoiled DNA [7, 9, 23]. Additional findings further revealed BRCA1 protein’s selectivity for four-way junction DNA over linear duplex DNA [23, 31]. It is therefore likely that BRCA1 exerts its regulation by been able to recognize and bind DNA targets with different conformations directly.
Here we analyzed the binding of BRCA1 protein to various DNA targets with B- and non B-DNA conformations. Using gel shift assay, magnetic beads immunoprecipitation and atomic force microscopy (AFM), we demonstrated a strong preference of the central region (aa 444–1057) of the BRCA1 protein to non-B DNA structures, especially to cruciform and quadruplex DNA structures. Our findings further pointed to BRCA1 protein’s potential in regulating cellular processes by its direct interaction with DNA structures broadly present in the genomic DNA.
BRCA1-L protein binds to different DNA targets
Preferential binding of BRCA1-L protein to non-B DNA structures in short oligonucleotides on PAGE gel
To determine the preference of BRCA1-L protein to different non-B DNA structures, competition assay was performed. BRCA1-L protein was bound to FAM-labeled CF structure oligonucleotides with and without different competitor non-labeled DNAs (Fig. 2). Only a small decrease in retarded band intensity was observed with high concentrations of SS competitor DNA, while a stronger decrease was seen with lower concentrations of quadruplex competitor DNA (Fig. 2a). Using the same approach, we tested also competition of BRCA1-L/CF complex by DS and CF competitor DNAs. The change in intensity of retarded bands was analyzed by densitometry (Fig. 2b). SS and DS DNAs were weak binding targets for BRCA1-L protein compare to cruciform and quadruplex DNAs. Even 20-fold molar excess of SS or DS B-DNA competitor was not able to compete with BRCA1-L complex with cruciform structure (Fig. 2b, SS-black column, DS-dashed column). The strongest BRCA1-L-binding partner was cruciform structure (Fig. 2b, speckle column) followed by quadruplex oligonucleotide (Fig. 2b, grey column). While fivefold excess of SS or DS competitor DNA decreased retarded band intensity by approximately 30 %, cruciform and quadruplex competitor DNAs decreased retarded band intensity by around 90 and 72 %, respectively. Notably, a 20-fold surplus of CF and Q oligonucleotides led to completely ablation of retarded band intensity. Importantly, statistically significant difference (p < 0.05) between BRCA1-L binding to non-B DNA structures and DS was observed.
Proof of the presence of non-B DNA structures in plasmid DNAs by atomic force microscopy
Preferential binding of BRCA1-L protein to non-B DNA structures in long plasmid DNA
BRCA1 is a multifunctional protein implicated in many important biological processes. It is a potent tumor suppressor and plays a major role in DNA repair and homologous recombination. BRCA1 protein is the most mutated gene in hereditary breast and ovarian cancers. Its mutation not only increased the lifetime risk of breast cancer to 65 %, but also increased the risk of other cancer types including prostate cancer . It was shown that BRCA1 protein binds to DNA  and regulates transcription of specific proteins . Strong preference of BRCA1 protein for cruciform structure has been demonstrated previously via gel shift assay on agarose gels . It was also revealed that superhelical density could increase BRCA1 protein binding to DNA . In this study we compared the binding of BRCA1 protein to DS DNA and non-B DNA structures and visualized these interactions using AFM. We showed a strong preference of BRCA1 protein for other non-B DNA structures such as quadruplex and triplex DNAs. Formation of non-B DNA structures is highly dependent on ion conditions, protein interactions and superhelical density of DNA. Magnesium ions are required for triplex DNA formation in oligonucleotide DNA, but they simultaneously inhibited BRCA1-DNA binding. Interestingly, we observed BRCA1 protein binding to DNA structures in plasmid DNA where these structures are stabilized by DNA supercoiling. Our results thereby demonstrated that native superhelical density is sufficient for non-B DNA structure formation. Furthermore, an array of experimental methods, including chromatin immunoprecipitation, confocal microscopy and functional assays, have illustrated that these structures are presented broadly in cells, with epigenetic modification being a potential mechanism of complex cell regulation. The presence of the magnesium could be an important factor which enables the formation of different DNA structures in cells [32, 33]. It was demonstrated that magnesium stabilizes DNA structures and plays a role in many enzymes’ catalytic action . Even if the amount of magnesium in the cell is relatively high compare to other ions, the concentration of free magnesium is in fact low and most Mg2+ ions are bound to ATP, proteins and other cellular components . Moreover, overexposure to magnesium is toxic . It was also noted that bivalent ion influences the DNA binding of other protein greatly . It is likely that tight regulation of the magnesium in the cell allows optimal BRCA1 DNA binding in living cells.
It has been revealed that BRCA1 protein plays a key role in homology-directed repair of DNA double strand breaks [38, 39] and facilitates end joining of DNA breaks . Interestingly, certain local DNA structures could be the source of the DNA breaks . Local DNA structures are known to facilitate different cellular processes including telomere length regulation, transcriptional modification, DNA replication and other events of cell maintenance. Hence, BRCA1’s ability to interact with these structures could be essential for cell survival and regulation. Over the last couple of years, it has brought to attention that non-B DNA structures, especially quadruplexes, are critical for transcriptional regulation of different genes including c-Myc proto-oncogene . The presence of G-quadruplexes is also evident in many important gene promoters such as Kras, Kit and TERT  and a large number of proteins have been characterized with preferential binding to these quadruplexes . It was reported that BRCA1 protein regulates telomerase and 3′ overhang length of telomeres . Importantly, BRCA1 protein interacts directly with human telomeres. This is established by telomeric ChIP assay and confocal microscopy, showing co-localization of the BRCA1 protein with telomeric DNA in cultured cells . Recently it was observed that BRCA1 mutation carriers have longer telomeres than their non-mutation carriers . Moreover, BRCA1 is repeatedly absent or significantly decreased in sporadic breast cancer . Given BRCA1 protein’s newly identified role in telomere regulation , its preferential binding to quadruplex DNA may indicate an important role in processes that are associated with quadruplex formation in the genome.
It is well understood that BRCA1 protein binds to damaged DNA and plays a role in transcriptional regulation of downstream target genes. However, BRCA1-DNA binding properties to local DNA structures have not yet been reported in detail. Our study suggests a strong influence of non-B DNA structures on BRCA1-DNA interactions. These findings propose a novel perspective on the understanding of how BRCA1 protein regulates various tasks through direct interaction with DNA. The ability of BRCA1 protein to bind preferentially to topologically folded non-B DNA further hinted the value of these structures not only in transcriptional regulation, but also in processes leading to cancer development and senescence.
Synthetic oligonucleotides with and without FAM-3′-end labeling were purchased from IDT, Inc. The oligonucleotide sequences and annealing buffers of single-stranded, double-stranded, cruciform, triplex and quadruplex DNAs are described in Additional file 1: Figure S3 (schema of DNA structures, Fig. 1a). Complementary oligonucleotides were annealed by incubation at 95 °C for 5 min with subsequent cooling to 4 °C at a rate of 1 °C/min. Oligonucleotide for quadruplex formation was incubated at room temperature for 16 h.
Supercoiled plasmid DNAs of pBluescript II SK (−), and derived plasmids pCFNO , pCMYC and pTA50 were isolated from bacterial strain DH5α as described in the QIAGEN protocol (QIAGEN GmbH, Germany). XhoI restriction enzyme (New England Biolabs, UK) was used for linearization of plasmids. pCMYC plasmid was constructed by cloning the 141 bp EcoRI/HindIII restriction fragment of pNHE plasmid  into the EcoRI/HindIII site of pBSK. pTA50 plasmid was constructed by cloning of (dT)50.(dA)50 sequence, forming a DNA triplex, into the EcoRV site of pBSK. Plasmids pCMYC and pTA50 were kindly provided by Dr. Marie Brazdova.
BRCA1 protein constructs
The coding region for the central region of BRCA1 protein (BRCA1-A, aa 219–498 and BRCA1-L, aa 444–1057) was PCR amplified from human BRCA1 cDNA, subcloned into the pET15b expression vector (Novagen), expressed, and purified as described .
Gel electrophoretic mobility shift assays on polyacrylamide gels
Labeled oligonucleotides (5 pmol) and BRCA1 protein constructs were mixed at different molar ratios (1:0.5/1/2/4) in 20 μl of the DNA binding buffer (5 mM Tris–HCl, pH 7.0, 1 mM EDTA, 50 mM KCl and 0.01 % Triton X-100). Competition assay contains increasing amount of competitor DNA (5/10/25/50 pmol) with 5 pmol of labeled cruciform oligonucleotide and 5 pmol of BRCA1-L protein in 20 μl of the DNA binding buffer. The samples were incubated for 15 min at 4 °C and loaded onto an 8 % non-denaturating polyacrylamide gel containing 0.33× Trisborate-EDTA buffer. Electrophoresis was performed for 60 min at 100 V at 4 °C. The gels were visualized on a LAS-3000 image analyzer (Fujifilm) and processed digitally.
The relative intensity of the BRCA1-L/DNA complexes is presented as the percentage of the bands without competitor DNAs. Data were analyzed by non-parametric methods to avoid assumptions about the distribution of the measured variables. Comparisons between groups were made with the Mann–Whitney U test (Statistica software). All values are reported as mean ± SD. Statistical significance was considered to be indicated by a value of p < 0.05.
Proof of the non-B DNA structures in plasmids by S1 nuclease cleavage
2 µg of plasmid DNA was digested by S1 nuclease (New England Biolabs, UK; 2 U/μg DNA) for 2 h at 37 °C in the S1 nuclease buffer (30 mM sodium acetate pH 4.6, 280 mM NaCl, 1 mM·ZnSO4). After digestion, samples were precipitated in ethanol, dissolved in water and digested by ScaI (New England Biolabs, UK) for 1 h at 37 °C before separation by electrophoresis on 1 % agarose gel.
Atomic force microscopy
BRCA1-L protein and 200 ng of plasmid DNA were mixed in a molar ratio of 20:1 in the binding buffer [(50 mM KCl, 5 mM Tris, 0.05 mM EDTA, 0.01 % Triton X-100), final volume 10 μl] and incubated on ice for 15 min. AFM imaging was performed on Grade V4 mica discs (SPI supplies, USA). The DNA samples and protein-DNA complexes were deposited on mica in a buffer containing 5 mM Na-Hepes pH 7.5, 20 mM KCl, 10 mM MgCl2,10 mM Tris in the concentration of 1 ng/μl DNA and incubated for 5 min, followed by rinsing with deionized water and air-dried. The images were obtained using AFM/STM Multimode eight electrochemical system, (Veeco, USA), operating in ScanAsyst mode in room temperature in air. The cantilever SCANASYST-AIR (Bruker) had a nominal spring constant of 0.4 N/m and the nominal scanning rate was set as 1 Hz. Obtained images were then analyzed using Gwyddion software package .
Competition assay by immunoprecipitation on magnetic beads
Superhelical and linear plasmids were incubated with protein G-coated magnetic beads (Dynabeads) using immobilized BRCA1-L immune complex with the anti-BRCA1 polyclonal antibody (Abcam) in the binding buffer. The samples were shaken gently for 30 min at 10 °C and then washed 3 times with the binding buffer. The BRCA-L/DNA complexes were disrupted by incubation with 0.5 % SDS for 5 min at 65 °C. The samples were loaded on a 1 % agarose gel containing 1x TAE (Tris–acetate-EDTA) buffer (Fig. 5).
amino acid residues
atomic force microscopy
breast cancer-associated protein-1
really interesting new gene
VB conceived the study; LH performed gel shift and AFM analysis; EJ performed the proof of the non-B DNA structures; HF isolated protein and performed competition assay. All authors contributed to the study design and manuscript writing. All authors read and approved the final manuscript.
This work was supported by the Grant Agency of the Czech Republic (15-21855S).
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Rosen EM. BRCA1 in the DNA damage response and at telomeres. Front Genet. 2013;4:85.View ArticlePubMedPubMed CentralGoogle Scholar
- Tu Z, Aird KM, Zhang R. Chromatin remodeling, BRCA1, SAHF and cellular senescence. Cell Cycle. 2013;12(11):1653–4.View ArticlePubMedPubMed CentralGoogle Scholar
- Xu Y, Price BD. Chromatin dynamics and the repair of DNA double strand breaks. Cell Cycle. 2011;10(2):261–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Wu J, Lu LY, Yu X. The role of BRCA1 in DNA damage response. Protein Cell. 2010;1(2):117–23.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):275–87.View ArticlePubMedGoogle Scholar
- 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):10265–72.View ArticlePubMedGoogle Scholar
- Paull TT, Cortez D, Bowers B, Elledge SJ, Gellert M. Direct DNA binding by Brca1. Proc Natl Acad Sci USA. 2001;98(11):6086–91.View ArticlePubMedPubMed CentralGoogle Scholar
- Parvin JD. BRCA1 at a branch point. Proc Natl Acad Sci USA. 2001;98(11):5952–4.View ArticlePubMedPubMed CentralGoogle Scholar
- 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.View ArticlePubMedGoogle Scholar
- Smith GR. Meeting DNA palindromes head-to-head. Genes Dev. 2008;22(19):2612–20.View ArticlePubMedPubMed CentralGoogle Scholar
- Palecek E. Local supercoil-stabilized DNA structures. Crit Rev Biochem Mol Biol. 1991;26(2):151–226.View ArticlePubMedGoogle Scholar
- van Holde K, Zlatanova J. Unusual DNA structures, chromatin and transcription. Bioessays. 1994;16(1):59–68.View ArticlePubMedGoogle Scholar
- Zlatanova J, van Holde K. Binding to four-way junction DNA: a common property of architectural proteins? Faseb J. 1998;12(6):421–31.PubMedGoogle Scholar
- 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):23622–35.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):24478–83.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):4381–9.PubMedPubMed CentralGoogle Scholar
- Kim E, Deppert W. The complex interactions of p53 with target DNA: we learn as we go. Biochem Cell Biol. 2003;81(3):141–50.View ArticlePubMedGoogle Scholar
- Zannis-Hadjopoulos M, Frappier L, Khoury M, Price GB. Effect of anti-cruciform DNA monoclonal antibodies on DNA replication. EMBO J. 1988;7(6):1837–44.PubMedPubMed CentralGoogle Scholar
- Zannis-Hadjopoulos M, Sibani S, Price GB. Eucaryotic replication origin binding proteins. Front Biosci. 2004;9:2133–43.View ArticlePubMedGoogle Scholar
- 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.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):1409–14.View ArticlePubMedGoogle Scholar
- 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):83–8.View ArticlePubMedGoogle Scholar
- 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.View ArticlePubMedPubMed CentralGoogle Scholar
- Klysik J. Cruciform extrusion facilitates intramolecular triplex formation between distal oligopurine.oligopyrimidine tracts: long range effects. J Biol Chem. 1992;267(24):17430–7.PubMedGoogle Scholar
- Frank-Kamenetskii M. DNA structure. The turn of the quadruplex? Nature. 1989;342(6251):737.View ArticlePubMedGoogle Scholar
- 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):144–56.View ArticlePubMedGoogle Scholar
- Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem. 2013;5(3):182–6.View ArticlePubMedPubMed CentralGoogle Scholar
- Huppert JL. Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chem Soc Rev. 2008;37(7):1375–84.View ArticlePubMedGoogle Scholar
- 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):1250–63.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):7560–5.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):529–35.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):1933–44.View ArticleGoogle Scholar
- 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):3781–5.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):29525–32.View ArticlePubMedGoogle Scholar
- 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):1017–32.View ArticlePubMedGoogle Scholar
- 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.PubMedGoogle Scholar
- 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):3617–25.View ArticlePubMedGoogle Scholar
- Coleman KA, Greenberg RA. The BRCA1-RAP80 complex regulates DNA repair mechanism utilization by restricting end resection. J Biol Chem. 2011;286(15):13669–80.View ArticlePubMedPubMed CentralGoogle Scholar
- Moynahan ME, Chiu JW, Koller BH, Jasin M. Brca1 controls homology-directed DNA repair. Mol Cell. 1999;4(4):511–8.View ArticlePubMedGoogle Scholar
- 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):28641–7.View ArticlePubMedGoogle Scholar
- Cote AG, Lewis SM. Mus81-dependent double-strand DNA breaks at in vivo-generated cruciform structures in S. cerevisiae. Mol Cell. 2008;31(6):800–12.View ArticlePubMedGoogle Scholar
- Balasubramanian S, Hurley LH, Neidle S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov. 2011;10(4):261–75.View ArticlePubMedPubMed CentralGoogle Scholar
- Brazda V, Haronikova L, Liao JC, Fojta M. DNA and RNA quadruplex-binding proteins. Int J Mol Sci. 2014;15(10):17493–517.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):8668–90.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):36083–98.View ArticlePubMedPubMed CentralGoogle Scholar
- 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):1018–24.View ArticlePubMedPubMed CentralGoogle Scholar
- Staff S, Isola J, Tanner M. Haplo-insufficiency of BRCA1 in sporadic breast cancer. Cancer Res. 2003;63(16):4978–83.PubMedGoogle Scholar
- 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.View ArticlePubMedGoogle Scholar
- Simonsson T, Pecinka P, Kubista M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 1998;26(5):1167–72.View ArticlePubMedPubMed CentralGoogle Scholar
- Necas D, Klapetek P. Gwyddion: an open-source software for SPM data analysis. Cent Eur J Phys. 2012;10(1):181–8.Google Scholar