Dai, J, Chen, D, Jones, RA, Hurley, LH and Yang, D. NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res 34: 5133-5144

College of Pharmacy, The University of Arizona, 1703 E. Mabel Street, Tucson, AZ 85721, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2006; 34(18):5133-44. DOI: 10.1093/nar/gkl610
Source: PubMed


BCL2 protein functions as an inhibitor of cell apoptosis and has been found to be aberrantly expressed in a wide range of
human diseases. A highly GC-rich region upstream of the P1 promoter plays an important role in the transcriptional regulation
of BCL2. Here we report the NMR solution structure of the major intramolecular G-quadruplex formed on the G-rich strand of
this region in K+ solution. This well-defined mixed parallel/antiparallel-stranded G-quadruplex structure contains three G-tetrads of mixed
G-arrangements, which are connected with two lateral loops and one side loop, and four grooves of different widths. The three
loops interact with the core G-tetrads in a specific way that defines and stabilizes the overall G-quadruplex structure. The
loop conformations are in accord with the experimental mutation and footprinting data. The first 3-nt loop adopts a lateral
loop conformation and appears to determine the overall folding of the BCL2 G-quadruplex. The third 1-nt double-chain-reversal
loop defines another example of a stable parallel-stranded structural motif using the G3NG3 sequence. Significantly, the distinct major BCL2 promoter G-quadruplex structure suggests that it can be specifically involved
in gene modulation and can be an attractive target for pathway-specific drug design.

Download full-text


Available from: Danzhou Yang, Jul 06, 2014
17 Reads
  • Source
    • "Introduction G-quadruplex DNA is a higher order structure of the G-rich nucleic acid assembly that is held together by Hoogsteen type hydrogen (H) bonds and stabilized by monovalent cation, which is distributed at the ends of eukaryotic chromosomes and the promoter regions such as c-MYC, c-KIT, k-RAS, and BCL-2 (Cogoi & Xodo, 2006; Dai, Chen, Jones, Hurley, & Yang, 2006; Phan, Kuryavyi, Burge, Neidle, & Patel, 2007; Rankin et al., 2005; Siddiqui-Jain, Grand, Bearss, & Hurley, 2002; Simonsson, Pecinka, & Kubista, 1998). Quadruplex structures may also be involved in translation process as indicated by its potential existence in messenger RNAs (Kolomietsa, Zarudnayaa, Potyahaylo, & Hovorun, 2015; Zarudnaya, Kolomiets, Potyahaylo, & Hovorun, 2003; Zarudnaya, Potyahaylo, Kolomiets, & Hovorun, 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: A series of cationic porphyrin-anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions, have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamic simulations. Three types of DNA G-quadruplexes were utilized, which comprise of parallel, antiparallel, and mixed-hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in antiparallel due to the presence of diagonal and lateral loops that crowd G-quartet. The binding to antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of total binding free energies that were calculated by using the MMPBSA method. Free energy analysis shows that the favorable contribution came from electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from van der Waals energy, which primarily contributed through end stacking interaction.
    Journal of biomolecular Structure & Dynamics 03/2015; DOI:10.1080/07391102.2015.1033015 · 2.92 Impact Factor
  • Source
    • "In this representation, a true Tm can be determined corresponding to the temperature at which half of the sample is folded and half is unfolded (Tm corresponded to θ = 0.5). Corresponding to the results of Dai and Dexheimer et al. [1-3], the CD spectra of Pu39WT displayed an absorption maximum at 264 nm and a minor shoulder at 295 nm, which inferred the formation of a single mixed hybrid G-quadruplex structure [13]. Only the CD amplitudes were smaller in the presence of 100 mM Na+ than 100 mM K+, which may reflect a decreased tetraplex population (Figure 1Ai). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background A 39-base-pair sequence (Pu39WT) located 58 to 19 base pairs upstream of the Bcl-2 P1 promoter has been implicated in the formation of an intramolecular mixed G-quadruplex structure and is believed to play a major role in the regulation of bcl-2 transcription. However, an extensive functional exploration requires further investigation. To further exploit the structure–function relationship of the Pu39WT-hemin DNAzyme, the secondary structure and peroxidase activity of the Pu39WT-hemin complex were investigated. Results Experimental results showed that when Pu39WT was incubated with hemin, it formed a uniparallel G-quadruplex-hemin complex in K+ or Na+ solution, rather than a mixed hybrid without bound hemin. Also, Pu39WT-hemin showed peroxidase activity (ABTS2−) in the presence of H2O2 to produce the colored radical anion (ABTS•-), which could then be used to determine the parameters governing the catalytic efficiency and reveal the peroxidase activity of the Pu39WT-hemin DNAzyme. Conclusions These results demonstrate the general peroxidase activity of Pu39WT-hemin DNAzyme, which is an intramolecular parallel G-quadruplex structure. This peroxidase activity of hemin complexed with the G-quadruplex-forming sequence in the Bcl-2 gene promoter may imply a potential mechanism of hemin-mediated cellular injury.
    Chemistry Central Journal 09/2014; 8(1):43. DOI:10.1186/1752-153X-8-43 · 2.19 Impact Factor
  • Source
    • "The P1 promoter, from which 90 to 95% of transcripts initiate [9], appears to be the primary driving force that regulates Bcl-2 transcription. Many transcription factors, including SP1, WT1, E2F, NGF, and IGF, bind to this region, indicating the importance for P1 promoter regulation [10]. The P1 promoter, especially the region upstream of the translation initiation site, is highly GC-rich [11], and the sequence within this region may tend to form G-quadruplex, a special secondary structure mediated by Hoogsteen hydrogen bonding [12] [13]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background: A new G-quadruplex structure located in the B-cell CLL/Iymphoma 2 (Bcl-2) P1 promoter and its physiological function related to Bcl-2 transcription have been studied to find a potential anticancer therapeutic target. Methods: Absorption, polyacrylamide gel electrophoresis, fluorescence, circular dichroism, and nuclear magnetic resonance spectra have been employed to determine G-quadruplex structure and the interaction between G-quadruplex and phenanthrolin-dicarboxylate. Real time polymerase chain reaction and luciferase assay were done to assess the physiological function of the G-quadruplex structure. Results: The UV-melting and polyactylamide gel electrophoresis studies show that the p32 DNA sequence forms an intramolecular G-quadruplex structure. Circular dichroism and nuclear magnetic resonance spectra indicate that the G-quadruplex is a hybrid-type structure with four G-tetrads. Fluorescence spectra show that a phenanthroline derivative has a higher binding affinity for p32 G-quadruplex than duplex. Further circular dichroism and nuclear magnetic resonance studies indicate that the phenanthroline derivative can regulate p32 G-quadruplex conformation. Real time polymerase chain reaction and luciferase assays show that the phenanthroline derivative has down-modulated Bcl-2 transcription activity in a concentration-dependent manner. However, no such effect was observed when p32 G-quadruplex was denatured through base mutation. Conclusion: The newly identified G-quadruplex located in the P1 promoter of Bcl-2 oncogene is intimately related with Bcl-2 transcription activity, which may be a promising anticancer therapeutic target. General significance: The newly identified G-quadruplex in the Bcl-2 P1 promoter may be a novel anticancer therapeutic target.
    Biochimica et Biophysica Acta (BBA) - General Subjects 07/2014; 1840(10). DOI:10.1016/j.bbagen.2014.07.014 · 4.38 Impact Factor
Show more