Publications

2024

• Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter
  
  • de Rache Aurore
  • Marquevielle Julien
  • Bouaziz Serge
  • Vialet Brune
  • Andreola Marie-Line
  • Mergny Jean-Louis
  • Amrane Samir
  Journal of Molecular Biology, Elsevier, 2024, 436 (2), pp.168359. Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacked on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reac- tivation or viral latency. (10.1016/j.jmb.2023.168359)
  DOI : 10.1016/j.jmb.2023.168359
• The control of nitric oxide dynamics and interaction with substituted zinc-phthalocyanines
  
  • Ben Brahim Nassim
  • Touaiti Sarra
  • Sellés Julien
  • Lambry Jean-Christophe
  • Negrerie Michel
  Dalton Transactions, Royal Society of Chemistry, 2024, 53 (2), pp.772-780. Phthalocyanines are artificial macrocycles that can harbour a central metal atom with four symmetric coordinations. Similar to metal-porphyrins, metal-phthalocyanines (M-PCs) may bind small molecules, especially diatomic gases such as NO and O2. Furthermore, various chemical chains can be grafted at the periphery of the M-PC macrocycle, which can change its properties, including the interaction with diatomic gases. In this study, we synthesized Zn-PCs with two different substituents and investigated their effects on the interaction and dynamics of nitric oxide (NO). Time-resolved absorption spectroscopy from picosecond to millisecond revealed that NO dynamics dramatically depends on the nature of the groups grafted to the Zn-PC macrocycle. These experimental results were rationalized by DFT calculations, which demonstrate that electrostatic interactions between NO and the quinoleinoxy substituent modify the potential energy surface and decrease the energy barrier for NO recombination, thus controlling its affinity. (10.1039/d3dt03356b)
  DOI : 10.1039/d3dt03356b
• Arginine-Modified Hemin Enhances G-Quadruplex DNAzyme Peroxidase Activity for High Sensitivity Detection
  
  • Liu Bin
  • Wang Tian
  • Qiu Dehui
  • Yan Xinrong
  • Liu Yuan
  • Mergny Jean-Louis
  • Zhang Xiaobo
  • Monchaud David
  • Ju Huangxian
  • Zhou Jun
  Analytical Chemistry, American Chemical Society, 2024, 96 (36), pp.14590-14597. Hemin/G-quadruplex (hG4) complexes are frequently used as artificial peroxidase-like enzymatic systems (referred to as G4 DNAzymes) in many biosensing applications, in spite of a rather low efficiency, notably in terms of detection limits. To tackle this issue, we report herein on a strategy in which hemin is chemically modified with the amino acids found in the active site of parent horseradish peroxidase (HRP), in the aim of recreating an environment conducive to a high catalytic activity. When hemin conjugated with a single arginine, it associates with G4 to create an arginine-hemin/G4 (R-hG4) DNAzyme that exhibits improved catalytic performances, characterized by kinetic analysis and DFT calculations. The practical relevance of this system was demonstrated with the implementation of biosensing assays enabling the chemiluminescent detection of G4-containing DNA and colorimetry detection of FEN1 enzyme with a high efficiency and sensitivity. Our results thus provide a guide for future enzyme engineering campaigns to create ever more efficient peroxidase-mimicking DNA-based systems. (10.1021/acs.analchem.4c03013)
  DOI : 10.1021/acs.analchem.4c03013
• Broadband rapid-scanning phase-modulated Fourier transform electronic spectroscopy
  
  • Javed Ariba
  • Lüttig Julian
  • Sanders Stephanie
  • Sessa Francesco
  • Gardiner Alastair
  • Joffre Manuel
  • Ogilvie Jennifer
  Optics Express, Optical Society of America - OSA Publishing, 2024, 32 (16), pp.28035. We present a phase-modulated approach for ultrabroadband Fourier transform electronic spectroscopy. To overcome the bandwidth limitations and spatial chirp introduced by acousto-optic modulators (AOMs), pulses from a 1 µm laser are modulated using AOMs prior to continuum generation. This phase modulation is transferred to the continuum generated in a yttrium aluminum garnet crystal. Separately generated phase-modulated continua in two arms of a Mach-Zehnder interferometer interfere with the difference of their modulation frequencies, enabling physical under-sampling of the signal and the suppression of low-frequency noise. By interferometrically tracking the relative time delay of the continua, we perform continuous, rapid-scanning Fourier transform electronic spectroscopy with a high signal-to-noise ratio and spectral resolution. As proof of principle, we measure the linear absorption and fluorescence excitation spectra of a laser dye and various biological samples. (10.1364/OE.530991)
  DOI : 10.1364/OE.530991