scholarly journals Interactions Between Spermine-Derivatized Tentacle Porphyrins and The Human Telomeric DNA G-Quadruplex

2018 ◽  
Vol 19 (11) ◽  
pp. 3686 ◽  
Author(s):  
Navin Sabharwal ◽  
Jessica Chen ◽  
Joo Lee ◽  
Chiara Gangemi ◽  
Alessandro D'Urso ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Binding Constants ◽  
Spectroscopic Studies ◽  
Resonance Light Scattering ◽  
Binding Modes ◽  
Telomeric Dna ◽  
Binding Stoichiometry ◽  
G Quadruplex

G-rich DNA sequences have the potential to fold into non-canonical G-Quadruplex (GQ) structures implicated in aging and human diseases, notably cancers. Because stabilization of GQs at telomeres and oncogene promoters may prevent cancer, there is an interest in developing small molecules that selectively target GQs. Herein, we investigate the interactions of meso-tetrakis-(4-carboxysperminephenyl)porphyrin (TCPPSpm4) and its Zn(II) derivative (ZnTCPPSpm4) with human telomeric DNA (Tel22) via UV-Vis, circular dichroism (CD), and fluorescence spectroscopies, resonance light scattering (RLS), and fluorescence resonance energy transfer (FRET) assays. UV-Vis titrations reveal binding constants of 4.7 × 106 and 1.4 × 107 M−1 and binding stoichiometry of 2–4:1 and 10–12:1 for TCPPSpm4 and ZnTCPPSpm4, respectively. High stoichiometry is supported by the Job plot data, CD titrations, and RLS data. FRET melting indicates that TCPPSpm4 stabilizes Tel22 by 36 ± 2 °C at 7.5 eq., and that ZnTCPPSpm4 stabilizes Tel22 by 33 ± 2 °C at ~20 eq.; at least 8 eq. of ZnTCPPSpm4 are required to achieve significant stabilization of Tel22, in agreement with its high binding stoichiometry. FRET competition studies show that both porphyrins are mildly selective for human telomeric GQ vs duplex DNA. Spectroscopic studies, combined, point to end-stacking and porphyrin self-association as major binding modes. This work advances our understanding of ligand interactions with GQ DNA.

scholarly journals PhenQE8, a Novel Ligand of the Human Telomeric Quadruplex

2021 ◽  
Vol 22 (2) ◽  
pp. 749
Author(s):  
Patricia B. Gratal ◽  
Julia G. Quero ◽  
Adrián Pérez-Redondo ◽  
Zoila Gándara ◽  
Lourdes Gude
Keyword(s):  
Equilibrium Dialysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
The Novel ◽  
X Ray Diffraction ◽  
Telomeric Dna ◽  
Healthy Human ◽  
Quadruplex Dna ◽  
Step Procedure ◽  
G Quadruplex

A novel quadruplex ligand based on 1,10-phenanthroline and incorporating two guanyl hydrazone functionalities, PhenQE8, is reported herein. Synthetic access was gained in a two-step procedure with an overall yield of 61%. X-ray diffraction studies revealed that PhenQE8 can adopt an extended conformation that may be optimal to favor recognition of quadruplex DNA. DNA interactions with polymorphic G-quadruplex telomeric structures were studied by different techniques, such as Fluorescence resonance energy transfer (FRET) DNA melting assays, circular dichroism and equilibrium dialysis. Our results reveal that the novel ligand PhenQE8 can efficiently recognize the hybrid quadruplex structures of the human telomeric DNA, with high binding affinity and quadruplex/duplex selectivity. Moreover, the compound shows significant cytotoxic activity against a selected panel of cultured tumor cells (PC-3, HeLa and MCF-7), whereas its cytotoxicity is considerably lower in healthy human cells (HFF-1 and RPWE-1).

scholarly journals Spectroscopic Studies on the Interaction Between Novel Antiviral Drug Favipiravir and Serum Albumins

2020 ◽  
Vol 8 (2) ◽  
pp. 93-103
Author(s):  
Alla Yegorova ◽  
Yulia Scrypynets ◽  
Georgy Maltsev ◽  
Inna Leonenko ◽  
Valery Antonovich ◽  
...  
Keyword(s):  
Antiviral Drug ◽  
Resonance Energy Transfer ◽  
Fluorescence Emission ◽  
Resonance Energy ◽  
Binding Constants ◽  
Spectroscopic Studies ◽  
Excitation Wavelength ◽  
Serum Albumins ◽  
Different Temperatures

Under physiological conditions, in vitro interaction between favipiravir (FAV) and serum albumins (BSA/HSA) was investigated at excitation wavelength 280 nm and at different temperatures (298 K, 313 K) by fluorescence emission spectroscopy. The hydrogen bond, van der Waals forces and electrostatic interaction plays a major role in stabilizing the complex; the binding constants KA at different temperatures were calculated. The distance r between donor (BSA/HSA) and acceptor (FAV) was obtained according to fluorescence resonance energy transfer (1.55/1.90 nm for BSA/HSA-FAV systems). The effect of FAV on the conformation of BSA/HSA was analyzed using synchronous fluorescence spectroscopy and UV/vis absorption spectroscopy.

Design of metalloporphyrins fused to imidazolium rings for binding DNA G-quadruplexes

2020 ◽  
Vol 24 (01n03) ◽  
pp. 340-349
Author(s):  
Francesca Caporaletti ◽  
Jenifer Rubio-Magnieto ◽  
Mamadou Lo ◽  
Jean-François Longevial ◽  
Clémence Rose ◽  
...  
Keyword(s):  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Cd Spectroscopy ◽  
Synthesis And Characterization ◽  
Binding Modes ◽  
Telomeric Dna ◽  
Relative Stabilities ◽  
X Ray ◽  
Imidazolium Ring

Synthesis and characterization of nickel(II) meso-tetraarylporphyrins fused to imidazolium rings across [Formula: see text],[Formula: see text]-pyrrolic positions and X-ray structure of the porphyrin where two opposed pyrrole units are fused to an imidazolium ring are presented. The interactions between these mono-, bis-, tris- and tetrakis(imidazolium) porphyrins with human telomeric DNA G-quadruplexes (G4) were investigated using UV-vis absorption spectroscopy, Circular Dichroism (CD) spectroscopy and Fluorescence Resonance Energy Transfer (FRET) melting assay. Possible binding modes between cationic porphyrins and a selected G4 sequence (d[AG3(T2AG[Formula: see text]]), and relative stabilities of porphyrin/G4 complexes are discussed. Excepting porphyrins fused to one imidazolium ring, the other derivatives interact with G4 structures and their stabilization strongly depends on the porphyrin structure (number and localization of the imidazolium rings).

Towards Single-Molecule Diagnostics Using Microfluidic Manipulation and Quantum Dot Nanosensors

2007 ◽  
Author(s):  
Hsin-Chih Yeh ◽  
Christopher M. Puleo ◽  
Yi-Ping Ho ◽  
Tza-Huei Wang
Keyword(s):  
Energy Transfer ◽  
Quantum Dot ◽  
Single Molecule ◽  
Dna Sequences ◽  
Mutational Analysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Single Molecule Detection ◽  
Specific Analysis ◽  
Low Volume

In this report, we review several single-molecule detection (SMD) methods and newly developed nanocrystal-mediated single-fluorophore strategies for ultrasensitive and specific analysis of genomic sequences. These include techniques, such as quantum dot (QD)-mediated fluorescence resonance energy transfer (FRET) technology and dual-color fluorescence coincidence and colocalization analysis, which allow separation-free detection of low-abundance DNA sequences and mutational analysis of oncogenes. Microfluidic approaches developed for use with single-molecule detection to achieve rapid, low-volume, and quantitative analysis of nucleic acids, such as electrokinetic manipulation of single molecules and confinement of sub-nanoliter samples using microfluidic networks integrated with valves, are also discussed.

scholarly journals G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

2021 ◽  
Vol 14 (8) ◽  
pp. 769
Author(s):  
Tiago Santos ◽  
Gilmar F. Salgado ◽  
Eurico J. Cabrita ◽  
Carla Cruz
Keyword(s):  
High Throughput ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Binding Mode ◽  
Titration Calorimetry ◽  
Apparent Affinity ◽  
G Quadruplex ◽  
Ligand Interactions ◽  
Types Of Information ◽  
Fluorescent Intercalator Displacement

Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.

Research Progress in the Typical Structure of Human Telomeric G-Quadruplex

2014 ◽  
Vol 955-959 ◽  
pp. 419-422
Author(s):  
Gui Lin Liu ◽  
Yan Ping Ding ◽  
Yan Ling Wu ◽  
Wen Zhang
Keyword(s):  
Cell Cycle ◽  
Dna Sequences ◽  
Research Progress ◽  
Human Chromosomes ◽  
Telomeric Dna ◽  
Typical Structure ◽  
Special Sequence ◽  
Physiological Processes ◽  
G Quadruplex ◽  
Small Molecule Ligands

Telomeric DNA of human chromosomes plays a significant role in physiological processes such as cell cycle, aging, cancer and genetic stability due to its special sequence and structure. The research on small molecule ligands targeting G-quadruplex formed by such special sequence has attracted considerable attention, and has achieved great breakthrough. In this paper, we summarize the DNA sequences and structures of three kinds of typical human telomeric G-quadruplex, providing an important reference for further research.

scholarly journals Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

2019 ◽  
Vol 116 (17) ◽  
pp. 8350-8359 ◽  
Author(s):  
Jaba Mitra ◽  
Monika A. Makurath ◽  
Thuy T. M. Ngo ◽  
Alice Troitskaia ◽  
Yann R. Chemla ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Conformational Changes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Force Spectroscopy ◽  
Telomeric Dna ◽  
Telomeric Sequences ◽  
Substitution Mutant

G-quadruplexes (GQs) can adopt diverse structures and are functionally implicated in transcription, replication, translation, and maintenance of telomere. Their conformational diversity under physiological levels of mechanical stress, however, is poorly understood. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to measure human telomeric sequences under tension. Abrupt GQ unfolding with K+in solution occurred at as many as four discrete levels of force. Added to an ultrastable state and a gradually unfolding state, there were six mechanically distinct structures. Extreme mechanical diversity was also observed with Na+, although GQs were mechanically weaker. Our ability to detect small conformational changes at low forces enabled the determination of refolding forces of about 2 pN. Refolding was rapid and stochastically redistributed molecules to mechanically distinct states. A single guanine-to-thymine substitution mutant required much higher ion concentrations to display GQ-like unfolding and refolded via intermediates, contrary to the wild type. Contradicting an earlier proposal, truncation to three hexanucleotide repeats resulted in a single-stranded DNA-like mechanical behavior under all conditions, indicating that at least four repeats are required to form mechanically stable structures.

Spectroscopic studies of the interaction of cationic water-soluble iron(III) meso-tetrakis(4-N-methylpyridiniumyl)porphyrin (FeTMPyP) with ionic and nonionic micelles

2005 ◽  
Vol 09 (02) ◽  
pp. 94-108 ◽  
Author(s):  
Patrícia S. Santiago ◽  
Shirley C. M. Gandini ◽  
Marcel Tabak
Keyword(s):  
Optical Absorption ◽  
Binding Constants ◽  
Spectroscopic Studies ◽  
Resonance Light Scattering ◽  
Water Soluble ◽  
Absorption Data ◽  
Additional Species ◽  
Surfactant Aggregates ◽  
Order Of Magnitude ◽  
Triton X

Interactions of cationic FeTMPyP with ionic and nonionic micelles have been studied by optical absorption, resonance light scattering (RLS) and 1 H NMR spectroscopies. The equilibrium behavior of FeTMPyP as a function of pH is described by several species in aqueous solution. The presence of phosphate anions leads to the existence of additional species in the acid p H region, probably due to the coordination of phosphates to the iron. FeTMPyP solution as a function of pH in the presence of anionic SDS showed a simplified equilibrium in acidic pH region, favoring the transition to the dimeric species. Titration of FeTMPyP as a function of SDS surfactant concentration showed the presence of three different porphyrin species: free metalloporphyrin monomers (or dimers depending on pH), metalloporphyrin monomers (or dimers) bound to the micelles, and nonmicellar metalloporphyrin/surfactant aggregates. In the case of zwitterionic LPC and HPS, and nonionic TRITON X-100 the nonmicellar metalloporphyrin/surfactant aggregates were not observed. Binding constants were calculated from optical absorption data and have values of 2 × 103 M −1 for SDS being much smaller for HPS (58 M −1), LPC and TRITON X-100. Comparison with our previous data for anionic FeTPPS 4 shows that both the electrostatic factor and hydrophobic forces are relevant in the porphyrin-surfactant interaction: for FeTPPS 4 binding constants to cationic CTAC and zwitterionic HPS are of the same order of magnitude, 1-3 × 104 M −1; for FeTMPyP the delocalization of the positive charges from the periphery substituents into the macrocycle ring leads to reduction of both electrostatic attraction to the micelle as well as hydrophobic character of the porphyrin ring, leading to a 10-fold reduction of binding to the micelles of opposite charge to the porphyrin. NMR data indicated that FeTMPyP is bound to the micelles as an equilibrium of two forms of monomer at pH 2.0, and at pH 9.0 the bound aggregated form (possibly dimers) is observed predominantly with some amount of a monomeric form.

scholarly journals A tunable assay for modulators of genome-destabilizing DNA structures

2019 ◽  
Vol 47 (13) ◽  
pp. e73-e73 ◽  
Author(s):  
Imee M A del Mundo ◽  
Eun Jeong Cho ◽  
Kevin N Dalby ◽  
Karen M Vasquez
Keyword(s):  
Dna Sequences ◽  
Genetic Instability ◽  
Human Cancer ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dna Structures ◽  
Myc Oncogene ◽  
Human Genomes ◽  
Complementary Oligonucleotide ◽  
Translocation Breakpoints

Abstract Regions of genomic instability are not random and often co-localize with DNA sequences that can adopt alternative DNA structures (i.e. non-B DNA, such as H-DNA). Non-B DNA-forming sequences are highly enriched at translocation breakpoints in human cancer genomes, representing an endogenous source of genetic instability. However, a further understanding of the mechanisms involved in non-B DNA-induced genetic instability is needed. Small molecules that can modulate the formation/stability of non-B DNA structures, and therefore the subsequent mutagenic outcome, represent valuable tools to study DNA structure-induced genetic instability. To this end, we have developed a tunable Förster resonance energy transfer (FRET)-based assay to detect triplex/H-DNA-destabilizing and -stabilizing ligands. The assay was designed by incorporating a fluorophore-quencher pair in a naturally-occurring H-DNA-forming sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. By tuning triplex stability via buffer composition, the assay functions as a dual-reporter that can identify stabilizers and destabilizers, simultaneously. The assay principle was demonstrated using known triplex stabilizers, BePI and coralyne, and a complementary oligonucleotide to mimic a destabilizer, MCRa2. The potential of the assay was validated in a 384-well plate with 320 custom-assembled compounds. The discovery of novel triplex stabilizers/destabilizers may allow the regulation of genetic instability in human genomes.

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