ABSTRACT
Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins.
Subject(s)
Base Pairing , Cytosine/chemistry , DNA, Z-Form/chemistry , DNA/chemistry , Fluorescence Resonance Energy Transfer , Nucleic Acid Conformation , Algorithms , Circular Dichroism , Kinetics , Models, Molecular , Models, Theoretical , Oligonucleotides/chemistryABSTRACT
Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds.
Subject(s)
Adenine/chemistry , Coloring Agents/chemistry , Fluorescent Dyes/chemistry , Nucleic Acids/chemistry , Base Pairing , Fluorescence , Spectrometry, FluorescenceABSTRACT
An efficient method for N-arylation of purines is reported. The N-arylation is catalysed by Cu(i) and 4,7-bis(2-hydroxyethylamino)-1,10-phenanthroline (BHPhen) in aqueous DMF or ethanol. The reaction generally proceeds with high selectivity for the N(9)-position.
Subject(s)
Hydrocarbons, Halogenated/chemistry , Purines/chemistry , Catalysis , Copper/chemistry , Molecular Structure , Phenanthrolines/chemistryABSTRACT
G-quadruplex (G4) ligands are currently receiving considerable attention as potential anticancer therapeutics. A series of phenanthroline-2,9-bistriazoles carrying tethered positive end groups has been synthesized and evaluated as G4 stabilizers. The compounds were efficiently assembled by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) in CH2Cl2 and water in the presence of a complexing agent. Characterization of the target compounds on telomeric and c-KIT G4 sequences led to the identification of guanidinium-substituted compounds as potent G4 DNA ligands with high selectivity over duplex DNA. The diisopropylguanidium ligands exhibited high selectivity for the proto-oncogenic sequence c-KIT over the human telomeric sequence in the surface plasmon resonance (SPR) assay, whereas the compounds appeared potent on both G4 structures in the FRET melting temperature assay. The phenanthroline-2,9-bistriazole ligands were thus identified as potent G4 ligands with high selectivity over duplex DNA, and preliminary results indicate that the scaffold may form basis for the development of subtype-specific G4 ligands.
Subject(s)
DNA/drug effects , G-Quadruplexes/drug effects , Phenanthrolines/pharmacology , Triazoles/pharmacology , DNA/chemistry , Dose-Response Relationship, Drug , Ligands , Molecular Structure , Phenanthrolines/chemical synthesis , Phenanthrolines/chemistry , Structure-Activity Relationship , Surface Plasmon Resonance , Triazoles/chemical synthesis , Triazoles/chemistryABSTRACT
A safe, practical, and scalable continuous flow protocol for the in situ generation of dimethylamine from DMF followed by nucleophilic aromatic substitution of a broad range of aromatic and heteroaromatic halides is reported.
ABSTRACT
Small molecules capable of stabilizing the G-quadruplex (G4) structure are of interest for the development of improved anticancer drugs. Novel 4,7-diamino-substituted 1,10-phenanthroline-2,9-dicarboxamides that represent hybrid structures of known phenanthroline-based ligands have been designed. An efficient synthetic route to the compounds has been developed and their interactions with various G4 sequences have been evaluated by Förster resonance energy transfer (FRET) melting assays, fluorescent intercalator displacement (FID), electrospray ionization mass spectrometry (ESI-MS), and circular dichroism (CD) spectroscopy. The preferred compounds have high aqueous solubility and are strong and potent G4 binders with a high selectivity over duplex DNA; thus, they represent a significant improvement over the lead compounds. Two of the compounds are inhibitors of HeLa and HT1080 cell proliferation.
Subject(s)
Antineoplastic Agents/chemical synthesis , DNA, Neoplasm/chemistry , Intercalating Agents/chemical synthesis , Phenanthrolines/chemical synthesis , Antineoplastic Agents/pharmacology , Cell Proliferation/drug effects , Circular Dichroism , DNA, Neoplasm/antagonists & inhibitors , Fluorescence Resonance Energy Transfer , G-Quadruplexes , HeLa Cells , Humans , Intercalating Agents/pharmacology , Ligands , Molecular Structure , Nucleic Acid Denaturation/drug effects , Phenanthrolines/pharmacology , Solubility , Spectrometry, Mass, Electrospray Ionization , Thermodynamics , WaterABSTRACT
A convenient and high-yielding multigram synthesis of the versatile intermediate 4,7-dichloro-1,10-phenanthroline-2,9-dicarboxylic acid is described. The intermediate is further efficiently derivatized to 4,7-diamino-1,10-phenanthroline-2,9-dicarboxamides with potential G-quadruplex stabilizing effects.
