Diketopyrrolo[3,4-c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures

Ramos, Catarina I. V.; Almodôvar, Vítor A. S.; Candeias, Nuno R.; Santos, Tiago; Cruz, Carla; Neves, Maria G. P. M. S.; Tomé, Augusto C.

doi:10.1016/j.bioorg.2022.105703

Cited by 11 publications

(11 citation statements)

References 84 publications

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“…Dipyridyl-DPP and the corresponding dicationic derivative MePyridyl-DPP were synthesized as recently reported (Scheme S1) (23). Dipyridyl-DPP was obtained from Pigment red 254 and 4-pyridylboronic acid, under Suzuki-Miyaura conditions, following a recently reported procedure (36).…”

Section: Synthesis Of Dpp Derivativesmentioning

confidence: 99%

“…Spectroscopic characteristics of DPP derivatives were determined in solution and photodynamic properties were investigated in presence of different molecular probes to sense the formation of ROS. Recently, it was demonstrated that MePyridyl‐DPP presents high affinity to G‐quadruplex structures and is particularly selective for oncogene promotors (23). Herein, antimicrobial activity sensitized by these DPPs was studied in a Gram‐positive bacterium Staphylococcus aureus .…”

Section: Introductionmentioning

confidence: 99%

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Diketopyrrolopyrrole Derivatives as Photosensitizing Agents against Staphylococcus aureus

Pérez

Almodôvar

Durantini

et al. 2022

Photochem & Photobiology

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Diketopyrrolopyrrole (DPP) derivatives containing sulfonamide (Sulfonamide‐DPP), pyridyl (Dipyridyl‐DPP) and N‐methylpyridyl (MePyridyl‐DPP) substituents were assessed as antibacterial photosensitizers. Non‐charged DPPs showed an intense absorption band centered at about 480 nm and green fluorescence emission (ΦF ~ 0.7) in acetonitrile. The absorption of MePyridyl‐DPP was bathochromically shifted at 510 nm, with decreased fluorescence emission. Sulfonamide‐DPP and Dipyridyl‐DPP photosensitized the formation of O2(1Δg) (ΦΔ ~ 0.15–0.17), while the production induced by MePyridyl‐DPP was at least 10 times lower. Furthermore, these DPPs produced a photoreduction of NBT similar to that of the control. Photodynamic inactivation induced by DPPs was first investigated at the single‐bacterium level of Staphylococcus aureus attached to a surface. After 30 min irradiation, MePyridyl‐DPP produced a complete eradication of the bacteria. In bacterial cell suspensions, dicationic DPP induced more than 7 log10 decrease in S. aureus cell survival after 30 min irradiation. Potentiation with iodide anions allowed a complete elimination of bacteria after 15 min therapy. This compound was also effective to eliminate S. aureus cells on biofilms. The results show that MePyridyl‐DPP bearing two positive groups provides an amphiphilic character to the structure that improves the interaction with the cell envelop. This effect enhances the photocytotoxic activity of MePyridyl‐DPP against bacteria.

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Section: Synthesis Of Dpp Derivativesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diketopyrrolopyrrole Derivatives as Photosensitizing Agents against Staphylococcus aureus

Pérez

Almodôvar

Durantini

et al. 2022

Photochem & Photobiology

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“…When visualizing PCR products with DNA-binding dye, the FP/RP ratio should strictly be 1. However, deviations in the FP/RP ratio can occur due to operational errors or issues with primer quality, leading to the appearance of extra bands caused by incomplete synthesis products. – The fluorescent labeling can make the range of effective primer FP/RP ratios wider and allow them to exceed 1 in order to avoid the generation of multiple bands. In particular, when calculating the binding constant with PCR-Stop results, misjudgment of double-stranded product bands may lead to objectively erroneous results.…”

Section: Discussionmentioning

confidence: 99%

“…In general, PCR-Stop has become an effective and efficient method to detect the interaction of the G4 structure and G4 ligand and is used to screen G4 ligands. However, the PCR-Stop assay may also generate some confused and puzzled results; for example, more than one PCR product band was generated – when the FP and RP were annealed. It is generally believed that the appearance of multiple bands is caused by nonspecific amplification due to complementary characteristics of the FP and RP or low annealing temperatures.…”

Section: Introductionmentioning

confidence: 99%

Ratio of the Primers Used in Polymerase Chain Reaction-Stop Analysis Impacts the Resultant Banding Pattern

Xiang,

Zhang,

et al. 2023

ACS Omega

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G-quadruplex (G4), as a dynamic nucleic acid secondary structure, widely exists in organism genomes and plays regulatory roles in a variety of cellular functions. Polymerase chain reaction stop assay (PCR-Stop) is a simple, quick, and low-cost widely used method for detection of the binding between G4 and its binding compounds. Different from the common PCR approach, no double-stranded DNA template is needed in the PCR-Stop assay, in which the forward and reverse primers extend against each other in the presence of DNA polymerase to produce a single DNA product. However, unexpected results, such as two or more PCR products, are often generated, and the mechanism is unclear. We found that the ratio of pair primers significantly impacts the generation and components of PCR-Stop products, which is crucial for the interpretation of the experiment results.

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“…The identification and stabilization of deoxyribonucleic acid (DNA) G-quadruplexes (G4s) assumes paramount importance in various well-known anticancer therapeutics, such as telomerase inhibition, [1][2][3][4] suppression of oncogenes transcription [5][6][7] and as drug delivery vehicles. [8][9][10] G4s arise from the non-canonical folding of guanine (G)-rich sequences and, from a structural point of view, comprise several stacked G-tetrads formed from the squared arrangement of four guanine nucleotides via Hoogsteen base pairing.…”

Section: Introductionmentioning

confidence: 99%

Arrays of graphene-quantum dots-supported DNA oligonucleotides as self-indicating porphyrin carriers

Monteiro¹,

Ramos²,

Fateixa³

et al. 2023

New J. Chem.

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Diketopyrrolo[3,4-c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures

Cited by 11 publications

References 84 publications

Diketopyrrolopyrrole Derivatives as Photosensitizing Agents against Staphylococcus aureus

Diketopyrrolopyrrole Derivatives as Photosensitizing Agents against Staphylococcus aureus

Ratio of the Primers Used in Polymerase Chain Reaction-Stop Analysis Impacts the Resultant Banding Pattern

Arrays of graphene-quantum dots-supported DNA oligonucleotides as self-indicating porphyrin carriers

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