Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

Stojković, Marijana Radić; Škugor, Marko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

doi:10.3762/bjoc.10.225

Cited by 7 publications

(5 citation statements)

References 23 publications

(53 reference statements)

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“…The design of small molecules that can selectively bind and discriminate different biomolecular structures (polynucleotides vs proteins, DNA or RNA, single or double-stranded polynucleotides, particular base composition…) and signalize binding by specific spectroscopic response is of great importance [ 1 – 2 ].…”

Section: Introductionmentioning

confidence: 99%

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

Matić¹,

Tandarić²,

Stojković³

et al. 2023

Beilstein J. Org. Chem.

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Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular modelling combined with spectrophotometric experiments revealed that in neutral and acidic buffered water solutions conjugates predominantly exist in intramolecularly stacked conformations because of the π–π stacking interaction between pyrene and phenanthridine moieties. The investigated systems exhibited a pH-dependent excimer formation that is significantly red-shifted relative to the pyrene and phenanthridine fluorescence. While the conjugate with a short linker showed negligible spectrophotometric changes due to the polynucleotide addition, the conjugate with a longer and more flexible linker exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated in the cell membrane.

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Section: Introductionmentioning

confidence: 99%

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

Matić¹,

Tandarić²,

Stojković³

et al. 2023

Beilstein J. Org. Chem.

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“…13; n=5 or n=6) successfully demonstrated the importance of the linker on recognition process. Moreover, DBTAA-propyladenine conjugate showed specific recognition of homogeneous AT-DNA sequence by an ICD band pattern, which was not observed for other ds-DNA/RNA [67].…”

Section: Dna/rna Binder Linked To Nucleobase By Inert Linkermentioning

confidence: 65%

Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications

Saftić

Ban

Matić

et al. 2019

CMC

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Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class are nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

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“…Therefore, for the control sequences we used a T 23 sequence that is completely unstructured, and two sequences from the literature that form G-quadruplexes but have different base compositions from the aptamer. Figure A shows that conjugation of the Ctrl1 sequence to the tail did not affect its antiparallel G-quadruplex structure, and the T 23 remained unstructured as an amphiphile. However, Ctrl2 formed parallel G-quadruplex as free ssDNA and a hybrid type parallel/antiparallel G-quadruplex as an amphiphile.…”

Section: Results and Discussionmentioning

confidence: 99%

Design of an Aptamer-Amphiphile for the Detection of β-Lactoglobulin on a Liquid Crystal Interface

et al. 2019

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An aptamer-amphiphile was designed that binds to β-lactoglobulin (β-LG), a major allergen from cow’s milk. For this work, a 23-nucleotide ssDNA aptamer β-LG-23, capable of forming antiparallel G-quadruplexes was used, and its specificity and binding affinity of 22 ± 2 nM for β-LG were evaluated via enzyme-linked apta-sorbent assay (ELASA). The β-LG-23 aptamer was synthesized as an amphiphile by conjugating it to a C16 double tail via different spacers, and the effect of the spacers on the binding affinity and secondary structure of the aptamer was investigated. From all amphiphiles tested, direct conjugation of the aptamer to the tail gave the lowest binding affinity to β-LG (37 ± 2 nM), while maintaining the antiparallel G-quadruplex secondary structure of the aptamer. As a proof of concept, the β-LG-23 aptamer-amphiphile was used to decorate the interface of a liquid crystal (LC) and effectively detected 10 nM or 0.18 ppm of β-LG with a 20 min equilibration time, thus demonstrating that it has the potential to be used for fast and label-free detection of β-LG.

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Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

Cited by 7 publications

References 23 publications

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications

Design of an Aptamer-Amphiphile for the Detection of β-Lactoglobulin on a Liquid Crystal Interface

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