Non-covalent ligand/DNA interactions: Minor groove binding agents

Nelson, Stephanie M.; Ferguson, Lynnette R.; Denny, William A.

doi:10.1016/j.mrfmmm.2007.03.012

Cited by 149 publications

(68 citation statements)

References 108 publications

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“…There are two main binding modes have been reported so far, end-stacking mode [13][14][15][16][17][18] and groove binding mode [19][20][21][22][23][24]. In both binding modes, besides the core scaffold (G-quartets), the roles of loops are also important to interaction and have been addressed in many studies [25,26].…”

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confidence: 99%

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

et al. 2013

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G-quadruplexes attract more and more attention in recent years. Numerous small molecules which can induce or stabilize the formation of G-quadruplexes have been investigated on the purpose of anticancer drug development. As a motif existed in physiological condition, flanking sequences are an important part of G-quadruplexes but the study on the impact of flanking sequences on (G-quadruplex)-ligand binding is rarely reported. In this paper, the effects of flanking sequences on binding affinity between a series of unimolecular parallel-stranded G-quadruplex sequences derived from c-myc oncogene promoter (termed as c-myc G-quadruplexes) and their ligands are discussed in detail. The results showed that the flanking sequences on c-myc G-quadruplexes play key roles in (G-quadruplex)-ligand interaction. When a c-myc G-quadruplex is bound to its ligands, the flanking sequences might form a binding cavity above the terminal G-quartet, which could provide a suitable site for ligands to dock in. Moreover, the bases on flanking sequences could interact with ligand through - stacking, and finally form a sandwich-stacking mode (terminal G-quartet, ligand and bases on the flanking sequence). This mode could stabilize the (G-quadruplex)-ligand complex effectively and enhance the binding affinity dramatically. However, flanking sequences are also found to exhibit steric hindrance effect which could impede the (G-quadruplex)-ligand binding. G-quadruplex

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confidence: 99%

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

et al. 2013

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“…Distamycin A (Figure 8) is a potent inhibitor of Werner and Bloom syndrome helicases and a dual inhibitor of topo I and II. It inhibits RNA polymerase II transcription by blocking chain elongation as well as intensifying transcription at natural RNA polymerase II pause sites (66). One signifi cant representative among distamycin Hoechst 33258, known as pibenzimol, is a fluorescent reagent with a head-to-tail bisbenzimidazole structure that initially showed activity against L1210 murine leukaemia (54).…”

Section: Dna Groove Bindersmentioning

confidence: 99%

“…Mithramycin (MTR) and chromomycine ( Figure 9) have a similar mode of binding to GC-rich DNA sequences in the minor groove and belong to the aureolic acid group of anticancer drugs (66).…”

Section: Dna Groove Bindersmentioning

confidence: 99%

Antineoplastic DNA-Binding Compounds: Intercalating and Minor Groove Binding Drugs

Mišković

Bujak

Lončar

et al. 2013

Archives of Industrial Hygiene and Toxicology

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DNA intercalating and minor groove binding compounds are new weapons in the battle against malignant diseases. These antineoplastic agents target the DNA molecule and interfere with the cell cycle leading to rapidly proliferating cell death. They are mainly derivates of a naturally occurring organic compound derived from a microorganism or plant. Intercalators usually act as topoisomerase I and/or II poisons, while the mechanisms of DNA minor groove binders are a combination of several steps including topoisomerase poisoning. This paper gives an overview of some of the developed DNA intercalating and minor groove binding compounds, as well as an explanation of their chemical structures, origins, and application in chemotherapy.

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“…Image quality was improved in the following two 19 centuries by optimized lens combinations and progress in glass production, but resolution, 20 contrast, noise, optical aberrations, sensitivity and specificity were still major problems. 21 Progression towards modern microscopy commenced when halfway the 19 th century, 22 fluorescence was being described by Stokes 1 and Von Lommel, creating the awareness that 23 substances could be identified by measuring their specific fluorescence spectrum.…”

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confidence: 99%

“…For decades, 16 researchers have fluorescently labeled nucleic acids with a variety of labeling strategies to gain 17 insight in the fate of these nucleic acids. While labeling short interference RNA (siRNA) or 18 antisense oligonucleotides is primarily done during chemical synthesis by the manufacturer, 19 several strategies exist for the labeling of larger polynucleotides, such as plasmid DNA (pDNA) 20 and messenger RNA (mRNA), in a research lab. These polynucleotides are of interest for any 21 biological application in which the expression of proteins is beneficial.…”

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confidence: 99%

Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies

2015

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7Live-cell imaging has provided the life sciences with insights into the cell biology and 8 dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In 9 this review, we focus on the current fluorescent labeling strategies for nucleic acids, and in 10 particular messenger RNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad 11 range of scientific fields. By giving a background of the available techniques and an evaluation 12 of the pros and cons, we try to supply scientists with all the information needed to come to an 13 informed choice of nucleic acid labeling strategy aimed at their particular needs. 14

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Non-covalent ligand/DNA interactions: Minor groove binding agents

Cited by 149 publications

References 108 publications

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

Antineoplastic DNA-Binding Compounds: Intercalating and Minor Groove Binding Drugs

Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies

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