Selective binding of small molecules to DNA: Application and perspectives

Wang, Bochu; Tan, Jun; Zhu, Lingyu

doi:10.1016/j.colsurfb.2010.03.048

Cited by 9 publications

(2 citation statements)

References 60 publications

(76 reference statements)

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“…Binuclear Ru II compounds such as L,L-B differ from both small molecules such as netropsin and many others, [28] as well as proteins [29] binding in the minor groove. Practically all DNA binding molecules utilise positive charges to offset the negative charges of the DNA backbone and the negative electrostatic potential in the grooves.…”

Section: Discussionmentioning

confidence: 99%

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂

Reymer

Persson

et al. 2013

Chemistry A European J

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Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one RuII, through the DNA base-pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear RuII compounds and DNA. We report a structural NMR study on the binuclear RuII intercalator Λ,Λ-B (Λ,Λ-[μ-bidppz(bipy)4Ru2]4+; bidppz=11,11′-bis(dipyrido[3,2-a:2′,3′-c]phenazinyl, bipy = 2,2′-bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]2. Threading of Λ,Λ-B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ-B is trapped in a well-defined surface-bound state consisting of an eccentric minor-groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ-B. Molecular dynamics simulations show that this minor-groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru2+ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ-B with natural calf thymus DNA. The present minor-groove binding mode is proposed to represent the initial surface interactions of binuclear RuII compounds prior to intercalation into AT-rich DNA.

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Section: Discussionmentioning

confidence: 99%

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂

Reymer

Persson

et al. 2013

Chemistry A European J

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“…Proflavine derivatives have seen clinical use as antibacterial agents and as probes to examine mutagenesis; the compound is also known to cause frameshift mutation in viruses, bacteriophages and bacteria, and even DNA-breaking activity in mammalian cells. This chromosomal mutation seems to be related to the ability of proflavine to stabilize DNA-topoisomerase intermediates (Biver et al, 2003;Gurova, 2009;Lang et al, 2013;Wang et al, 2010;Yang et al, 2005). Proflavine is an acridine dye and has been shown (Moloney et al, 2001) to bind directly with nucleic acids; the conjugate of this interaction becomes highly photosensitive.…”

Section: Synthesis Of Thioureasmentioning

confidence: 99%

A review on acridinylthioureas and its derivatives: biological and cytotoxic activity

2017

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Acridines possess two characteristics that have led many researchers to consider the agents interesting targets for future development as potential farmacophores: the planar acridine skeleton, which is able to intercalate into DNA, and the intense fluorescence of the agents. This review offers a study of the multifunctional character of acridines and the synthesis of novel acridine derivatives, with particular focus being placed on isothiocyanates and their congeners, e.g. thioureas, isothioureas, quaternary ammonium salts and platinum/gold conjugates. The review provides an overview of the structure, spectral properties, DNA binding and biological activity of acridinylthiourea congeners. These acridinylthiourea derivatives display significant cytotoxic activities against different types of cancer cell lines at micromolar concentrations. Copyright © 2017 John Wiley & Sons, Ltd.

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Luminescent Sensing

Kitchen

Parkesh

Veale

et al. 2012

Supramolecular Chemistry

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The development of luminescent sensing has been central to the field of supramolecular chemistry. Herein, we give a some insight into some of the developments that have taken place in recent times, focusing most of our effort on the discussion of luminescent sensors for cations, anions, and neutral molecules, by presenting a selected number of examples from this fast, broad, and ever expanding research field. We also demonstrate how the use of luminescent sensors has helped in the development of contrast and imaging agents, and in particular show examples of their use in cellular imaging and sensing within competitive biological environments.

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Selective binding of small molecules to DNA: Application and perspectives

Cited by 9 publications

References 60 publications

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂

A review on acridinylthioureas and its derivatives: biological and cytotoxic activity

Luminescent Sensing

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Selective binding of small molecules to DNA: Application and perspectives

Cited by 9 publications

References 60 publications

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

A review on acridinylthioureas and its derivatives: biological and cytotoxic activity

Luminescent Sensing

Contact Info

Product

Resources

About

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺: An NMR Study with [d(CGCGAATTCGCG)]₂