The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

Biebricher, Andreas S.; Heller, Iddo; Roijmans, Roel F H; Hoekstra, Tjalle P.; Peterman, Erwin J. G.; Wuite, Gijs J. L.

doi:10.1038/ncomms8304

Cited by 180 publications

(240 citation statements)

References 51 publications

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“…Dye molecules induce structural changes in DNA [46], which disrupt the functions of DNA-binding proteins and enzymes [47]. A detailed understanding of how fluorescent dyes bind with host DNA may prove essential to drug development efforts [48], or DNA curtains studies [49].…”

Section: Resultsmentioning

confidence: 99%

Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements

Backer¹,

Lee²,

Moerner³

2016

Optica

115

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Single-molecule orientation measurements provide unparalleled insight into a multitude of biological and polymeric systems. We report a simple, high-throughput technique for measuring the azimuthal orientation and rotational dynamics of single fluorescent molecules, which is compatible with localization microscopy. Our method involves modulating the polarization of an excitation laser, and analyzing the corresponding intensities emitted by single dye molecules and their modulation amplitudes. To demonstrate our approach, we use intercalating and groove-binding dyes to obtain super-resolved images of stretched DNA strands through binding-induced turn-on of fluorescence. By combining our image data with thousands of dye molecule orientation measurements, we develop a means of probing the structure of individual DNA strands, while also characterizing dye-DNA interactions. This approach may hold promise as a method for monitoring DNA conformation changes resulting from DNA-binding proteins.

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Section: Resultsmentioning

confidence: 99%

Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements

Backer¹,

Lee²,

Moerner³

2016

Optica

115

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“…Other studies have demonstrated the capability of optical tweezers techniques to measure the persistence length of the CIS-DNA complex and have shown that CIS binds cooperatively to the DNA molecule (19,20). In the same vein, using optical tweezers, still other authors have observed a reduction of DNA persistence length and DNA extension in the presence of intercalants (21)(22)(23), noting also that the measured values of the persistence length depend on the maximum stretching force (24). Finally, magnetic tweezers (MT) measurements have revealed the effect of drug binding on DNA nanomechanics by detecting persistence-length variations (15,25), or the presence of two different persistence lengths depending on the applied force (9), or the various effects of combining CIS and transplatin (26).…”

Section: Introductionmentioning

confidence: 92%

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Salerno

Beretta

Zanchetta

et al. 2016

Biophysical Journal

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Platinum-containing molecules are widely used as anticancer drugs. These molecules exert cytotoxic effects by binding to DNA through various mechanisms. The binding between DNA and platinum-based drugs hinders the opening of DNA, and therefore, DNA duplication and transcription are severely hampered. Overall, impeding the above-mentioned important DNA mechanisms results in irreversible DNA damage and the induction of apoptosis. Several molecules, including multinuclear platinum compounds, belong to the family of platinum drugs, and there is a body of research devoted to developing more efficient and less toxic versions of these compounds. In this study, we combined different biophysical methods, including single-molecule assays (magnetic tweezers) and bulk experiments (ultraviolet absorption for thermal denaturation) to analyze the differential stability of double-stranded DNA in complex with either cisplatin or multinuclear platinum agents. Specifically, we analyzed how the binding of BBR3005 and BBR3464, two representative multinuclear platinum-based compounds, to DNA affects its stability as compared with cisplatin binding. Our results suggest that single-molecule approaches can provide insights into the drug-DNA interactions that underlie drug potency and provide information that is complementary to that generated from bulk analysis; thus, single-molecule approaches have the potential to facilitate the selection and design of optimized drug compounds. In particular, relevant differences in DNA stability at the single-molecule level are demonstrated by analyzing nanomechanically induced DNA denaturation. On the basis of the comparison between the single-molecule and bulk analyses, we suggest that transplatinated drugs are able to locally destabilize small portions of the DNA chain, whereas other regions are stabilized.

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“…1(a)], thereby lengthening the DNA upon binding. 8,9 Both groove binders and intercalators have a well-defined orientation with respect to the helix axis of the DNA. For intercalators, the absorption and emission dipole moments are roughly perpendicular to the DNA helix axis.…”

Section: Introductionmentioning

confidence: 99%

A polarized view on DNA under tension

Mameren

Vermeulen

Wuite

2017

The Journal of Chemical Physics

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In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of doublestranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.

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The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

Cited by 180 publications

References 51 publications

Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements

Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

A polarized view on DNA under tension

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