Decorating a single giant DNA with gold nanoparticles

Carnerero, José M.; Masuoka, Shinsuke; Baba, Hikari; Yoshikawa, Yuko; Prado‐Gotor, Rafael; Yoshikawa, Kunio

doi:10.1039/c8ra05088k

Cited by 12 publications

(17 citation statements)

References 55 publications

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“…To evaluate the intramolecular Brownian motion of DNA ( Figure 7), we quantified the fluctuation of single DNA molecules in the fluorescence images [32][33][34][35]. Autocorrelation of DNA obtained from the time-dependent fluctuation of the long-axis length is shown in Figure 8, and the deduced spring and damping constants are summarized in Figure 9.…”

Section: Visco-elasticity and Hydrodynamic Radius R H Of The Dna Molementioning

confidence: 99%

“…In addition to the aforementioned analysis of the intrachain fluctuation (Figures 7-9), we analyzed the translational motion to evaluate the R H . Although the fluorescence images do not give precise information on the actual sizes of individual DNA molecules because of the presence of a blurring effect of 0.3-0.5 µm [33][34][35], the analysis of the Brownian motion, or translational fluctuation, can provide the R H as a reliable measure of the size of individual DNA molecules. It was apparent that the effect on the hydrodynamic radius R H was observed in a very similar manner, although the hydrodynamic radius R H did not change greatly and the visco-elastic properties of the platinum compound-DNA complex changed more clearly.…”

Section: Visco-elasticity and Hydrodynamic Radius R H Of The Dna Molementioning

confidence: 99%

“…We evaluated the autocorrelation C(t) from the time-dependent fluctuation of the long-axis length, L(t) [33]:…”

Section: Evaluation Of Visco-elasticity and Hydrodynamic Radius R H Fmentioning

confidence: 99%

“…where r is a two-dimensional positional vector of the center of mass of DNA molecules and the symbol t denotes a time average. In the actual analysis of the fluctuation, we used a modified equation [32][33][34][35] when a convectional flow was noticed. The hydrodynamic radius R H was calculated from D based on the Stokes-Einstein relationship:…”

Section: Evaluation Of Visco-elasticity and Hydrodynamic Radius R H Fmentioning

confidence: 99%

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Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression

Kishimoto

Yoshikawa

et al. 2019

IJMS

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Despite the effectiveness of cisplatin as an anticancer agent, its trans-isomer, transplatin, is clinically ineffective. Although both isomers target nuclear DNA, there is a large difference in the magnitude of their biological effects. Here, we compared their effects on gene expression in an in vitro luciferase assay and quantified their effects on the higher-order structure of DNA using fluorescence microscopy (FM) and atomic force microscopy (AFM). The inhibitory effect of cisplatin on gene expression was about 7 times that of transplatin. Analysis of the fluctuation autocorrelation function of the intrachain Brownian motion of individual DNA molecules showed that cisplatin increases the spring and damping constants of DNA by one order of magnitude and these visco-elastic characteristics tend to increase gradually over several hours. Transplatin had a weaker effect, which tended to decrease with time. These results agree with a stronger inhibitory effect of cisplatin on gene expression. We discussed the characteristic effects of the two compounds on the higher-order DNA structure and gene expression in terms of the differences in their binding to DNA.

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Section: Visco-elasticity and Hydrodynamic Radius R H Of The Dna Molementioning

confidence: 99%

Section: Visco-elasticity and Hydrodynamic Radius R H Of The Dna Molementioning

confidence: 99%

“…We evaluated the autocorrelation C(t) from the time-dependent fluctuation of the long-axis length, L(t) [33]:…”

Section: Evaluation Of Visco-elasticity and Hydrodynamic Radius R H Fmentioning

confidence: 99%

Section: Evaluation Of Visco-elasticity and Hydrodynamic Radius R H Fmentioning

confidence: 99%

See 2 more Smart Citations

Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression

Kishimoto

Yoshikawa

et al. 2019

IJMS

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“…In addition, a single giant DNA strand was coated with gold nanoparticles, following Ref. (Carnerero et al 2018), which allowed a probing of its dynamics by means of fluorescence microscopy, TEM, and CD spectra. Since the T4 DNA strands studied in this paper are quite large in size (a few tens of microns), their local motion corresponds to the application of image-time correlation spectroscopy (with a sampling time of 30 fps).…”

Section: Introductionmentioning

confidence: 99%

Direct visualization of local activities of long DNA strands via image–time correlation

Kang

Sadakane

2021

Eur Biophys J

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Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5–10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of $$\upmu m$$ μ m ) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image–time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.

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Small DNA additives to polyelectrolyte multilayers promote formation of ultrafine gold nanoparticles with enhanced catalytic activity

Nagahama

Zinchenko

2018

Colloid Polym Sci

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Decorating a single giant DNA with gold nanoparticles

Abstract: We decorated a single giant DNA (1.66 × 105 base pairs) with gold nanoparticles through the simple procedure of mild warming, without denaturation of the DNA molecule.

Cited by 12 publications

References 55 publications

Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression

Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression

Direct visualization of local activities of long DNA strands via image–time correlation

Small DNA additives to polyelectrolyte multilayers promote formation of ultrafine gold nanoparticles with enhanced catalytic activity

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