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5 results for “cyanine dye”
Dataset of "Thermal Truncation of Heptamethine Cyanine Dyes"
<p>Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. Unlike phototruncation, the thermal truncation (chain-shortening) reaction is a phenomenon that has rarely been described for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3′ and C4′ positions of the chain and different heterocyclic end groups, the presence of different bases, nucleophiles and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, demonstrating the need to model catalytic reactions by highly correlated wavefunction-based methods. We show that entropic effects control the course of this process. The study provides a critical insight into the reactivity of the polyene chains of cyanines and offers new approaches to the synthesis of meso-substituted symmetrical and unsymmetrical pentamethine cyanines from Cy7 derivatives.</p>
Far-red pentamethine cyanine dyes as fluorescent probes for detection of serum albumins
<p><span>Benzothiazole based cyanine dyes with bridged groups in pentamethine chain were studied as potential far-red fluorescent probes for protein detection. Spectral-luminescent properties were characterized for unbound dyes and in the presence of serum albumins (bovine (BSA), human (HSA), equine (ESA)), and globular proteins (β-lactoglobulin, ovalbumin). We have observed that the addition of albumins leads to a significant increase in dyes fluorescence intensity. However, the fluorescent response of dyes in the presence of other globular proteins was noticeably lower. The value of fluorescence quantum yield for dye bearing sulfonate group complexed with HSA amounted to 42% compared with 0.2 % for the free dye. The detection limit of HSA by this dye was about > 0.003 mg/ml that indicates the high sensitivity of dye to low HSA concentrations. Modeling of structure of the dyes complexes with albumin molecules was performed by molecular docking. According to these data, dyes could bind to up to five sites on the HSA molecule; the most preferable are the hemin-binding site in subdomain IB and <span>the dye-binding site in the pocket between subdomains IA, IIA, and IIIA.</span> This work confirms that pentamethine cyanine dyes could be proposed as powerful far-red fluorescent probes applicable for highly sensitive detection of albumins.</span></p>
Interplay between a heptamethine cyanine dye sensitizer (IR806) and lanthanide upconversion nanoparticles
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to </strong><strong><em>Angewandte Chemie</em></strong><strong>, and entitled:</strong></p> <p><strong>Interplay between a heptamethine cyanine dye sensitizer (IR806) and lanthanide upconversion nanoparticles</strong></p> <p><strong>Authored by:</strong></p> <p>Haichun Liu<sup>1</sup>, Abhilash Kulkarni<sup>1</sup>, Uliana Kostiv<sup>1</sup>, Elin Sandberg<sup>1</sup>, Anbharasi Lakshmanan<sup>1</sup>, Georgios A. Sotiriou<sup>2</sup>, Jerker Widengren<sup>1,*</sup></p> <p><em><sup>1</sup></em><em> Department of Applied Physics, KTH Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden</em></p> <p><em><sup>2</sup></em><em>Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden</em></p> <p>Corresponding author:</p> <p>*<u>jwideng@kth.se</u></p> <p><strong>The data files containing raw data and results of the analysis are grouped according to the different figures in the manuscript where the extracted results are presented.</strong></p> <p><strong>ABSTRACT</strong></p> <p><span>Lanthanide-doped upconversion nanoparticles (UCNPs) have attractive emission properties but suffer from weak light-absorbing capacities and thereby relatively low brightnesses. This motivates using strongly absorbing dye molecules as antennas and sensitizers. However, despite much effort, understanding of this dye-UCNP interplay is still limited. Major sensitization mechanisms are still under discussion, largely because there is a lack of effective means to observe key factors such as dark state transitions within the dyes. Here, we established a combined spectroscopic procedure to systematically investigate the photophysics behind the dye-UCNP interaction, embracing fluorescence-based transient-state excitation-modulation, lifetime and correlation spectroscopy, and spectrofluorometry/spectrophotometry. With this procedure we studied the heptamethine cyanine dye IR806, a typical UCNP sensitizer, established its photophysical model, deciphered its photophysics in UCL-sensitization-related environments and could identify energy transfer from the IR806 singlet excited state to Yb<sup>3+</sup> (UCNP sensitizer ion) as the dominant sensitization mechanism. Our studies suggest that IR806 can form non-emissive H-aggregates at the nanoparticle surfaces, which can be dissociated after certain light excitation duration (typically>100µs). Moreover, buildup of a non-fluorescent, photo-redox state of IR806 after longer irradiation times (10–100ms) can deleteriously affect its UCL sensitization, inferring an optimal excitation duration for dye-sensitized UCNPs, relevant for e.g. optical imaging applications.</span></p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Far-red pentamethine cyanine dyes as fluorescent probes for detection of serum albumins
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