Mikroakışkan Temelli Floresans Mikroskop Sistemi ile Otofloresan Flavin Koenzimlerinin Fotofiziksel Geçişleri Üzerine Nümerik Modelleme Çalışmaları

International Journal of Advances in Engineering and Pure Sciences, Год журнала: 2025, Номер 37(1), С. 73 - 91

Опубликована: Март 19, 2025

Bu araştırmada ışığa ve çözücü ortamına oldukça hassas, çok küçük uyarım kesit alanına sahip zayıf floresan ışıma yapabilen flavin mononükleotit (FMN) adenin dinükleotit (FAD) koenzimlerinin fotofiziksel geçişlerini çözümleme kapasitesine mikroakışkan temelli bir floresans mikroskop sistemi için nümerik modelleme çalışmaları sunulmuştur. FMN FAD’nin moleküler yapısı, özellikleri girdikleri kimyasal reaksiyonlar dikkate alınarak her iki molekül farklı modeller kullanılmıştır. modellerde yer alan elektronik durumlar 1. mertebeden lineer diferansiyel denklem olarak ele alınmış olup durum popülasyonu zamana bağlı çözülmüş, çip ile lazer alanının geometrik boyutları parametreleri kullanılarak görüntü sinyal verisi elde edilmiştir. İki akış hızında şiddeti, çözücüye eklenen etanol, askorbat triptofan gibi redoks ajanlarının normalize sinyaline popülasyonlarına olan etkisi simüle Sinyal analizlerine ek sinyallerin oluşturulmasında kullanılan sCMOS verileri deneysel koşullar edilmiş alanıyla kıyaslanmıştır. Araştırmada önerilen yöntem hızlarında karanlık popülasyonlarının birbirinden ayırt edilebilirliğini koşullarda değişen durumların kamera görüntülerine etkisini olduğunu göstermiştir. Mevcut yöntemlerle kıyaslandığında, edilen sayısal bulgular, çalışmada sunulan yöntemin foto-bozunumunu büyük ölçüde önleyebilme potansiyelini ispatlamıştır moleküllerin özelliklerinin hangi gözlemlenebileceği ilgili optimizasyon çalışmalarının yapılmasına olanak sağlamaktadır.

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Multiplexed Near-IR Detection of Single-Molecule Fluorescence Fluctuations Using a Single Superconducting Nanowire Single-Photon Detector

ACS Photonics, Год журнала: 2025, Номер unknown

Опубликована: Март 28, 2025

Язык: Английский

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All-Optical Strategies to Minimize Photo-Bleaching in Reversibly Switchable Fluorescent Proteins

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

Abstract Photo-bleaching is a general hurdle of fluorescence-based techniques that becomes even more severe in high- resolution microscopy relies on prolonged, focused and complex illumination sequences. Strategies to reduce photo-bleaching require chemical modifications the cell media, which often stave off physiological cellular conditions. Here, we outline an all-optical strategy minimize reversibly switching fluorescent proteins (RSFPs), class probes used several super-resolution protein-multiplexing imaging techniques. By identifying photobleaching pathways, developed novel schemes increase number ON- OFF photo-switching cycles based designed modulation on-switching light or co-irradiation with red- shifted light. rationalizing photo-cycle, expand multiplexing strategies RSFPs spatiotemporal resolutions while maintaining accuracy recording longer time-lapse sub-cellular structures both confocal parallelized RESOLFT nanoscopy.

Язык: Английский

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Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(37), С. 24261 - 24278

Опубликована: Янв. 1, 2024

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented steady-state time-resolved fluorescence phosphorescence measurements. The processes the dichloromethane are resolved sub-100 fs temporal resolution using SWIR, near-IR, visible photoexcitation. Different population members ground-state inhomogeneous ensemble found to equilibrate

Язык: Английский

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Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties

Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(7), С. 6235 - 6241

Опубликована: Янв. 1, 2024

The aim of this study is to investigate the photophysical properties a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT.

Язык: Английский

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Photoisomerization of heptamethine cyanine (Cy7) dyes: A theoretical study

Dyes and Pigments, Год журнала: 2024, Номер 230, С. 112354 - 112354

Опубликована: Июль 27, 2024

In this study, density functional theory (DFT) combined with time-dependent (TD) DFT calculations were employed to investigate the photoisomerization reaction kinetics of two near infrared (NIR) heptamethine cyanine (Cy7-NH3 and Cy7-SO3) dyes in ground singlet state first excited state. We found that all-trans Cy7 molecules results at least one mono-cis all-cis species demonstrate redshifted emission, agreement recently published transient excitation modulation spectroscopy fluorescence correlation measurements. The transition states estimated for a whole pathway both potential energy surfaces. have isomers studied can be achieved through sequential two-step within surface, along double CC bond adjacent edge group (leading isomer 1) central-chain 2). Computations show all-trans→ 1→all-cis is limited by trans→ 1 stage, while 2→all-cis second stage. Accounting fact 2 demonstrates red-shifted emission compared form reachable energetically favorable we concluded experimentally observed Cy7-NH3 Cy7-SO3 should assigned formation species. If populated double-step it also considered as source emission. However, follows from our simulations, kinetically intricate achieve 2.

Язык: Английский

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Photophysics in Biomembranes: Computational Insight into the Interaction between Lipid Bilayers and Chromophores

Accounts of Chemical Research, Год журнала: 2024, Номер 57(16), С. 2245 - 2254

Опубликована: Авг. 6, 2024

ConspectusLight is ubiquitously available to probe the structure and dynamics of biomolecules biological tissues. Generally, this cannot be done directly with visible light, because absence absorption by those biomolecules. This problem can overcome incorporating organic molecules (chromophores) that show an optical response in vicinity Since properties are strongly dependent on chromophore's environment, time-resolved spectroscopic studies provide a wealth information biosystems at molecular scale nondestructive way. In work, we give overview multiscale computational strategy developed us last eight years prove theoretical simulations needed explain, guide, predict observations fluorescence experiments. As challenge accepted views existing probes, discover unexplored abilities discriminate surrounding lipid bilayers their temperature-dependent as well solvent-dependent properties. We focus three archetypal chromophores: diphenylhexatriene (DPH), Laurdan, azobenzene. Our method shows conformational changes should not neglected for prototype rod-shaped molecule DPH. They determine its position orientation liquid-ordered (Lo) sphingomyelin/cholesterol (SM/Chol) bilayer responsible strong differentiation spectra decay times dioleoylphosphatidylcholine (DOPC) dipalmitoylphosphatidylcholine (DPPC) membranes, which room temperature liquid-disordered (Ld) solid-gel (So) phases, respectively. Thanks pronounced first excited state dipole moment, Laurdan has long been known solvatochromic probe. however two conformers, they exhibit different membrane phases. see conformers only blocked one phase but another. Supported anisotropy simulations, therefore regarded rotor. Finally, versatility azobenzene saturated Ld simulated, along photoisomerization pathways. By means nonadiabatic QM/MM surface hopping analyses (QM/MM-SH), dual mechanism found torsional slow conversion trans-to-cis. For cis-to-trans, much higher quantum yield so-called "pedal-like" mechanism. The differences related potential energy surfaces interactions alkyl chains. When tails increased length attached probe, cis pushed toward polar surface, while trans pulled center membrane.

Язык: Английский

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Interplay between a Heptamethine Cyanine Dye Sensitizer (IR806) and Lanthanide Upconversion Nanoparticles

Advanced Optical Materials, Год журнала: 2024, Номер 12(29)

Опубликована: Июль 5, 2024

Abstract 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 sensitizers. However, despite much effort, understanding of this dye‐UCNP interplay is still limited. Major sensitization mechanisms are under discussion, largely because there a lack effective means to observe key factors such dark state transitions within the dyes. Here, combined spectroscopic procedure established systematically investigate photophysics behind interaction, embracing fluorescence‐based transient‐state excitation‐modulation, lifetime correlation spectroscopy, spectrofluorometry/spectrophotometry. With heptamethine cyanine IR806, typical UCNP sensitizer studied, its photophysical model established, in UCL‐sensitization‐related environments deciphered, energy transfer IR806 singlet excited Yb 3+ (UCNP ion) can be identified dominant mechanism. These studies suggest that form non‐emissive H‐aggregates at nanoparticle surfaces, which dissociated after certain light excitation duration (typically>100 µs). Moreover, buildup non‐fluorescent, photo‐redox longer irradiation times (10–100 ms) deleteriously affect UCL effect, inferring an optimal for dye‐sensitized UCNPs, relevant for, e.g., optical imaging applications.

Язык: Английский

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Dual-band vibrational lasing emission from cyanine derivatives

Dyes and Pigments, Год журнала: 2024, Номер 224, С. 112016 - 112016

Опубликована: Фев. 7, 2024

Язык: Английский

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Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 28, 2024

Abstract MINimal photon FLUXes (MINFLUX) offers super-resolution microscopy (SRM) with nanometer localization precision, more relaxed fluorophore brightness and photostability requirements than for other SRM techniques. Nonetheless, low probabilities have been reported in several MINFLUX studies, a broader use of less bright photostable fluorophores, including near-infrared (NIR) fluorophores has difficult to realize. In this work, we identified blinking as main cause erroneous (and dismissed) localizations imaging devised strategies overcome these effects. We systematically studied the blinking/switching properties cyanine emitting far-red or NIR range, over typical time scales (µs-10ms), sample excitation conditions used imaging. By subsequent simulations representative procedures, found that trans-cis isomerization, particular photo-reduction can generate significant errors. However, errors could be suppressed by balanced redox buffers repetitive beam scans. Implementing strategies, replacing slower, intrinsic switching needed transient binding fluorophore-labelled DNA strands complementary attached targets (DNA-PAINT), first demonstrate NIR-MINFLUX precision. This work presents an overall strategy, where characterization make it possible design optimal conditions, opening imaging, well related studies.

Язык: Английский

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