Time-resolved single molecule fluorescence spectroscopy of Cy5-dCTP: influence of the immobilization strategy

Solvent-Free and Efficient One-Pot Strategy for Synthesis of the Triazine-Heterocycle Azacyanines

A novel method with great universality for preparing the electron-rich and electron-deficient triazine-heterocycle azacyanines was presented by using only dibromomethane as a catalysis and solution. The high boiling temperature of dibromomethane has a more flexible reaction condition, allowing all three azacyanine products a chance to yield over 80%. The FT-IR element analysis and all necessary tests, even signal-crystal tests, were executed to firmly confirm that the molecular structure of the azacyanines was accurate. This principal reaction route design that provides a new opportunity for the preparation of azacyanines and their derivatives in a cost-effective and simple process shows great potential for industrial-scale preparation of this important azacyanine intermediate product.

Novel Fluorescent Azacyanine Compounds: Improved Synthesis and Optical Properties

Benzothiazoles are known to possess a number of biological activities and therefore are considered to be an important scaffold in the design and synthesis of pharmacophores. In this study, an improved synthesis method for novel fluorescent benzothiazole-based cyclic azacyanine (CAC) dyes bearing different electron-donating/withdrawing groups on their scaffold is presented. The improved method enabled us to increase the synthesis yield for the previously reported CACs. More importantly, it allowed us to synthesize new CAC dyes that were not synthesizable with the previously reported method. The synthesized dyes were characterized by ¹H and ¹³C NMR spectroscopy, elemental analysis, and mass spectrometry and their optical (absorption and fluorescence) properties were investigated. All of the synthesized CACs were found to be displaying strong absorption within the range of 387-407 nm. The spectral shifts observed in the absorption and fluorescence measurements suggested that the spectroscopic and optical properties of CACs can be directly modulated by the nature of the electron-donating/withdrawing substituents. The fluorescence quantum yields (QYs) of the unsubstituted (parent CAC) and substituted CACs were also measured and compared. The fluorescence QY of CACs with electron-donating substituents (methoxy or ethoxy) was found to be at least four times higher than that of the parent CAC with no substitutions.

DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes

Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.

Cyclic azacyanines: experimental and computational studies on spectroscopic properties and unique reactivity

The absorption and fluorescence properties of cyclic azacyanine (CAC) derivatives were examined in several solvents. The presence of electron donating or withdrawing groups on the CAC impacts spectroscopic properties. The general solvent relaxation displayed by azacyanine derivatives is in accordance with Lippert-Mataga's prediction but exception is noted in the case of protic solvent due to specific hydrogen bonding interactions. Fluorescence lifetime decay studies indicate a relaxation time in the nanosecond timescale with mono exponential decay. Donating substituents markedly increase the excited state lifetime, whereas withdrawing groups marginally decrease the excited state lifetime. Quantum chemical computations were used to explore the origins of the reactivity and spectroscopic properties of CACs; results are consistent with a model in which regioselectivity results from differences in mechanistic steps occurring after initial attack by hydroxide on the CAC.

SOLVING SINGLE BIOMOLECULES BY ADVANCED FRET-BASED SINGLE-MOLECULE FLUORESCENCE TECHNIQUES

The use of Förster resonance energy transfer (FRET) has undergone a renaissance in the last two decades, especially in the study of structure of biomolecules, biomolecular interactions, and dynamics. Thanks to powerful advances in single-molecule fluorescence (SMF) techniques, seeing molecules at work is a reality, which has helped to build up the mindset of molecular machines. In the last few years, many technical developments have broadened the applications of SMF-FRET, expanding the amount of information that can be recovered from individual molecules. Here, we focus on the non-standard SMF-FRET techniques, such as two-color coincidence detection (TCCD), alternating laser excitation (ALEX), multiparameter fluorescence detection (MFD); the addition of fluorescence lifetime as an orthogonal dimension in single-molecule experiments; or the development of novel and improved methods of analysis constituting to a set of advanced methodologies that may become routine tools in a close future.

[Formula: see text]Special Issue Comment: This review about advanced single-molecule FRET techniques is specially related to the review by Jørgensen and Hatzakis,6 who detail experimetal strategies to solve the activity of single enzymes. The advanced techniques described in our paper may serve as interesting alternatives when applied to enzyme studies. Our manuscript is also related to the reviews in this Special Issue that deal with model solving.22,130