Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair

Sobek, Jens; Schlapbach, Ralph

doi:10.3390/molecules25225369

Cited by 9 publications

(13 citation statements)

References 102 publications

(159 reference statements)

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“…When Cy3 is used to label systems like proteins and DNA, it is usually attached to these systems via saturated aliphatic hydrocarbon linkers ( N -alkyl groups). ,,,, If the N -alkyl groups affect the electronic properties of the monomer, then one must account for them while deriving the atomic transition charges of the monomer. To investigate the effect of the N -alkyl groups on the monomer, we extended our electronic structure calculations on the Cy3 with N -methyl groups to N -ethyl and N -propyl groups, as shown in Figure .…”

Section: Results and Discussionmentioning

confidence: 99%

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

et al. 2021

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Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.

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Section: Results and Discussionmentioning

confidence: 99%

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

et al. 2021

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“…ZMWs have been applied to numerous biomolecular in vitro single-molecule studies, aiding in the elucidation of molecular interactions [ 26 , 32 – 68 , 70 – 76 ] and enzymatic reactions [ 8 , 18 , 20 , 31 , 76 , 77 ]. However, the successful implementation of ZMWs in in vitro single-molecule experiments necessitates the circumvention of several barriers, preventing the widespread use of ZMWs.…”

Section: Zmws For Single-molecule Fluorescence Imagingmentioning

confidence: 99%

Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies

2022

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Single-molecule technologies can provide detailed information regarding molecular mechanisms and interactions that cannot easily be studied on the bulk scale; generally, individual molecular behaviors cannot be distinguished, and only average characteristics can be measured. Nevertheless, the development of the single-molecule sequencer had a significant impact on conventional in vitro single-molecule research, featuring automated equipment, high-throughput chips, and automated analysis systems. However, the utilization of sequencing technology in in vitro single-molecule research is not yet globally prevalent, owing to the large gap between highly organized single-molecule sequencing and manual-based in vitro single-molecule research. Here, we describe the principles of zero-mode waveguides (ZMWs) and nanopore methods used as single-molecule DNA sequencing techniques, and provide examples of functional biological measurements beyond DNA sequencing that contribute to a global understanding of the current applications of these sequencing technologies. Furthermore, through a comparison of these two technologies, we discuss future applications of DNA sequencing technologies in in vitro single-molecule research.

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“…Fluorophores attached to DNA or RNA oligomers have enabled monitoring their migration during gel electrophoresis experiments [1] and the tracking of these polymers in single-molecule experiments. [2,3] Additionally, the binding interactions between DNA or RNA with other nucleic acids, [4] proteins, [5] or ligands, [6] as well as in sequencing-by-synthesis experiments, can be followed. [7] There exist many fluorophores tailored for various applications in which fluorescein, rhodamine, BODIPY, and cyanine3 (Cy3) or variants thereof are used with some frequency in nucleic acid visualization (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Fluorophore‐mediated photooxidation of the guanine heterocycle

Fleming

Xiao

Chabot

et al. 2022

J of Physical Organic Chem

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Fluorescent dyes are routinely used to visualize DNA or RNA in various experiments, and some dyes also act as photosensitizers capable of catalyzing oxidation reactions. The present studies explored whether the common labeling dyes fluorescein, rhodamine, BODIPY, or cyanine3 (Cy3) can function as photosensitizers to oxidize nucleic acid polymers. Photoirradiation of each dye in the presence of the guanine (G) heterocycle, which is the most sensitive toward oxidation, identified slow rates of nucleobase oxidation in the nucleoside and DNA contexts. For all four fluorophores studied, the only product detected was spiroiminodihydantoin (Sp), suggesting that the dyes functioned as Type II photosensitizers and generate singlet oxygen ( 1 O 2 ). The nucleoside reactions were then conducted in D 2 O solutions, known to increase the lifetime of 1 O 2 , which resulted in an $6-fold increase in the Sp yield, further supporting the classification of these dyes as Type II photosensitizers. Lastly, we inspected the pattern of G reactivity with the dyes upon photoirradiation in the context of a parallel-stranded G quadruplex. The G nucleotides in the two exterior G tetrads were found to be oxidation prone, providing the third line of evidence that the dyes are Type II photooxidants. The present work found that the common dyes fluorescein, rhodamine, BODIPY, or Cy3 can drive G oxidation but with a slow rate and low overall yield. This will likely not impact many experiments using dyes to study nucleic acids except for those that have long exposures with high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.

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Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair

Cited by 9 publications

References 102 publications

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies

Fluorophore‐mediated photooxidation of the guanine heterocycle

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