1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer

Astakhova, Kira; Malakhov, Andrei D.; Степанова, И. А.; Устинов, Алексей Владимирович; Бондарев, С. Л.; Paramonov, Alexander S.; Korshun, Vladimir A.

doi:10.1021/bc700280h

Cited by 42 publications

(35 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In moving systems, more complex imaging setups are required, including rapid filter wheel changes or multichannel imaging systems, increasing the complexity and cost of the instrumentation. [12] The synthesis is shown in Scheme S1 of the Supporting Information, in addition details and spectral characterization are given. Inorganic quantum dots can address this problem in part by taking advantage of a single UV excitation; [7] however, they present some of their own limitations as biological labels, including large size, multivalency, toxicity, and limited cellular permeability.…”

mentioning

confidence: 99%

DNA Polyfluorophores for Real‐Time Multicolor Tracking of Dynamic Biological Systems

et al. 2012

View full text Add to dashboard Cite

It is becoming widely appreciated that complex biological networks and interaction events need to be understood not only in the three spatial dimensions but also in the fourth dimension, time. To address this need, fluorescence imaging with light microscopy has entered a dynamic era. A series of time-lapsed images or an aggregated video of a dynamic event imparts much more information than a single still image, better revealing the natural organization and flow of biological processes. The widespread application of fluorescent proteins, [1] quantum dots, [2] and small-molecule fluorophores [3] in time-lapsed imaging, along with state-of-the-art optical technologies, such as super-resolution microscopy, [4] and integrated systems, such as intravital microscopy, [5] have aided enormous advances in understanding cellular and organismal biology. Tracking the movements of molecular and cellular targets has helped reveal processes such as metastasis, [6] secretory pathway cargo transfer, [1] and many more. The timeframe of the studied events can vary from hours to minutes, or even seconds.Although it is possible to track sub-second motions by light microscopy, simultaneously tracking vectors of multiple species is hindered by the spectral limitations of common organic dyes and proteins, which require separate excitation wavelengths and emission filters. This drawback prevents the experimenter from recording visualization of multiple colors in real time, and thus most current multicolor labeling studies are based on post-image merging of multiple false-colored images. In moving systems, more complex imaging setups are required, including rapid filter wheel changes or multichannel imaging systems, increasing the complexity and cost of the instrumentation. Even with this added sophistication, timescales and numbers of colors are limited. Inorganic quantum dots can address this problem in part by taking advantage of a single UV excitation; [7] however, they present some of their own limitations as biological labels, including large size, multivalency, toxicity, and limited cellular permeability. [8] Ideally, small-molecule, water-soluble organic dyes could be useful in multicolor dynamic imaging if they could be excited at one wavelength. In previous studies, we developed a new class of fluorescent dyes (oligodeoxyfluorosides (ODFs)) in which fluorescent aromatic species replace nucleobases in short DNA-like oligomers. [9] This molecular design has the advantage of rapid automated synthesis of thousands of possible composite dyes from a few components. In addition, the short DNA-like oligomers retain small size, are water-soluble, and are easily conjugated to small molecules and biomacromolecules. [10] An early study of a set of ODF fluorophores demonstrated multicolor emissions (in excess of ten colors) with single long wavelength UV excitation. [9] However, this first-generation set of dyes exhibited some limitations, such as low quantum yields of some monomers and oligomers, the chemical instability of one monomer...

show abstract

mentioning

confidence: 99%

DNA Polyfluorophores for Real‐Time Multicolor Tracking of Dynamic Biological Systems

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Recently, several groups reported the synthesis of nucleic acid structures with continuous helical arrangement of several pyrene moieties, which resulted in the formation of the strong excimer band 20–26. As highlighted in several articles, the spectroscopic properties of alkynylpyrene analogues are derived from those of the parent pyrene 27–30. Thus, substitutions of pyrene at positions 1, 3, 6, and/or 8 via an acetylene bridge leads to a bathochromic shift in the absorption/emission spectra accompanied by high fluorescence quantum yields, even in the presence of oxygen 27–29.…”

Section: Introductionmentioning

confidence: 99%

1‐, 2‐, and 4‐Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship

Filichev

Astakhova

Malakhov

et al. 2008

Chemistry A European J

View full text Add to dashboard Cite

A postsynthetic, on-column Sonogashira reaction was applied on DNA molecules modified by 2- or 4-iodophenylmethylglycerol in the middle of the sequence, to give the corresponding ortho- and para-twisted intercalating nucleic acids (TINA) with 1-, 2-, and 4-ethynylpyrene residues. The convenient synthesis of 2- and 4-ethynylpyrenes started from the hydrogenolysis of pyrene that has had the sulfur removed and separation of 4,5,9,10-tetrahydropyrene and 1,2,3,6,7,8-hexahydropyrene, which were later converted to the final compounds by successive Friedel-Crafts acetylation, aromatization by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone, and a Vilsmeier-Haack-Arnold transformation followed by a Bodendorf fragmentation. Significant alterations in thermal stability of parallel triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in homopyrimidine TINAs. Thus, for para-TINAs the bulge insertion of an intercalator led to high thermal stability of Hoogsteen-type parallel triplexes and duplexes, whereas Watson-Crick-type duplexes were destabilized. In the case of ortho-TINA, both Hoogsteen and Watson-Crick-type complexes were stabilized. Alterations in the thermal stability were highly influenced by the ethynylpyrene isomers used. This also led to TINAs with different changes in fluorescence spectra depending on the secondary structures formed. Stokes shift of approximately 100 nm was detected for pyren-2-ylethynylphenyl derivatives, whereas values for 1- and 4-ethynylpyrenylphenyl conjugates were 10 and 40 nm, respectively. In contrast with para-TINAs, insertion of two ortho-TINAs opposite each other in the duplex as a pseudo-pair resulted in formation of an excimer band at 505 nm for both 1- and 4-ethynylpyrene analogues, which was also accompanied with higher thermal stability.

show abstract

“…[26,27] One of the primary reasons for the positive effect of the modifications on stability is their tendency to develop stacking interactions among themselves or with the nucleobases. [16,17,28,29] Anthraquinone and its derivatives are well-known intercalators. [30,31] They are a frequently found motif in DNA targeting drugs.…”

Section: Introductionmentioning

confidence: 99%

Anthraquinones as Artificial DNA Building Blocks

2008

View full text Add to dashboard Cite

Synthesis and properties of oligodeoxynucleotides containing anthraquinone-derived building blocks with flexible linkers are described. Starting from the 1,4-, 1,5-, 1,8-and 2,6-dihydroxyanthraquinone isomers, the corresponding phosphoramidites were prepared and incorporated into oligonucleotides. The site of linker attachment was found to be of critical importance for hybrid stability. Whereas the 2,6-iso-

show abstract

1-Phenylethynylpyrene (1-PEPy) as Refined Excimer Forming Alternative to Pyrene: Case of DNA Major Groove Excimer

Cited by 42 publications

References 60 publications

DNA Polyfluorophores for Real‐Time Multicolor Tracking of Dynamic Biological Systems

DNA Polyfluorophores for Real‐Time Multicolor Tracking of Dynamic Biological Systems

1‐, 2‐, and 4‐Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship

Anthraquinones as Artificial DNA Building Blocks

Contact Info

Product

Resources

About