2‐(1‐Ethynylpyrene)‐Adenosine as a Folding Probe for RNA—Pyrene in or out

Abstract

A series of short RNA duplexes containing one or two 1-ethynylpyrene-modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature-dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene-rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A-U base pairs. Flanking G-C base pairs, even only in the 5'-direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene-pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.

The Three Possible 2‐(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers

“…Substitution of pyrene at a single position is possible—for symmetry reasons, only the positions 1, 2 and 4 are distinct—and has frequently been utilized to generate various fluorescent nucleoside analogues for nucleic acids research . In general, both, the position of the substitution and their nature were found to affect the electronic and spectral properties of pyrene derivatives .…”

“…[7,8] Substitution of pyrene at as ingle position is possible-for symmetry reasons, only the positions 1, 2a nd 4a re distinctand has frequently been utilized to generate various fluorescent nucleoside analogues for nucleic acids research. [9][10][11][12][13][14][15] In general, both, the position of the substitution and their nature were found to affect the electronic and spectral properties of pyrene derivatives. [16][17][18][19][20] Linked to nucleosides,p yrene often forms pronouncedc harget ransfer( CT) states after excitation, acting as electron donor and acceptor when linked to pyrimidines andg uanosine, respectively.…”

Fluorescent nucleobases as tools for studying DNA and RNA

“…The pyrene fluorophore appended on adenine A PY , A P and G P has allowed these nucleobases to be excited at long ultraviolet to short blue ranges (380 to 420 nm) while emitting blue light (450 to 480 nm) (Fig. 3d) 32–34 . In some rarer cases, the 7 position can also be appended with fluorescence extensions, with replacement of the nitrogen at the 7 position with carbon to preserve aromaticity.…”

Photophysical processes of the spectroscopic RNA probe 2-(1-ethynylpyrene)-adenosine (PyA)

“…Another favorable characteristic is the ability to form excimers upon close proximity of two PyAs of complementary strands in the minor groove [4]. Experiments revealed that PyA is also able to intercalate into RNA depending on the flanking bases in 5' direction of the modified base [5,6]. A G-C base pair leads to the intercalation of PyA, whereas A-U base pairs do not show this behavior.…”