RNA as scaffold for pyrene excited complexes

Grünewald, Christian; Kwon, Tae-Dong; Piton, Nelly; Förster, Ute; Wachtveitl, Josef; Engels, Joachim W.

doi:10.1016/j.bmc.2007.04.058

Cited by 49 publications

(52 citation statements)

References 22 publications

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“…After desalting, the oligonucleotides were analysed by using MALDI-TOF mass spectrometry (see ref. [36] and Figures S1 and S2 in the Supporting Information for experimental details). Sequences and pyrene positions of the chosen compounds are listed in Table 1.…”

Section: Synthesismentioning

confidence: 97%

“…Synthesis of the modified oligonucleotides was carried out as previously described. [36] In short, synthesis of oligonucleotides followed standard procedures using the well-established 2'-O-bis(2-acetoxyethoxy)-methyl (ACE) orthoester chemistry. [37] Site-specific modification with 1-ethynylpyrene was accomplished by using Sonogashira cross-coupling to an iodinated nucleobase (adenine) within the strand while still on solid support; [38] this exploited the general advantages of solid-phase synthesis (high yield, ease of purification, etc.…”

Section: Synthesismentioning

confidence: 99%

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

et al. 2010

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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.

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Section: Synthesismentioning

confidence: 97%

Section: Synthesismentioning

confidence: 99%

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

et al. 2010

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“…act as an universal RNA folding probe which only slightly disturbs the RNA structure. The pyrene moiety is thought to point out into the minor groove of RNA in an A-form helix [4]. Another favorable characteristic is the ability to form excimers upon close proximity of two PyAs of complementary strands in the minor groove [4].…”

Section: Introductionmentioning

confidence: 99%

“…The pyrene moiety is thought to point out into the minor groove of RNA in an A-form helix [4]. 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].…”

Section: Introductionmentioning

confidence: 99%

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

Trojanowski

Plötner

Grünewald

et al. 2013

EPJ Web of Conferences

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Abstract. We examine the photoinduced excited state dynamics of pyrene modified adenosine, a versatile probe for folding and hybridization of ribonucleic acids. Measurements in different solvents revealed complex ultrafast dynamics, but high robustness since the overall fluorescence quantum yield ( f ) is hardly affected. The result is a strong fluorescent RNA-probe whose spectral properties change in a defined way upon environmental changes.

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Tris(2-acetoxyethoxy)orthoformate

Desaulniers

2010

Encyclopedia of Reagents for Organic Synthesis

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RNA as scaffold for pyrene excited complexes

Cited by 49 publications

References 22 publications

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

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

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

Tris(2-acetoxyethoxy)orthoformate

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