Of pyrene fluoresce violet, at higher concentrations the fluorescence shifts 100 nm and becomes blue. This unstructured, long-wavelength emission arises from the formation of a charge-transfer complex between a pyrene in the excited state and another pyrene in the ground state. Since this complex must form within the lifetime of the excited state, the two pyrene molecules must be in close proximity – an ideal situation for developing DNA probes. By having two pyrene-labeled DNA probes, one with the pyrene on the 5′ terminus and the other on the 3′, the two pyrenes could be brought together by hybridizing in tandem to the target sequence, leading to excimer formation.2 This technique has been used recently to probe mRNA in cells, taking advantage of the relatively long fluorescence life time of the pyrene excimer.3 An interesting development came when Korshun attached the pyrene to the 5 position of deoxyuridine through a triple bond (Figure 1).4 By doing so, the pyrene is electronically coupled to the deoxyuridine base as shown by the redshifting of the pyrene absorbance by more than 50 nm compared to the unsubstituted 1-ethynylpyrene. 5 This electronic coupling of the base and the pyrene makes the fluorescence of the pyrene sensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.104987-11-3 custom synthesis 6 This coupling also allows photoinduced charge transfer to occur upon excitation of the pyrene, essentially `injecting’ electrons into the duplex.587871-26-9 site 7 The only downside is a substantial reduction of the Stokes’ shift of the excimer’s fluorescence compared to the monomer, dropping from circa 100 to 14 nm, as shown in Figure 2A on the Back Page.PMID:25905390 To complement the Pyrene-dU, we are also introducing its longer wavelength cousin, Perylene-dU (Figure 1). The PerylenedU is another fluorescent polycyclic aromatic hydrocarbon that can form excimers. As with the Pyrene-dU, the Perylene analog has been shown to be sensitive to its hybridization state. 8 When used in tandem, perylene and pyrene have been shown to form exciplexes9 giving rise to a broad range of fluorescence 12
emission depending upon the sequence and spacing between the fluorophores. Absorption and emisssion data for Pyrene-dU and Perylene-dU are collected in the Table and the emission spectrum for Perylene-dU with the absorption spectrum as an insert is shown in Figure 2B on the Back Page. We are happy to introduce these interesting new products to our repertoire of unusual bases. TECHNICAL BRIEF – ABOUT ACTIVATORS: NOW AND TOMORROW
1H-Tetrazole One of the first activators described for phosphoramidite chemistry was 1HTetrazole and this has been the mainstay since its introduction for use with DNA synthesis. Other products have been introduced that have advantages over 1Htetrazole, however none has been truly a universal replacement for 1H-Tetrazole. Nevertheless, the sun may be setting on 1HTetrazole as the activator of choice for DNA and RNA synthesis and this note discusses the properties 1H-Tetrazole and its inherent weaknesses as an activator. Several other choices for activator are also described. The study of the mechanism of 1HTetrazole activation by Dahl 1, Berner 2, as well as others, led to the proposal of a two step reaction of tetrazole with phosphoramidites. First, tetrazole protonates the diisopropylamino group of the phosphoramidite and then displaces diisopropylamine by nucleophilic substitution to form the a.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com