A short, rigid linker between pyrene and guanidiniocarbonyl-pyrrole induced a new set of spectroscopic responses to the ds-DNA secondary structure

Abstract

A novel pyrene-guanidiniocarbonyl-pyrrole dye, characterised by a short, rigid linker between the two chromophores, interacts strongly with ds-DNA but only negligibly with ds-RNA. Under neutral conditions the dye shows strong selectivity toward AT-DNA (with respect to GC-DNA). Binding is accompanied by a specific ICD band at 350 nm and fluorescence quenching for all DNAs/RNAs studied. At pH 5 the affinity of the dye is reversed, now favouring GC-DNA over AT-DNA. A strong emission increase for AT-DNA is observed but with quenching for GC-DNA.

Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate

“…Intriguingly, the fluorimetric response of 1 was identical to experiments done at pH 7, while 2 showed a slightly different fluorescence recognition pattern at pH 5, showing a small fluorimetric preference for mixed ct-DNA, followed by GC-DNA and AU-RNA. The reason why both new dyes ( 1 , 2 ) did not show a pronounced impact of pH on their fluorimetric response, as previously noted for e.g., series of pyrene—GCP analogs [ 13 , 14 , 15 ], is probably because cyanine fluorophore is cationic itself, and thus not so dependent in binding to DNA/RNA on the additional positive charge of GCP present only at pH 5.…”

“…At variance to all previously studied aryl-GCP conjugates [ 10 , 11 , 12 , 13 , 14 , 15 ] and even the Cy-GCP [ 17 ] (very close analog of 2 ), no ICD bands of GCP chromophore (at λ = 300 nm) were observed, pointing out that for both, 1 and 2 , GCP moiety was not uniformly oriented in respect to the polynucleotide chiral axis [ 32 ], similar as previously noted for nucleobase-GCP analogs [ 33 ].…”

“…For instance, pyrene-GCP analogs have been shown to be very efficient single-molecule- multipurpose probes, being able to recognize between various ds-DNA and ds-RNA by simultaneous specific responses in fluorescence and circular dichroism [ 13 , 14 ]. Moreover, recently reported pyrene-GCP analog fluorimetric recognition of DNA/RNA could be reversibly controlled by pH [ 15 ].…”

A Quadrupolar Bis‐Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins

“…Furthermore, 1 binds to ds‐DNA/RNA as a groove binder but, in contrast with most groove binders, it also interacts strongly with ss‐RNA, by acting as a spindle around which ss‐RNAs are wrapped due to a combination of electrostatic, H‐bonding and hydrophobic interactions. As most small molecule interactions with ss‐RNA are based on an intercalative binding mode, often combined with additional H‐bonding, whereby helicity of ss‐RNA is preserved or even enhanced, the binding mode of 1 presented herein is unique. Such ss‐RNA condensation due to complexation (extended strand to globular transformation) could protect its backbone against RNAase degradation and also facilitate its cellular uptake and distribution, opening new possibilities for RNA‐based applications.…”

Syntheses of Enantiopure 1,2-Ethylenediamines with Tethered Secondary Amines of the Formula H2NCH2CH[(CH2) n NHMe]NH2 (n = 1–4) from α-Amino Acids: New Agents for Asymmetric Catalysis

“…12 As for all 'new steps' in this study, the product was characterized by NMR ( 1 H, 13 C{ 1 H}) and microanalysis. Per an earlier report, 13 a modern version of the Hofmann rearrangement that uses an iodine(III) oxidant was employed to convert 1 into the primary amine 2 in 85% yield. The amine was subsequently treated with ethyl chloroformate to give the ethyl carbamate 3, a new compound.…”