The conjugates of cyanine dye and guanidiniocarbonyl-pyrrole as a fluorescent and CD probes for distinguishing between various double stranded DNA or double stranded RNA secondary structures

U sklopu rada okarakterizirana su dva nova konstitucijska izomera gvanidinijkarbonil-pirola (GCP) i 6-bromo-tiazol oranž (cijanin), koji se razlikuju u svojoj povezanosti: kod jednog konjugata GCP je s cijaninom vezan preko atoma dušika u benzotiazolu, a drugi konjugat je povezan preko dušika u kinolinu. Spojevi pokazuju različita svojstva u vodenom mediju, kao i različitost u prepoznavanju raznih dvolančanih DNA i dvolančanih RNA. Specifična karakteristika cijanina je povećana sklonost agregiranja u vodenom mediju. Oba spoja se efikasno vežu na dvolančane DNA i RNA s mikromolarnim afinitetom, s tim da je benzotiazolni izomer pokazao izrazitu fluorescentnu selektivnost prema dvolančanoj RNA, u usporedbi s ostalim ispitivanim dvolančanim DNA uzvojnicama, dok je kinolinski analog pokazao slabu fluorescencijsku selektivnost prema dvolančanoj GC-DNA. Vezanjem na DNA ili RNA, samo je izomer povezan preko kinolina pokazao, po vezanju na DNA/RNA, pojavu induciranog cirkularnog dikroizma (ICD; λ=450-550 nm), s tim da je pomoću ICD vrpci moguće pouzdano razlikovati A-T(U) polinukleotide od G-C polinukleotida.Two novel constitutional isomers of guanidiniocarbonyl-pyrrole (GCP) and 6-bromo-thiazole orange (cyanine) were characterized, differing only in linker connectivity between GCP and cyanine (benzothiazole nitrogen vs quinoline nitrogen). Conjugates revealed distinctively different properties in aqueous medium, as well as different recognition pattern of various ds-DNA or ds-RNA sequences. Namely, quinolone-linked was more prone to aggregation in aqueous medium. Both compounds effectively bind, with micromolar affinity, to double-stranded DNA and RNA, whereby benzothiazole-linked isomer showed distinct fluorimetric selectivity toward ds-RNA in comparison to any other tested ds-DNA, whereas the quinolone-linked analog showed similar fluorescence response to all studied DNA/RNA. By binding to DNA or RNA, only the quinoline analogue showed induced circular dichroism bands (ICD; λ = 450-550 nm), whereby it was possible to use an ICD bands to reliably differentiate AT (U) polynucleotides from GC polynucleotides