Title
Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response
Author
Ivo Crnolatac, Iva Rogan, Boris Majić, Sanja Tomić, Todor Deligeorgiev, Gordan Horvat, Damjan Makuc, Janez Plavec, Gennaro Pescitelli, Ivo Piantanid
Year
2016
Journal
Analytica Chimica Acta
Abstract
Two small molecules showed intriguing properties of analytical multipurpose probes, whereby one chromophore gives different signal for many different DNA/RNA by application of several highly sensitive spectroscopic methods. Dyes revealed pronounced fluorescence ratiomeric differentiation between ds-AU-RNA, AT-DNA and GC-DNA in approximate order 10:8:1. Particularly interesting, dyes showed specific fluorimetric response for poly rA even at 10-fold excess of any other ss-RNA, and moreover such emission selectivity is preserved in multicomponent ss-RNA mixtures. The dyes also showed specific chiral recognition of poly rU in respect to the other ss-RNA by induced CD (ICD) pattern in visible range (400-500 nm), which was attributed to the dye-side-chain contribution to binding (confirmed by absence of any ICD band for reference compound lacking side-chain). Most intriguingly, minor difference in the side-chain attached to dye chromophore resulted in opposite sign of dye-ICD pattern, whereby differences in NMR NOESY contacts and proton chemical shifts between two dye/oligo rU complexes combined with MD simulations and CD calculations attributed observed bisignate ICD to the dimeric dye aggregate within oligo rU.
Instrument
J-815
Keywords
Circular dichroism, Secondary structure, DNA structure, Ligand binding, Biochemistry