Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response.
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.
Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia.
Ivo
I
Crnolatac
Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia.
Iva
I
Rogan
Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia.
Boris
B
Majić
Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia.
Sanja
S
Tomić
Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria.
Todor
T
Deligeorgiev
Department of Physical Chemistry, Faculty of Science/Chemistry, Horvatovac 102A, HR-10000 Zagreb, Croatia.
Gordan
G
Horvat
Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana, Slovenia.
Damjan
D
Makuc
Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, Ljubljana, Slovenia.
Janez
J
Plavec
Department of Chemistry, University of Pisa, Via Moruzzi 13, Pisa, Italy.
Gennaro
G
Pescitelli
Division of Organic Chemistry and Biochemistry, Division of Physical Chemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia. Electronic address: pianta@irb.hr.
Ivo
I
Piantanida
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D015335:Molecular Probes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
D015335:Molecular Probes; D004247:DNA
Chiral recognition; DNA/RNA recognition; Fluorescence; Induced circular dichroism; Molecular modelling