Binding study of bisbenzimide Hoechst 33258 with DNA/RNA using surface-enhanced Raman scattering spectroscopy

Spektroskopijom površinski pojačanog Ramanovog raspršenja (SERS) istražene su interakcije molekula Hoechst 33258 (H33258) s dvolančanim sintetskim DNA/RNA polinukleotidima (poli dA-poli dT, poli dG-poli dC, poli rA-poli rU) te prirodnom ct-DNA. Kompleksi su pripravljeni u molarnim omjerima [H33258]/[polinukleotid] = 1/1, 1/5 i 1/10 u koloidnim suspenzijama srebrovih nanočestica stabiliziranih površinskim slojem negativno nabijenih kloridnih iona (AgNP_Cl) i pozitivno nabijenih molekula spermina (AgNP_sp). Prije analize načina vezanja s polinukleotidima, istražena je agregacija H33258 u rasponu koncentracija 1×106–1×104 mol/L, pri čemu su opaženi SERS spektri karakteristični za agregirane i monomerne vrste. SERS spektri H33258 s DNA analozima ukazali su na vezanje molekula u mali utor AT polinukleotida te djelomično interkaliranje između parova baza gvanina i citozina pristupom kroz veliki utor GC polinukleotida. Promjene u SERS spektrima kompleksa s RNA analogom, upućuju na interakcije male molekule s adeninom. Spektralne karakteristike H33258 dominiraju u spektrima kompleksa s ct-DNA, najvjerojatnije zbog nasumičnih sljedova AT i GC prirodnog polinukleotida.Interactions of Hoechst 33258 (H33258) molecules with double-stranded synthetic DNA/RNA polynucleotides (poly dA-poly dT, poly dG-poly dC, poly rA-poly rU) and natural ct-DNA were studied by surface-enhanced Raman scattering (SERS) spectroscopy. Complexes were prepared in molar ratios [H33258]/[polynucleotide] = 1/1, 1/5 and 1/10 in colloidal suspensions of silver nanoparticles stabilized by a surface layer of negatively charged chloride ions (AgNP_Cl) and positively charged spermine molecules (AgNP_sp). Prior to the polynucleotide binding assay, aggregation of H33258 in the concentration range 1×106–1×104 mol/L was investigated, whereby SERS spectra characteristic of aggregated and monomeric species were observed. The SERS spectra of H33258 with DNA analogs indicated binding of molecules into the minor groove of AT polynucleotide and partial intercalation between guanine and cytosine base pairs by access through the major groove of GC polynucleotide. Changes in the SERS spectra of the complex with the RNA analog implied interactions of small molecules with adenine. The spectral characteristics of H33258 dominated in the spectra of complexes with ct-DNA, most likely due to random AT and GC sequences of the natural polynucleotide