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Guanidino-aryl derivatives: protonation and structure tuning for spectrophotometric recognition of ds-DNA and ds-RNA

A series of aryl-substituted guanidines revealed pKa about 10 in aqueous medium, thus positioning themselves between more basic aliphatic guanidines (pKa >13) and acidic guanidinocarbonyl-pyrrole (pKa 6). The study revealed that for the biorelevant (micromolar) affinity toward ds-DNA and ds-RNA the minimal size of aryl-unit is anthracene. Further aryl-increase (pyrene, porphyrin) did not result in stronger affinity toward ds-DNA/RNA, nor gave significant thermal stabilisation of DNA/RNA double helix, thus suggesting that aromatic stacking interactions between compounds and DNA/RNA are not dominant binding interaction. Generally, results suggested that aryl- guanidines binding to DNA/RNA grooves by combination of hydrophobic, electrostatic, H-bonding and Van der Waals interactions, whereby fluorescence of the two largest aromatics (pyrene, porphyrin) was highly sensitive in fine probing of DNA/RNA groove properties. In addition, pyrene and porphyrin analogues at excess to polynucleotide binding sites aggregated within polynucleotide groove, yielding fine recognition between various ds- DNA and ds-RNA by induced circular dichroism signals.

Aryl-guanidine ; DNA/RNA recognition ; Fluorescence ; Circular dichroism ; Dye aggregation

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