Journal
CHEMISTRY-A EUROPEAN JOURNAL
Volume 26, Issue 20, Pages 4539-4551Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/chem.201904396
Keywords
base pairs; biosensors; diamidines; DNA; minor groove binders
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A series of small diamidines with thiophene and modified N-alkylbenzimidazole sigma-hole module represent specific binding to single G.C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3)(3)](2)) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G.C bp highly specific binders extend the compound database for future biological applications.
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