Simultaneous recognition of nucleobase and sites of DNA damage: Effect of tethered cation on the binding affinity

Arivazhagan Rajendran, Viruthachalam Thiagarajan, Burki Rajendar, Seiichi Nishizawa, Norio Teramae

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)


Background: The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH2) has been synthesized and characterized by Mass and 1H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (Tm) and fluorescence measurements. Methods: Thermal denaturation study of DNA duplex containing T target base revealed the ΔTm of 5.1 °C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH2 is quenched only upon adding the DNA containing T target base. Results: The binding constant for the interaction of the ligand to T target base containing DNA duplex was determined to be 4.7 (± 0.3) × 106 M- 1. The tethered cation in the ligand is found to enhance the binding constant. The ligand binds to both a target nucleotide and an AP site on the complimentary strand for the target strand in a DNA duplex. General significance: Interestingly, the electronic behavior of the ligand depends on the bases flanking the AP site. Its fluorescence is quenched with guanine flanking bases, while it is enhanced with DNA duplex containing T bases flanking an AP site. Finally, the binding modes were visualized by molecular modeling.

Original languageEnglish
Pages (from-to)95-100
Number of pages6
JournalBiochimica et Biophysica Acta - General Subjects
Issue number2
Publication statusPublished - 2009 Feb


  • Abasic site
  • Flanking base
  • Molecular modeling
  • Nucleobase recognition
  • Single nucleotide polymorphism


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