NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA

Viruthachalam Thiagarajan, Arivazhagan Rajendran, Hiroyuki Satake, Seiichi Nishizawa, Norio Teramae

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)

Abstract

The binding behavior of green fluorescent ligands, derivatives of 7-nitrobenzo-2-oxa-1,3-diazole (NBD), with DNA duplexes containing an abasic (AP) site is studied by thermal denaturation and fluorescence experiments. Among NBD derivatives, N1-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)propane-1, 3-diamine (NBD-NH2) is found to bind selectively to the thymine base opposite an AP site in a DNA duplex with a binding affinity of 1.52X10 6m-1. From molecular modeling studies, it is suggested that the NBD moiety binds to thymine at the AP site and a protonated amino group tethered to the NBD moiety interacts with the guanine base flanking the AP site. Green fluorescent NBD-NH2 is successfully applied for simultaneous G>T genotyping of PCR amplification products in a single cuvette in combination with a blue fluorescent ligand, 2-amino-6,7-dimethyl-4- hydroxypteridine (diMe-pteridine).

Original languageEnglish
Pages (from-to)94-100
Number of pages7
JournalChemBioChem
Volume11
Issue number1
DOIs
Publication statusPublished - 2010 Jan 4

Keywords

  • Abasic site
  • DNA
  • DNA recognition
  • Fluorescence
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Organic Chemistry

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