NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA.
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, N(1)-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)propane-1,3-diamine (NBD-NH(2)) is found to bind selectively to the thymine base opposite an AP site in a DNA duplex with a binding affinity of 1.52 x 10(6) M(-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-NH(2) 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).
Thiagarajan
Viruthachalam
V
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Japan.
Rajendran
Arivazhagan
A
Satake
Hiroyuki
H
Nishizawa
Seiichi
S
Teramae
Norio
N
D001393:Azoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D009578:Nitrobenzenes / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D011621:Pteridines / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*; D044366:Transition Temperature
C510797:7-nitrobenz-2-oxa-1,3-diazol-4-yl; D001393:Azoles; D015342:DNA Probes; D005456:Fluorescent Dyes; D008024:Ligands; D009578:Nitrobenzenes; D011621:Pteridines; D004247:DNA; C006542:2-amino-4-hydroxypteridine; D013941:Thymine