Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity.
BACKGROUND
The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH(2)) has been synthesized and characterized by Mass and (1)H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (T(m)) and fluorescence measurements.


METHODS
Thermal denaturation study of DNA duplex containing T target base revealed the DeltaT(m) of 5.1 degrees C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH(2) 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)x10(6) 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.


CONCLUSIONS
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.
Rajendran
Arivazhagan
A
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan. compubiol@gmail.com
Thiagarajan
Viruthachalam
V
Rajendar
Burki
B
Nishizawa
Seiichi
S
Teramae
Norio
N
D000042:Absorption; D001665:Binding Sites; D002412:Cations / Q000737:chemistry / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004249:DNA Damage / Q000502:physiology; D005453:Fluorescence; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D009711:Nucleotides / Q000378:metabolism*; D011719:Pyrazines / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity; D013997:Time Factors
C539380:3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide; D002412:Cations; D008024:Ligands; D009711:Nucleotides; D011719:Pyrazines; D004247:DNA