Cd Spectral And Thermal Denaturation Profiles For The Ct-Dna Binding Of Cationic Methylene Blue Dye

Mudasir^*,1, Nurul Hidayat Aprilita¹ and Naoki Yoshioka^2
1Chemistry Department, Gadjah Mada University, Sekip Utara P.O. Box Bls. 21,Yogyakarta 5528, Indonesia
²Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku,Yokohama 223-8522, Japan
^*Corresponding author: mudasir@ugm.ac.id; dasir01(at)yahoo.com

Abstract
The circular dichroism (CD) spectral and thermal denaturation (Tm) profiles of the binding of methylene blue (MB) to calf-thymus (CT)-DNA has been systematically investigated. The induced CD signals of MB/CT-DNA complex are relatively small and change sign and shape on going from low to high ionic strength (NaCl). These CD spectral profiles suggest that the binding of the dye at low ionic strength to CT-DNA appears to be intercalative and to occur likely at GC-like sites. With increasing ionic strength, the dye appears to change binding preference and move to AT-likes sites. The CD spectral profiles of MB/CT-DNA complex at ionic strength of 50 mM are independent of temperature, showing no change in sign and shape upon increasing temparature in the range of 11-39 ^oC. A moderate stabilization of double helix ct-DNA occurs when the MB dye binds to ct-DNA indicated by the increase in Tm of ct-DNA of about 5.5 ^oC in the presence of MB. This suggests that MB dye possibly binds to ct-DNA via both electrostatic and intercalation modes.

Keywords: methylene blue, DNA-binding ligand, circular dichroism, thermal denaturation, cationic dye

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