Effects of Na+ ions on breathing vibrational modes of poly (dT) center dotpoly (dA) center dot poly (dT)

A lattice dynamics model for poly (dT) (.) poly (dA) (.) poly (dT), which i s one of the best important triplex DNA was presented based on its screw sy mmetry. In this model, the presence of Na+ ions was included explicitly. Th e breathing modes of poly (dT) (.) poly (dA) (.) poly (dT) were calculated. By comparing the isolated triplex vibrational modes, it was found that the addition of Na' ions could extinguish very strong breathing modes of Hooge nsteen hydrogen bond located in 18. 4cm-1.36. 4cm-1 and 43. 8cm-1. The brea thing modes of Watson-Crick hydrogen bond were not changed obviously. These results indicate that Na' ions can increase the stability of poly(dT) (.) poly(dA) (.) poly(dT) and reasonably explain the melting experiment of poly (dT) (.) poly(dA) (.) poly (dT).