Development of novel polymer-coated substrates for straightening and fixing DNA

We developed polymer-coated glass substrates for DNA stretching and fixation to analyze the precise gene location on DNA by fluorescence microscopy and atomic force microscopy (AFM). We observed partially stretched and many aggregated DNA molecules on uncoated glass, indicating that DNA interacted rigidly with the surface because of the strong polarity of the glass surface. Few DNA molecules were fixed on polyvinylbutyral (PVB) coated glasses, however, indicating that the interaction between DNA and the surface was weaker than that on the uncoated surface because of the strong hydrophobic surfaces. Observed images demonstrated that DNA was sufficiently fixed and stretched on poly(vinylcarbazole) (PVCz) and polyphenazasiline (PPhenaz) coated surfaces. Furthermore, PPhenaz- and PVCz-coated surfaces provided adequate AFM observation of stretched DNA molecules. This specific interaction is considered to be attributed to pi-pi interaction (pi-stacking) between aromatic amines in polymers and base pairs in DNA molecules.