Single Molecular Film for Recognizing Biological Molecular Interaction: DNA-Protein Interaction and Enzyme Reaction

Abstract

Protein–protein and protein–substrate interactions play essential roles in biological functions. Surface forces measurement and atomic force microscopy, which directly measure the interaction forces as a function of the surface separation, enable us to quantitatively evaluate these interactions [1–3]. We have employed the surface forces measurement [4] and colloidal probe atomic force microscopy [5] to study interactions involved in specific molecular recognition of DNA–protein and enzyme–substrate reaction. Studied are interactions between nucleic acid bases (adenine and thymine) [6], Spo0A–DB (the DNA-binding site of a transcription factor Spo0A), and DNA [7,8], those between subunits I and II of heptaprenyl diphosphate (HepPP) synthase in the presence of a substrate ((E,E)-farnesyl diphosphate, FPP) and a cofactor (Mg²⁺) [9–11], and the selectivity of the substrates in this enzymatic reaction [12]. Keys of our approach are the preparation of well-defined samples and the appropriate analysis. We have modified he substrate surfaces with these proteins using the Langmuir–Blodgett (LB) method. This chapter reviews the LB modification method and subsequent demonstrations of biological specific interactions employing this approach.