Self-Assembly Properties and Dynamics of Synthetic Proteo–Nucleic Building Blocks in Solution and on Surfaces

Abstract

Synthetic proteo-nucleic structures (PDNAs) encompassing a single-stranded DNA sequence covalently attached to a redox protein domain able to interact with surface or matrix were designed and characterized. They constitute versatile building blocks alternative to regular DNA for creating scaffolds with optical, electrical, or catalytic properties. PDNAs self-assemble in the presence of complementary oligonucleotides, to form a network of protein domains linked by double-stranded DNA segments. Electrophoretic and hydrodynamic behaviors of PDNAs and corresponding DNA were compared under electrophoresis and gel filtration conditions. Hybridization rates between small and large assemblies were characterized by rapid-mixing experiments. Results showed that the protein part significantly contributes to hydrodynamic behaviors of structures but marginally affects the conformation and hybridization properties of the nucleic domain. PDNA metal-mediated complexes with nitriloacetate-modified phospholipids can diffuse and interact at the surface of vesicles or supported membranes. Surface plasmon resonance analysis of membrane-PDNA interactions indicated that two protein units are required to allow stable surface association and that surface occupancy constrains assembly sizes. High-speed atomic force microscopy illustrated rapid lateral diffusion of assemblies on mica, revealing transient association between noncomplementary PDNA extremities and frequent trapping by surface defects. Regularly organized protein domains were visualized using a larger DNA framework.

Filming Biomolecular Processes by High-Speed Atomic Force Microscopy

“…Importantly, the function of fragile molecules is not disturbed by the interaction with the cantilever tip (detailed in section , Minimizing Invasiveness: The Tip–Sample Interaction). This performance made it possible to directly observe the structural dynamics and dynamic processes of biomolecules in action, providing a straightforward understanding of how the biomolecules operate to function. − In the past few years, various biomolecular systems and their dynamic events have been studied using HS-AFM, continuously demonstrating the innovative power of this novel microscopy to reveal details of molecular action inaccessible to other approaches. − Very recently, the analysis of dynamic events occurring in live cells has also become possible. − Most of the biological HS-AFM studies on proteins and cells performed since 2006 are listed in Table .…”

Biochip data normalization using multifunctional probes

“…To multifunctionalize the probes in the general field of biomolecular interactions, an ssDNA calibration sequence can be conveniently used whenever possible, for ssDNA type probes as illustrated in this communication, or possibly in a more general case for protein type probes using the so-called PDNAs. 30 Such a patented methodology 31 could be generalized to different systems. As it is not specific to the reading system, it could be used identically in any dynamic reading system allowing sequential injections and readings of different target solutions.…”

Microwave Spectroscopic Detection of Human Hsp70 Protein on Annealed Gold Nanostructures on ITO Glass Strips

“…The field of exploitation of this prototype of high-speed AFM in biology is vast, because the additional dimension of the temporal evolution of biological processes is evaluated (structural and functional dynamics). The authors focused on the study of membrane-related processes (important in signaling, transport, and energy generation), protein–DNA complexes [9] (important in gene regulation and transcription process), and the effect of the surface nature and confinement on the selectivity, reactivity, and biological activity of proteins [10] (interactions between proteins and inorganic materials) important for the development of the biosensor.…”