Molecular sponges give atomic structures of trace substances

Ever since Richard Feynman lamented in his 1959 talk “There’s Plenty of Room at the Bottom” that the electron microscope failed by two orders of magnitude to image individual atoms, a general method of imaging nanostructures to atomic resolution has been an integral part of the Feynman vision of what was later called nanotechnology: the construction of atomically-precise products through the use of molecular machine systems. Imaging proteins to atomic resolution is a necessary subgoal of Eric Drexler’s 1981 proposal that protein design could provide an approach to develop general capabilities for molecular engineering and molecular manipulation. X-ray crystallography has been the gold standard for obtaining atomically precise structures for proteins and other nanostructures, but this method requires substantial amounts of crystalline material, and not all proteins, and certainly not all nanostructures, are available in crystalline form. Nadrian C. Seeman, the pioneer of DNA nanotechnology, one of the most promising roads to atomically precise manufacturing (APM), has said that “The first goal is to use our branched DNA system to scaffold the organization of biological macromolecules into crystalline arrays, thus overcoming the crystallization problem of biological crystallography. This will enable the 3D structural characterization of potential drug targets, leading to rational drug design.” The electron microscope has been greatly improved since Feynman’s time and some success has been obtained in using DNA nanotechnology to organize proteins for structure determination. However, another option is now available. A blog by Derek Lowe discusses a paper from a group at the University of Tokyo published in Nature earlier this year [abstract] that uses porous metal-organic frameworks (MOFs) as ‘chemical sponges’ as ‘hosts’ to soak up very small quantities of small to mid-sized molecules as ‘guests’ so that X-ray crystallography of the host-guest complex provides the structure of the guest molecule. From “X-Ray Structures Of Everything. Without Crystals. Holy Cow“:.

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