Nucleobase pairing and photodimerization in a biologically derived metal-organic framework nanoreactor

Biologically derived metal-organic frameworks (bio-MOFs) are of great importance as they can be used as models for bio-mimicking and in catalysis, allowing us to gain insights into how large biological molecules function. Through rational design, here we report the synthesis of a novel bio-MOF featuring unobstructed Watson-Crick faces of adenine (Ade) pointing towards the MOF cavities. We show, through a combined experimental and computational approach, that thymine (Thy) molecules diffuse through the pores of the MOF and become base-paired with Ade. The Ade-Thy pair binding at 40-45% loading reveals that Thy molecules are packed within the channels in a way that fulfill both the Woodward-Hoffmann and Schmidt rules, and upon UV irradiation, Thy molecules dimerize into ThyThy. This study highlights the utility of accessible functional groups within the pores of MOFs, and their ability to 'lock' molecules in specific positions that can be subsequently dimerized upon light irradiation, extending the use of MOFs as nanoreactors for the synthesis of molecules that are otherwise challenging to isolate.

Synthesis, Characterization, and Applications of Visible Light Active Metal-Organic Frameworks

Samantha Lynn Anderson

Understanding how crystalline materials are assembled is important for the rational design of metal-organic frameworks (MOFs). Controlling their formation can allow researchers to streamline the synthesis of new materials as well as control their properties for targeted applications. In the first chapter of this thesis we report the construction of two 3-dimensional TbIII based MOFs (SION-1 and SION-2). Here, SION-2 acts as a metastable MOF and intermediate phase that partially dissolves and transforms into the thermodynamically stable MOF, SION-1. This chemical transformation occurs in a DMF/water solvent mixture, and is triggered when additional energy is provided to the reaction. In situ studies reveal the partial dissolution of the metastable phase after which the MOF components are reassembled into the thermodynamically stable phase. The marked difference in thermal and chemical stability between the kinetically and thermodynamically controlled phases is contrasted by their identical chemical building unit composition. Following the understanding of this transformation, an isostructural family of SION-1 and SION-2 had been constructed using lanthanide metal salts, where LnIII-SION-1 is comprised of Ce, Nd, Eu, Gd, Tb, Dy, Ho, Er, Yb and Lu and LnIII-SION-2 is formed using Ce, Nd, Eu, Gd, Tb and Yb. The electronic properties of lanthanide based MOFs have not been extensively studied due to the general cognizance that LnIII ions behave as isolated free ions as their 4f orbitals do not contribute to bonding. Here, we systematically studied the electronic properties (UV-vis) of LnIII-SION-1 and LnIII-SION-2 and show that the higher the intensity of this absorption band in LnIII-SION-1 is due to the better overlap between Ln(5d) and ligand(pi*) orbitals and reveals that the lowest unoccupied crystalline orbitals are dispersed over an energy range and can be considered as a conduction band. We validated this observation by the non-linear I-V curves collected on CeIII- and YbIII-SION-1, both of which display dielectric properties. In the second chapter of this thesis, we rationally design a novel biologically derived MOF featuring unobstructed Watson-Crick faces of Ade pointing towards the MOF cavities. We show, through a combined experimental and computational approach, that Thy molecules diffuse through the pores of the MOF and become base-paired with Ade. The Ade-Thy pair binding at 40-45% loading reveals that Thy molecules are packed within the channels in a way that fulfill both the Woodward-Hoffmann and Schmidt rules, and upon UV irradiation, Thy molecules dimerize into ThyThy. This study highlights the utility of MOFs as nanoreactors for the synthesis of molecules that are otherwise difficult. Concluding this thesis, a biologically derived multimodal sensor MOF is synthesized and a formed into a device. The MOF, SION-9, is comprised of Ade and a porphyrin based ligand, and has tuneable conductive properties ranged from 2.69-4.20 x 10-8 - 7.43-7.34 x 10-6 S/cm. SION-9 is sensitive to both pressure and temperature simultaneously, and demonstrated both fast response times (< 60 ms) and a long shelf life (> 6 months).

EPFL2019

Effects of base-pair sequence, nicks and gaps on DNA minicircle shapes

Arnaud Amzallag

DNA is a long polymer with the form of a double helix of about two nanometers diameter (2.10-9 meters). It is composed of nucleotides whose sequence carries the information of heredity. The four possible nucleotides have slightly different geometries, and their sequence along the DNA molecule are thought to influence the shape and the stiffness of the double helix on a scale of few tens to a few hundred base pairs, and thereby its biological activity. DNA minicircles (or miniplasmids) are closed loops with lengths of the order of a few tens or hundreds of base pairs in which the double helix bends around to close on its own tail with some number of twists. Its minimal energy shape and its energy of formation depend on the sequence of base pairs, and can be efficiently computed by polymer and rod models, if shape and stiffness parameters of DNA are provided as inputs. This structure is therefore an interesting experimental motif to test sequence-dependent mechanical properties of the DNA molecule. The purpose of this thesis is to explore the experimental methods to determine the shape and free energy of formation of DNA minicircles. The shapes have been be determined from cryo-electron micrographs. Efficiency of formation has been investigated by a novel method called annealing-cyclization. Cryo-electron microscopy allows observation of very small molecules (here 17 or 11 nm diameter) in vitrified water, in order to keep the 3D shape of the molecules as close as possible to the shape they had in solution. In Chapter 1, I used stereo cryo-electron micrographs to determine and compare the three-dimensional shape of 95 individual DNA minicircles of 158 base pairs, which were identical in sequence except within a 18 bp block which contained either a TATA box sequence or a CAP site. I defined the notion of shape-distance which I used to estimate the error of reconstruction, and I detected clusters of shapes using an appropriate sorting algorithm. However the cluster did not seem to be associated with the variable sequence (TATA or CAP). I then analyzed (in Chapter 2) two-dimensional shapes of shorter DNA minicircles (94 bp) determined by negative staining electron microscopy, designed with either two nicks (breaks in one of the strands) or two gaps (missing nucleotides) at diametrically opposite sites of the minicircles. I observed that the gapped minicircles have an elongated shape with respect to the nicked minicircles, and I used this result together with the results of atomic level molecular dynamics simulations to conclude that the gap flexibility, perhaps together with base unpairing at the gap site, is responsible for this elongated minicircle shape. Finally, I proposed a ligase-free assay to measure the minicircle formation efficiency, which can give a high yield of nicked minicircles. The method avoids the use of ligase and the associated concerns about the effect of ligase concentration on the measurements. I determined an equation from a chemical model of the reaction that fits the experimental data, and I defined the Ja factor which gives a measure of the cyclization yield independent of DNA initial concentration. This method seems to confirm that minicircles with two gaps cyclize more efficiently that minicircles with two nicks, probably because of the gap flexibility. As a perspective, the conclusions of this thesis could be used for the design of minicircle constructs whose shape would be sensitive enough to sequence mutation in order to be detected by electron microscopy. Such shapes could be then compared, thanks to the shape-distance tool defined herein, to shapes computed with known or putative DNA models.

EPFL2008

Taking lanthanides out of isolation: tuning the optical properties of metal-organic frameworks

Samantha Lynn Anderson, Gloria Capano, Maria Fumanal Quintana, Andrzej Gladysiak, Nestor Guijarro Carratala, Christopher Patrick Ireland, Stavroula Kampouri, Kevin Sivula, Berend Smit, Kyriakos Stylianou, Davide Tiana

Metal organic frameworks (MOFs) are increasingly used in applications that rely on the optical and electronic properties of these materials. These applications require a fundamental understanding on how the structure of these materials, and in particular the electronic interactions of the metal node and organic linker, determines these properties. Herein, we report a combined experimental and computational study on two families of lanthanide-based MOFs: Ln-SION-1 and Ln-SION-2. Both comprise the same metal and ligand but with differing structural topologies. In the Ln-SION-2 series the optical absorption is dominated by the ligand and using different lanthanides has no impact on the absorption spectrum. The Ln-SION-1 series shows a completely different behavior in which the ligand and the metal node do interact electronically. By changing the lanthanide in Ln-SION-1, we were able to tune the optical absorption from the UV region to absorption that includes a large part of the visible region. For the early lanthanides we observe intraligand (electronic) transitions in the UV region, while for the late lanthanides a new band appears in the visible. DFT calculations showed that the new band in the visible originates in the spatial orbital overlap between the ligand and metal node. Our quantum calculations indicated that Ln-SION-1 with late lanthanides might be (photo)conductive. Experimentally, we confirm that these materials are weakly conductive and that with an appropriate co-catalysts they can generate hydrogen from a water solution using visible light. Our experimental and theoretical analysis provides fundamental insights for the rational design of Ln-MOFs with the desired optical and electronic properties.

2020