Insights into the Structure and Energy of DNA Nanoassemblies

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.     

Insights into Light‐driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory

Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6‐4 photoproducts. (6‐4) Photolyases are light‐activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6‐4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH^?) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron‐induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.     

Ribonuclease T1: Structure,Function, and Stability

Proteins carry out the most important and difficult tasks in all living organisms. To do so, they must often interact specifically with other small and large molecules. This requires that they fold to a globular conformation with a unique active site that is used for the specific interaction. Consequently, protein folding can be regarded as the “secret of life”. Biochemists and chemists have a great interest in elucidating the mechanism by which proteins fold and in predicting the folded conformation and its stability given just the amino acid sequence. This challenge is sometimes called the “protein folding problem”. The ability to construct proteins differing in sequence by one or more amino acids and to analyze their three-dimensional structures by X-ray crystallography and NMR spectroscopy is a powerful tool for investigating the conformational stability and folding of proteins. Several proteins are now under intensive study by this approach. One of these is ribonuclease T1.     

Further Insights into the Porous Structure of TEOS Derived Silica Gels

The porous structure of TEOS derived silica gels was studied using nitrogen adsorption at 77 K. Silica gels were prepared using TEOS, H₂O and ethanol for different molar ratios. No catalyst was used in this study. Silica gels were also heat treated up to 1000°C. The nitrogen sorption isotherms were analyzed by two models: Fractal and Percolation Theories. Using the fractal analysis approach, the surface roughness of the porous structure of silica gels was determined. The surface fractal dimension depends on the hydrolysis conditions and heat treatment. The surface fractal dimension decreases with increasing H₂O/TEOS molar ratio or heating temperature. For the silica gels studied, the surface fractal dimension changed from 2.6 to 2.5 after heating the gels, and from 2.4 to 2.6 with decreasing H₂O/TEOS ratio.Using the Percolation theory, we have determined the connectivity of the porous structure of silica gels. The extent of sorption hysteresis of the nitrogen isotherms reflects the connectivity of the pore network. The mean coordination number (connectivity) Z, and the linear dimension of the network, L, have been calculated from the hysteresis of the isotherms. For the as-prepared silica gels, Z was about 8 and L close to 2. On heating the gels, Z decreases to 4 and L increases to 7, results which are in accordance with the collapse of the porous network.     

Insights into Structure Direction of Microporous Aluminophosphates: Competition between Organic Molecules and Water

A combination of experimental characterisation techniques and computational modelling has allowed us to gain insight into the molecular features governing structure direction in the synthesis of microporous aluminophosphates. The occlusion of three different structure‐directing agents (SDAs), triethylamine (TEA), benzylpyrrolidine (BP) and (S )‐(?)‐N‐benzylpyrrolidine‐2‐methanol (BPM), within the AFI structure during its crystallisation, together with the simultaneous incorporation of water, has been experimentally measured. We found a higher incorporation of organic molecules in the structure obtained with BPM, while a higher water (and lower organic) content is found for the ones obtained with TEA and BP as SDAs. The computational study provides a thermodynamic explanation for the observed behaviour in terms of the relative stabilisation energy of the SDAs and water molecules within the AFI framework compared with when they are in aqueous solution, and demonstrates that a competition for preferential occupation exists between water and organic SDAs, which is a function of the interaction with the inorganic framework. The lower interaction of TEA and BP molecules with the AFI structure promotes the simultaneous incorporation of water molecules in the 12‐membered‐ring (MR) channel, to increase the host–guest interaction energy and thus the thermodynamic stability. The presence of strongly interacting methanol groups in the BPM molecules leads to the incorporation of only organic molecules within the 12‐MR channels. Our results demonstrate the essential role that water molecules play in the stabilisation of hydrophilic microporous aluminophosphates; a minimum amount of organic SDA is, however, essential for a templating role of the microporous architecture.     

Electronic Structure Insights into the Solvation of Magnesium Ions with Cyclic and Acyclic Carbonates

A computational framework to rank the solvation behavior of Mg²⁺ in carbonates by using molecular dynamics simulations and density functional theory is reported. Based on the binding energies and enthalpies of solvation calculated at the M06‐2X/6‐311++G(d,p) level of theory and the free energies of solvation from ABF‐MD simulations, we find that ethylene carbonate (EC) and the ethylene carbonate:propylene carbonate (EC:PC) binary mixture are the best carbonate solvents for interacting with Mg²⁺. Natural bond orbital and quantum theory of atoms in molecules analyses support the thermochemistry calculations with the highest values of charge transfer, perturbative stabilization energies, electron densities, and Wiberg bond indices being observed in the Mg²⁺(EC) and Mg²⁺(EC:PC) complexes. The plots of the noncovalent interactions indicate that those responsible for the formation of Mg²⁺ carbonate complexes are strong‐to‐weak attractive interactions, depending on the regions that are interacting. Finally, density of state calculations indicate that the interactions between Mg²⁺ and the carbonate solvents affects the HOMO and LUMO states of all carbonate solvents and moves them to more negative energy values.     

Theoretical Insights into the Formation, Structure, and Energetics of Some Cyclodextrin Complexes

To investigate the physicochemical aspects relevant for the formation of various cyclodextrin inclusion complexes and to search for corresponding general structure–complex-stability relationships, stability data of 1 : 1 complexes for 179, 310, and 51 guest molecules with unsubstituted -, -, and -cyclodextrin were collected. Statistical analysis using structure-based parameters such as molecular size, hydrophobicity, rotatable bonds, electronic properties, and the presence or absence of more than 150 various functional or structural moieties were performed. The complexation thermodynamics could be well described within the framework of our recently introduced molecular size-based model for nonassociative liquids. With increasing guest size, 1 : 1 complex stability, as measured by ln K or G⁰, increases linearly up to a size limit characteristic for each CD, and the corresponding slopes and intercepts are in agreement with those predicted by the model. For larger structures, values level off and are scattered around an average value depending on shape, goodness of fit, and possibly lipophilicity and some specific effects (e.g. such as those caused by presence of phenol functionality). The complexation between -cyclodextrin and certain large steroidal guest molecules, especially a brain-targeted estradiol chemical delivery systems (E₂-CDS) that is under clinical development, was investigated in details based on fully relaxed semiempirical AM1 quantum chemical calculations. A deformation index (DI) of the CD ring computed using these fully optimized host-guest geometries could be used to characterize the conformational change of the guest.     

Recent Insights into Inhibition,Structure, and Mechanism of Configuration-Retaining Glycosidases

Not “from above”, but “from the side” : Configuration-retaining β-glycosidases protonate their substrate either anti or syn to the endocyclic C1−O bond as the first step in the enzymic cleavage of the glycosidic bond (see schematic drawing). Insights into the mechanism of action of glycosidases have been gained by a combination of the synthesis of inhibitors, the study of the kinetics of their inhibition, and the analysis of the crystal structures of glycosidases and glycosidase–ligand complexes.     

Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and pi stacking

Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol (-1) difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a significant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and pi-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H...X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.     

Insights into the Relationship of Catalytic Activity and Structure: A Comparison Study of Three Carbonic Anhydrase Mimics

Density functional theory (DFT) calculations were used to study the mechanism of CO₂ hydrolysis by Zn‐(1,5,9‐triazacyclododecane) and Zn‐cyclam and evaluate the associated thermodynamic and kinetic parameters. Microkinetic models were then built based on the kinetics and thermodynamics derived from first principles. Both catalysts showed very similar behavior to Zn‐cyclen, which we have reported previously, but with multiple distinctions. The intrinsic reaction rate constants for Zn‐(1,5,9‐triazacyclododecane) and Zn‐cyclam were calculated to be 2693 and 4623 M^?1 s^?1, respectively, which is in reasonable agreement with experimental values reported or estimated. The CO₂ adsorption step was found to be a rate‐limiting step for all three catalysts. Zn‐cyclam has the lowest barrier for this step due to the highest pK_a or nucleophilicity of the Zn‐OH^? form, and_, therefore, the highest intrinsic activity. However, the observed reaction rate constant also depends on the availability of the catalyst. The decrease in the observed reaction rate constant over 0–12 ms was ascribed to the decrease in the concentration of the catalytic form, Zn‐OH^?, which was primarily converted to Zn‐HCO₃^?. The reaction rate constant of Zn‐cyclam dropped much faster than those of Zn‐cyclen and Zn‐(1,5,9‐triazacyclododecane) due to lower energy of the Zn‐HCO₃^? form. The conversion of CO₂ at 1000 ms as a function of pH was calculated to compare the relative activity of these catalysts, and Zn‐cyclen was found to be the best catalyst.     

Insights into the Structure of Large-Ring Cyclodextrins through Molecular Dynamics Simulations in Solution

Molecular dynamics simulations were carried out using the AMBER parm99 force field and explicit water molecules (TIP3P) to gain insight into the structural deformations and energetics of several large-ring cyclodextrins (with a degree of polymerization 26, 30, 55, 70, 85, and 100) in solution. The structures displayed by CD26 during the MD simulation (10.0 ns) did not correspond to the conformation in the crystalline state. The two "flips" present in the macroring of CD26 in the crystal state disappeared after 1.5 and 3.0 ns simulations, respectively. The larger CDs bear a considerable degree of flexibility. They display different modes of folding and cavity-like regions of different sizes and shapes: circular and elongated loops of variable size, orientated in different fashion; portions of a double helical strand with the two single helices parallel to each other (CD30, CD70); a helix of three turns and a serpentiform portion containing six loops (CD55); a cone-shaped spiral region (CD70); a rounded dendritic fold with several arbitrarily oriented small loops on the surface of the clustering (CD85); three spiral portions and a tendency for bending into two (CD100). These results support the hypothesis for the existence of more than one cavity in large-ring cyclodextrins.     

Using Diffusion NMR To Characterize Guanosine Self‐Association: Insights into Structure and Mechanism

This paper presents results from a series of pulsed field gradient (PFG) NMR studies on lipophilic guanosine nucleosides that undergo cation‐templated assembly in organic solvents. The use of PFG‐NMR to measure diffusion coefficients for the different aggregates allowed us to observe the influences of cation, solvent and anion on the self‐assembly process. Three case studies are presented. In the first study, diffusion NMR confirmed formation of a hexadecameric G‐quadruplex [G 1 ]₁₆ ? 4 K⁺ ? 4 pic^? in CD₃CN. Furthermore, hexadecamer formation from 5′‐TBDMS‐2′,3′‐isopropylidene G 1 and K⁺ picrate was shown to be a cooperative process in CD₃CN. In the second study, diffusion NMR studies on 5′‐(3,5‐bis(methoxy)benzoyl)‐2′,3′‐isopropylidene G 4 showed that hierarchical self‐association of G₈‐octamers is controlled by the K⁺ cation. Evidence for formation of both discrete G₈‐octamers and G₁₆‐hexadecamers in CD₂Cl₂ was obtained. The position of this octamer–hexadecamer equilibrium was shown to depend on the K⁺ concentration. In the third case, diffusion NMR was used to determine the size of a guanosine self‐assembly where NMR signal integration was ambiguous. Thus, both diffusion NMR and ESI‐MS show that 5′‐O‐acetyl‐2′,3′‐O‐isopropylidene G 7 and Na⁺ picrate form a doubly charged octamer [G 7 ]₈ ? 2 Na⁺ ? 2 pic^? 9 in CD₂Cl₂. The anion's role in stabilizing this particular complex is discussed. In all three cases the information gained from the diffusion NMR technique enabled us to better understand the self‐assembly processes, especially regarding the roles of cation, anion and solvent.     

Insights into the interactions between DNA and an infinite clamp-like copper (II) complex

Transition Metal Chemistry - A Cu(II) complex [Cu2(phen)2(NAB)2(HO)]n (phen?=?1, 10-phenanthroline and NABH?=?p-N, N-(2-hydroxyethyl)amino benzoic acid) was synthesized, and...     

Insights into the Pamamycin Biosynthesis

Pamamycins are macrodiolides of polyketide origin with antibacterial activities. Their biosynthesis has been proposed to utilize succinate as a building block. However, the mechanism of succinate incorporation into a polyketide was unclear. Here, we report identification of a pamamycin biosynthesis gene cluster by aligning genomes of two pamamycin‐producing strains. This unique cluster contains polyketide synthase (PKS) genes encoding seven discrete ketosynthase (KS) enzymes and one acyl‐carrier protein (ACP)‐encoding gene. A cosmid containing the entire set of genes required for pamamycin biosynthesis was successfully expressed in a heterologous host. Genetic and biochemical studies allowed complete delineation of pamamycin biosynthesis. The pathway proceeds through 3‐oxoadipyl‐CoA, a key intermediate in the primary metabolism of the degradation of aromatic compounds. 3‐Oxoadipyl‐CoA could be used as an extender unit in polyketide assembly to facilitate the incorporation of succinate.     

Replication of a DNA microarray

A mechanical method for efficient replication of DNA microarrays is described. The approach consists of three steps. First, a master DNA microarray consisting of single-stranded DNA elements is exposed to a solution containing the biotin-functionalized complement of each array element. Following hybridization, a replica surface modified with streptavidin is brought into contact with the master. This results in linking of the biotin-functionalized complement with the replica surface. Next, the replica is separated from the master, and the complementary strands are transferred to the replica surface. The resulting complementary DNA microarray contains position-coded sequences that mirror the information contained on the master DNA microarray. Multiple replicas can be prepared from a single master, the replicas efficiently hybridize only their complement, and DNA not labeled with biotin is not transferred to the replica surface.     

Structure of the Dioxygenase AsqJ: Mechanistic Insights into a One‐Pot Multistep Quinolone Antibiotic Biosynthesis

Multienzymatic cascades are responsible for the biosynthesis of natural products and represent a source of inspiration for synthetic chemists. The Fe^II/α‐ketoglutarate‐dependent dioxygenase AsqJ from Aspergillus nidulans is outstanding because it stereoselectively catalyzes both a ferryl‐induced desaturation reaction and epoxidation on a benzodiazepinedione. Interestingly, the enzymatically formed spiro epoxide spring‐loads the 6,7‐bicyclic skeleton for non‐enzymatic rearrangement into the 6,6‐bicyclic scaffold of the quinolone alkaloid 4′‐methoxyviridicatin. Herein, we report different crystal structures of the protein in the absence and presence of synthesized substrates, surrogates, and intermediates that mimic the various stages of the reaction cycle of this exceptional dioxygenase.     

Effects of Pressure and pH on the Physical Stability of an I-Motif DNA Structure

The thermodynamic stability of a cytosine(C)-rich i-motif tract of DNA, which features pH-sensitive [C..H..C]⁺ moieties, has been studied as function of both pressure (0.1–200 MPa) and pH (3.7–6.2). Careful attention was paid to correcting citrate buffer pH for known variations that stem from changes in pressure. Once pH-corrected, (i) at pH >4.6 the i-motif becomes less stable as pressure is increased (K_D decreases), giving a small negative volume change for dissociation (Δ_DV°) of the i-motif – a conclusion opposite to that which would be drawn if the buffer pH was not corrected for the effects of pressure; (ii) the i-motif's melting temperature increases by more than 30 K between pH 6.5 and 4.5, the consequence of an enthalpy for dissociation (Δ_DH°) of 77(3) and 90(3) kJ (mol H⁺)⁻¹ at 0.1 and 200 MPa, respectively; (iii) below pH 4.6 at 0.1 MPa (pH 4.3 at 200 MPa) the melting temperature decreases as a result of double protonation of cytosine pairs, and Δ_DH° and Δ_DV° change signs; and (iv) the combination of Δ_DH° and Δ_DV° lead to the melting temperature at pH 4.3 being 3 K higher at 200 MPa than at 0.1 MPa.