Jesús Mosquera

DNA Recognition by Synthetic Constructs

The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein–DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non‐natural agents that can reproduce the DNA‐recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double‐stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability.

Aqueous Anion Receptors through Reduction of Subcomponent Self‐Assembled Structures

To prepare new functional covalent architectures that are difficult to synthesize using conventional organic methods, we developed a strategy that employs metal-organic assemblies as precursors, which are then reduced and demetalated. The host-guest chemistry of the larger receptor thus prepared was studied using NMR spectroscopy and fluorescence experiments. This host was observed to strongly bind aromatic polyanions in water, including the fluorescent dye molecule pyranine with nanomolar affinity, thus allowing for the design of an indicator-displacement assay.

Subcomponent Flexibility Enables Conversion between D4-Symmetric CdII8L8 and T-Symmetric CdII4L4 Assemblies

A flexible tris-formylpyridine subcomponent A was observed to produce three distinct products following Cd(II)-templated self-assembly with different anilines. Two of the products were Cd(II)4L4 tetrahedra, one with ligands puckered inward, and the other outward. The third product was a Cd(II)8L8 structure having all mer stereochemistry, contrasting with the fac stereochemistry of the tetrahedra. These three complexes were observed to coexist in solution. The equilibrium between them could be influenced through guest binding and specific interactions between aniline subcomponents, allowing a selected one of the three to predominate under defined conditions.

Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl–Bis(benzamidine) Components†

At specific DNA sites, nickel(II) salts promote the assembly of designed components, namely a bis(histidine)-modified peptide that is derived from a bZIP transcription factor and a bis(benzamidine) unit that is equipped with a bipyridine. This programmed supramolecular system with emergent properties reproduces some key characteristics of naturally occurring DNA-binding proteins, such as bivalence, selectivity, responsiveness to external agents, and reversibility.

Anion Binding in Water Drives Structural Adaptation in an Azaphosphatrane-Functionalized FeII4L4 Tetrahedron

Anion-templated aqueous self-assembly resulted in the formation of an endohedrally functionalized FeII4L4 tetrahedron from azaphosphatrane-based subcomponents. This new water-soluble cage is flexible and able to encapsulate anions with volumes ranging from 35 to 219 Å3 via hydrogen bonding and electrostatic interactions. It structurally adapts in response to the size and shape of the template anions, dynamically adopting a conformation either where all four azaphosphatrane +P-H vectors point inward, or else where one points outward and the other three inward. The two cage isomers can coexist in solution and interconvert. A shape memory phenomenon was observed during guest displacement because guest exchange occurs more rapidly than structural reconfiguration.

Sequence-selective encapsulation and protection of long peptides by a self-assembled Fe II 8 L 6 cubic cage

Self-assembly offers a general strategy for the preparation of large, hollow high-symmetry structures. Although biological capsules, such as virus capsids, are capable of selectively recognizing complex cargoes, synthetic encapsulants have lacked the capability to specifically bind large and complex biomolecules. Here we describe a cubic host obtained from the self-assembly of FeII and a zinc-porphyrin-containing ligand. This cubic cage is flexible and compatible with aqueous media. Its selectivity of encapsulation is driven by the coordination of guest functional groups to the zinc porphyrins. This new host thus specifically encapsulates guests incorporating imidazole and thiazole moieties, including drugs and peptides. Once encapsulated, the reactivity of a peptide is dramatically altered: encapsulated peptides are protected from trypsin hydrolysis, whereas physicochemically similar peptides that do not bind are cleaved.

Anion Recognition as a Supramolecular Switch of Cell Internalization

The cell internalization of designed oligoarginine peptides equipped with six glutamic acid residues and an anionic pyranine at the N-terminus is triggered upon addition of a supramolecular host. This host binds specifically to the pyranine moiety, enabling the complex to traverse the cell membrane. Interestingly, none of the components, neither the host nor the guest, are able to cross the cell membrane on their own.

Selective Anion Extraction and Recovery Using a FeII4L4 Cage

Abstract Selective anion extraction is useful for the recovery and purification of valuable chemicals, and in the removal of pollutants from the environment. Here we report that FeII 4L4 cage 1 is able to extract an equimolar amount of ReO4 −, a high‐value anion and a nonradioactive surrogate of TcO4 −, from water into nitromethane. Importantly, the extraction was efficiently performed even in the presence of 10 other common anions in water, highlighting the high selectivity of 1 for ReO4 −. The extracted guest could be released into water as the cage disassembled in ethyl acetate, and then 1 could be recycled by switching the solvent to acetonitrile. The versatile solubility of the cage also enabled complete extraction of ReO4 − (as the tetrabutylammonium salt) from an organic phase into water by using the sulfate salt of 1 as the extractant.

Selective DNA-Binding by Designed Bisbenzamidine-Homeodomain Chimeras

We report the construction of conjugates between three variants of the helix 3 region of a Q50K engrailed homeodomain and bisbenzamidine minor‐groove DNA binders. The hybrid featuring the sequence of the native protein failed to bind to DNA; however, modifications that increased the α‐helical folding propensity of the peptide allowed specific DNA binding by a bipartite (major/minor groove) interaction.

Ruthenation of Non-stacked Guanines in DNA G-Quadruplex Structures: Enhancement of c-MYC Expression.

Abstract Guanine quadruplexes (GQs) are compact four‐stranded DNA structures that play a key role in the control of a variety of biological processes, including gene transcription. Bulky ruthenium complexes featuring a bipyridine, a terpyridine, and one exchangeable ligand ([Ru(terpy)(bpy)X]n+) are able to metalate exposed guanines present in the GQ of the c‐MYC promoter region that are not involved in quadruplex base pairing. qRT‐PCR and western‐blot experiments indicated that the complexes promote a remarkable increase in the expression of this oncogene. We also show that exchangeable thioether ligands (X=RSR′, Met) allow regulation of the metalating activity of the complex with visible light.