Selective and Cooperative Ligand Binding to Antiparallel Human Telomeric DNA G‐Quadruplexes

The quest for ligands that specifically bind to particular G‐quadruplex nucleic acid structures is particularly important to conceive molecules with specific effects on gene expression or telomere maintenance, or conceive structure‐specific molecular probes. Using electrospray mass spectrometry in native conditions, we reveal a highly cooperative and selective 2:1 binding of Cu^II‐tolylterpyridine complexes to human telomeric G‐quadruplexes. Circular dichroism and comparisons of affinities for different sequences reveal a marked preference for antiparallel structures with diagonal loops and/or wide‐medium–narrow‐medium groove‐width order. The cooperativity is attributed to conformational changes in the polymorphic telomeric G‐quadruplex sequences, which convert preferably into an antiparallel three‐quartet topology upon binding of two ligands.     

In Vivo Spectrum of UVC‐induced Mutation in Mouse Skin Epidermis May Reflect the Cytosine Deamination Propensity of Cyclobutane Pyrimidine Dimers

Although ultraviolet radiation (UVR) has a genotoxicity for inducing skin cancers, the skin may tolerate UVC component because the epidermal layer prevents this short wavelength range from passing through. Here, UVC genotoxicity for mouse skin was evaluated in terms of DNA damage formation and mutagenicity. UVC induced UVR photolesions and mutations remarkably in the epidermis but poorly in the dermis, confirming the barrier ability of the epidermis against shorter UVR wavelengths. Moreover, the epidermis itself responded to UVC mutagenicity with mutation induction suppression, which suppressed the mutant frequencies to a remarkably low, constant level regardless of UVC dose. The mutation spectrum observed in UVC‐exposed epidermis showed a predominance of UV‐signature mutation, which occurred frequently in 5′‐TCG‐3′, 5′‐TCA‐3′ and 5′‐CCA‐3′ contexts. Especially, for the former two contexts, the mutations recurred at several sites with more remarkable recurrences at the 5′‐TCG‐3′ sites. Comparison of the UVC mutation spectrum with those observed in longer UVR wavelength ranges led us to a mechanism that explains why the sequence context preference of UV‐signature mutation changes according to the wavelength, which is based on the difference in the mCpG preference of cyclobutane pyrimidine dimer (CPD) formation among UVR ranges and the sequence context‐dependent cytosine deamination propensity of CPD.     

Changes in the Enantiomeric Composition of Chiral Mixtures Upon Adsorption on a Non‐Chiral Surface

The adsorption of propylene oxide, a chiral molecule, on a Pt(111) single‐crystal surface was studied as a function of enantiomeric composition by temperature programmed desorption (TPD) and molecular beams. Two opposing trends were observed leading to variations in the enantiomeric excess (ee) of the chemisorbed layers with respect to the composition of the gas‐phase mixtures: a kinetic effect dominant during the initial uptake, with a preference toward the formation of enantiopure layers, and a steady‐state effect seen after approximately monolayer half‐saturation, at which point the preference is toward racemization. These effects may account for important phenomena such as the bias toward one chirality in biological systems and the selective crystallization of some chiral compounds, and may also be used in practical applications for chemical separations and catalysis.     

The Effect of Dispersion on the Structure of Diphenyl Ether Aggregates

Dispersion interactions can play an important role in understanding unusual binding behaviors. This is illustrated by a systematic study of the structural preferences of diphenyl ether (DPE)–alcohol aggregates, for which OH???O‐bound or OH???π‐bound isomers can be formed. The investigation was performed through a multi‐spectroscopic approach including IR/UV and microwave methods, combined with a detailed theoretical analysis. The resulting solvent‐size‐dependent trend for the structural preference turns out to be counter‐intuitive: the hydrogen‐bonded OH???O structures become more stable for larger alcohols, which are expected to be stronger dispersion energy donors and thus should prefer an OH???π arrangement. Dispersion interactions in combination with the twisting of the ether upon solvent aggregation are key for understanding this preference.     

Foldamer‐Mediated Remote Stereocontrol: >1,60 Asymmetric Induction

An N‐terminal L ‐α‐methylvaline dimer induces complete conformational control over the screw sense of an otherwise achiral helical peptide foldamer formed from the achiral quaternary amino acids Aib and Ac₆c. The persistent right‐handed screw‐sense preference of the helix enables remote reactive sites to fall under the influence of the terminal chiral residues, and permits diastereoselective reactions such as alkene hydrogenation or iminium ion addition to take place with 1,16‐, 1,31‐, 1,46‐ and even 1,61‐asymmetric induction. Stereochemical information may be communicated in this way over distances of up to 4 nm.     

Influence of β‐Alanine on Hairpin Polyamide Orientation in the DNA Minor Groove

Antiparallel polyamides containing 1H‐pyrrole, 1H‐imidazole, and 3‐hydroxy‐1H‐pyrrole amino acids display a preference for minor‐groove binding oriented N? C with respect to the 5′‐3′ direction of the DNA helix. We find that replacement of a central Py/Py pair with a β/β pair within a ten‐ring hairpin relaxes the orientation preference and, for some DNA sequences, causes the polyamide to prefer the opposite C? N orientation. Substitution of the achiral γ‐aminobutanoic acid (γ) with either (R)(or S)‐2‐(acetylamino)‐4‐aminobutanoic acid moderates the orientation preference of the 2‐β‐2‐hairpin.     

Surface Chemistry of tert‐Butylphosphine (TBP) on Si(001) in the Nucleation Phase of Thin‐Film Growth

We combine density functional theory calculations and scanning tunneling microscopy investigations to identify the relevant chemical species and reactions in the nucleation phase of chemical vapor deposition. tert‐Butylphosphine (TBP) was deposited on a silicon substrate under conditions typical for surface functionalization and growth of semiconductor materials. On the activated hydrogen‐covered surface H/Si(001) it forms a strong covalent P?Si bond without loss of the tert‐butyl group. Calculations show that site preference for multiple adsorption of TBP is influenced by steric repulsion of the adsorbate's bulky substituent. STM imaging furthermore revealed an anisotropic distribution of TBP with a preference for adsorption perpendicular to the surface dimer rows. The adsorption patterns found can be understood by a mechanism invoking stabilization of surface hydrogen vacancies through electron donation by an adsorbate. The now improved understanding of nucleation in thin‐film growth may help to optimize molecular precursors and experimental conditions and will ultimately lead to higher quality materials.     

Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected “GxyG” host–guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest‐neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above‐the‐average preference for turn‐like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above‐the‐average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of ³J(H^N,H^α) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII?β equilibrium indicating a significant residue dependent temperature dependence of the peptides’ conformational ensembles. These results suggest that nearest‐neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy–entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures.     

NMR and Luminescence Binding Studies of Ytterbium,Thulium, and Europium Macrocyclic Complexes with Phosphorus(V) Oxy Anions

The binding of a series of phosphate anions to coordinatively unsaturated macrocyclic complexes of Yb, Tm, and Eu was studied by ¹H‐NMR, emission and circularly polarized luminescence (CPL) spectroscopy. Each ternary adduct was distinguished by its spectral profile. With O‐phosphorylated amino acids and peptides, chemoselective ligation of the phosphate moiety was favored by Eu over chelation involving the terminal amino group, which was competitive for Tm and Yb. A preference for binding O‐phosphono‐L ‐tyrosine sites was found with various Eu complexes, and was signalled by ratiometric changes in metal‐based emission and CPL spectra.     

Complete Switch of Reaction Specificity of an Aldolase by Directed Evolution In Vitro: Synthesis of Generic Aliphatic Aldol Products

A structure‐guided engineering of fructose‐6‐phosphate aldolase was performed to expand its substrate promiscuity toward aliphatic nucleophiles, that is, unsubstituted alkanones and alkanals. A “smart” combinatorial library was created targeting residues D6, T26, and N28, which form a binding pocket around the nucleophilic carbon atom. Double‐selectivity screening was executed by high‐performance TLC that allowed simultaneous determination of total activity as well as a preference for acetone versus propanal as competing nucleophiles. D6 turned out to be the key residue that enabled activity with non‐hydroxylated nucleophiles. Altogether 25 single‐ and double‐site variants (D6X and D6X/T26X) were discovered that show useful synthetic activity and a varying preference for ketone or aldehyde as the aldol nucleophiles. Remarkably, all of the novel variants had completely lost their native activity for cleavage of fructose 6‐phosphate.     

pH‐dependent Interaction of Rhodopsin with Cyanidin‐3‐glucoside. 1. Structural Aspects†

Anthocyanins are a class of natural compounds common in flowers and vegetables. Because of the increasing preference of consumers for food containing natural colorants and the demonstrated beneficial effects of anthocyanins on human health, it is important to decipher the molecular mechanisms of their action. Previous studies indicated that the anthocyanin cyanidin‐3‐glucoside (C3G) modulates the function of the photoreceptor rhodopsin. In this paper, we show using selective excitation ¹H NMR spectroscopy that C3G binds to rhodopsin. Ligand resonances broaden upon rhodopsin addition and rhodopsin resonances exhibit chemical shift changes as well as broadening effects in specific resonances, in an activation state‐dependent manner. Furthermore, dark‐adapted and light‐activated states of rhodopsin show preferences for different C3G species. Molecular docking studies of the flavylium cation, quinoidal base, carbinol pseudobase and chalcone forms of C3G to models of the dark, light‐activated and opsin structures of rhodopsin also support this conclusion. The results provide new insights into anthocyanin–protein interactions and may have relevance for the enhancement of night vision by this class of compounds. This work is also the first report of the study of ligand binding to a full‐length membrane receptor in detergent micelles by ¹H NMR spectroscopy. Such studies were previously hampered by the presence of detergent micelle resonances, a problem overcome by the selective excitation approach.     

Diastereodivergent Asymmetric 1,4‐Addition of Oxindoles to Nitroolefins by Using Polyfunctional Nickel‐Hydrogen‐Bond‐Azolium Catalysts

Diastereodivergency is a challenge for catalytic asymmetric synthesis. For many reaction types, the generation of one diastereomer is inherently preferred, while the other diastereomers are not directly accessible with high efficiency and require circuitous synthetic approaches. Overwriting the inherent preference by means of a catalyst requires control over the spatial positions of both reaction partners. We report a novel polyfunctional catalyst type in which a Ni^II‐bis(phenoxyimine) unit, free hydroxy groups, and an axially chiral bisimidazolium entity participate in the stereocontrol of the direct 1,4‐addition of oxindoles to nitroolefins. Both epimers of the 1,4‐adduct are accessible in excess on demand by changes to the ligand constitution and configuration. As the products have been reported to be valuable precursors to indole alkaloids, this method should allow access to their epimeric derivatives.     

Reversal of a Single Base‐Pair Step Controls Guanine Photo‐Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)₂(dppz)]²⁺ have been compared in 5′‐{CCGG AT CCGG}₂ and 5′‐{CCGG TA CCGG}₂ using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.     

Sugar–Edge Interactions in a DNA–RNA G‐Quadruplex: Evidence of Sequential C−H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding

DNA G‐quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti‐dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA–RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3′‐side within the quadruplex core strongly suggest the presence of C8?H???O hydrogen‐bonding interactions with the O2′ position of the C2′‐endo ribonucleotide. A geometric analysis of reported high‐resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.     

From Concept to Crystals via Prediction: Multi‐Component Organic Cage Pots by Social Self‐Sorting

We describe the a priori computational prediction and realization of multi‐component cage pots, starting with molecular predictions based on candidate precursors through to crystal structure prediction and synthesis using robotic screening. The molecules were formed by the social self‐sorting of a tri‐topic aldehyde with both a tri‐topic amine and di‐topic amine, without using orthogonal reactivity or precursors of the same topicity. Crystal structure prediction suggested a rich polymorphic landscape, where there was an overall preference for chiral recognition to form heterochiral rather than homochiral packings, with heterochiral pairs being more likely to pack window‐to‐window to form two‐component capsules. These crystal packing preferences were then observed in experimental crystal structures.     

Origin of the “endo rule” in Diels–Alder reactions

Detailed density functional theory calculations definitively rationalize the preference for the endo cycloadduct (also known as endo rule) in text‐book thermal Diels–Alder reactions involving maleic anhydride and cyclopentadiene or butadiene. This selectivity is mainly caused by an unfavorable steric arrangement in the transition‐state region of the exo pathway which translates into a more destabilizing activation strain. In contrast with the widely accepted, orbital‐interaction‐based explanation for the endo rule, it is found that neither the orbital interactions nor the total interaction between the deformed reactants contributes to the endo selectivity. © 2013 Wiley Periodicals, Inc.     

Probing the Adhesion of Hepatocellular Carcinoma HepG2 and SK‐Hep‐1 Cells

Carcinoma cell differentiation stage is an important indicator of cell behavior. For example, cell mobility is much higher for poorly‐differentiated hepatocellular carcinoma SK‐Hep‐1 cells than for well‐differentiated HepG2 cells. In this study, we have cultured HepG2 and SK‐Hep‐1 cells on chemically patterned polydimethylsiloxane (PDMS) substrates to observe differences in the adhesion properties and cell structure that occur due to the patterns. Both cell lines showed a preference for the hydrophobic regions on the patterned PDMS surface with SK‐Hep‐1 cells achieving a higher density than HepG2 for the same cell‐count solutions. Further, SK‐Hep‐1 cells adopted the square or hexagonal shape of the surface patterns while HepG2 cells maintained their more rounded shape. AFM force measurement arrays were also performed on the cell surfaces to measure and map adhesion values between the tip and cell surface membrane. These results demonstrate that, in addition to cell shape and size, adhesion expression in hepatocellular carcinoma cells is differentiation stage dependent. Further, the ability of the SK‐Hep‐1 cells to adopt the shape of the substrate pattern indicates they are more structurally labile, which may contribute to their higher mobility.     

Conformational analysis of trinucleotides containing a single abasic residue; mimics of DNA damage

The conformations of three deoxytrinucleotide analogues [d(TpXpT), where X = T, tetrahydrofuran (THF) or propyl (Pr)] were investigated using ¹H NMR spectroscopy as part of our studies of DNA‐base damage. The phosphorus‐decoupled ¹H NMR spectrum of each compound was simulated and values for the vicinal proton–proton coupling constants of the sugar ring hydrogens were extracted at several different temperatures, for use in conformational analyses. It was found that the south‐pucker preference of the sugar 3′ to the modification is increased whereas that of the 5′ is decreased relative to the puckers observed for the non‐modified system. The conformational change is <25%. This subtle effect may be sufficient for recognition by DNA repair enzymes. Copyright © 2003 John Wiley & Sons, Ltd.     

Triple‐Helix‐Stabilizing Effects in Collagen Model Peptides Containing PPII‐Helix‐Preorganized Diproline Modules

Collagen model peptides (CMPs) serve as tools for understanding stability and function of the collagen triple helix and have a potential for biomedical applications. In the past, interstrand cross‐linking or conformational preconditioning of proline units through stereoelectronic effects have been utilized in the design of stabilized CMPs. To further study the effects determining collagen triple helix stability we investigated a series of CMPs containing synthetic diproline‐mimicking modules (ProMs), which were preorganized in a PPII‐helix‐type conformation by a functionalizable intrastrand C₂ bridge. Results of CD‐based denaturation studies were correlated with calculated (DFT) conformational preferences of the ProM units, revealing that the relative helix stability is mainly governed by an interplay of main‐chain preorganization, ring‐flip preference, adaptability, and steric effects. Triple helix integrity was proven by crystal structure analysis and binding to HSP47.