Guanidiniocarbonylpyrrole–Aryl Derivatives: Structure Tuning for Spectrophotometric Recognition of Specific DNA and RNA Sequences and for Antiproliferative Activity

We present a systematic study of different guanidiniocarbonylpyrrole‐aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12 , is also needed. Compound 12 allows for base‐pair‐selective recognition of ds‐DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.     

Synthesis and Crystallochromy of 1,4,7,10‐Tetraalkyltetracenes: Tuning of Solid‐State Optical Properties of Tetracenes by Alkyl Side‐Chain Length

We synthesized a series of 1,4,7,10‐tetraalkyltetracenes using a new 2,6‐naphthodiyne precursor and 2,5‐dialkylfurans as starting materials (alkyl=methyl to hexyl). Surprisingly, the solid‐state color of the tetracenes ranges through yellow, orange, and red. Both yellow and red solids are obtained for the butyl derivative. Optical properties in solution show no marked differences; however, those in the solid state show characteristics that vary with alkyl side‐chain length: methyl, propyl, and pentyl derivatives are orange; ethyl and butyl derivatives are yellow; and another butyl and hexyl derivative are red. X‐ray analyses reveal that the molecular structures are planar, semi‐chair, or chair forms; the chair form takes a herringbone‐like arrangement and the other forms take slipped parallel arrangements. The mechanism of crystallochromy is discussed in terms of molecular structure, crystal packing, and calculations that take account of exciton coupling.     

Macrocyclic DNA‐Mismatch‐Binding Ligands: Structural Determinants of Selectivity

A collection of 15 homodimeric and 5 heterodimeric macrocyclic bisintercalators was prepared by one‐ or two‐step condensation of aromatic dialdehydes with aliphatic diamines; notably, the heterodimeric scaffolds were synthesized for the first time. The binding of these macrocycles to DNA duplexes containing a mispaired thymine residue (TX), as well as to the fully paired control (TA), was investigated by thermal denaturation and fluorescent‐intercalator‐displacement experiments. The bisnaphthalene derivatives, in particular, the 2,7‐disubstituted ones, have the highest selectivity for the TX mismatches, as these macrocycles show no apparent binding to the fully paired DNA. By contrast, other macrocyclic ligands, as well as seven conventional DNA binders, show lesser or no selectivity for the mismatch sites. The study demonstrates that the topology of the ligands plays a crucial role in determining the mismatch‐binding affinity and selectivity of the macrocyclic bisintercalators.     

Quantum‐based models of charge‐dependent potential energy surfaces: Three‐state models

Quantum‐based models of how potential energies depend on charge are developed from a three‐state model, at the level of neglecting state‐to‐state overlap. The energy as a function of charge is defined as proposed previously (Valone and Atlas, J Chem Phys 2004, 120, 7262). With this definition, addition of a third state smooths the derivatives of the energy model with respect to charge at integer values of charge that are in the interior of the allowed charge range. These derivatives are related to the chemical potential. At the dissociation limit, this model converges to established limits. Another dependence is proposed that uses two different charges simultaneously. The concepts are illustrated, with calculations on an OH molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

7,7′‐Diamino‐2,2′‐diindolylmethane: A Building Block for Highly Efficient and Selective Anion Receptors—Studies in Solution and in the Solid State

The easy‐to‐make 7,7′‐diamino‐2,2′‐diindolylmethane was used as a building block for the construction of anion receptors operating by hydrogen bonds. Its various bisamide and bisurea derivatives were designed and synthesised as acyclic as well as macrocyclic molecules, then their structural and anion binding properties were studied in solution and in the solid state. The bisamide receptors demonstrate high affinity towards oxoanions in highly polar and partially aqueous solutions (DMSO with up to 25 % H₂O) with significant selectivity for dihydrogen phosphate. Remarkably, the bisurea‐based molecules are able to bind anionic guests even in pure methanol and show selectivity toward tetrahedral oxoanions, that is, hydrogen sulphate and dihydrogen phosphate. X‐ray analysis revealed that both classes of molecules adopt a similar conformation in the solid state: a bent sheet shape with a binding pocket equipped with hydrogen‐bond donors (four for the amides and six for the bisureas), whose orientation is particularly tailored for oxoanions. The results of ROESY NMR experiments are in agreement with the findings for the solid state and confirmed that both bisamides and bisureas can easily adapt the conformation with convergent hydrogen‐bond donors, which is highly suitable for anion binding.     

Binding Cofactors with Triplex‐Based DNA Motifs

Cofactors are pivotal compounds for the cell and many biotechnological processes. It is therefore interesting to ask how well cofactors can be bound by oligonucleotides designed not to convert but to store and release these biomolecules. Here we show that triplex‐based DNA binding motifs can be used to bind nucleotides and cofactors, including NADH, FAD, SAM, acetyl CoA, and tetrahydrofolate (THF). Dissociation constants between 0.1 μM for SAM and 35 μM for THF were measured. A two‐nucleotide gap still binds NADH. The selectivity for one ligand over the others can be changed by changing the sequence of the binding pocket. For example, a mismatch placed in one of the two triplets adjacent to the base‐pairing site changes the selectivity, favoring the binding of FAD over that of ATP. Further, changing one of the two thymines of an A‐binding motif to cytosine gives significant affinity for G, whereas changing the other does not. Immobilization of DNA motifs gives beads that store NADH. Exploratory experiments show that the beads release the cofactor upon warming to body temperature.     

From Intercalation to Groove Binding: Switching the DNA‐Binding Mode of Isostructural Transition‐Metal Complexes

The interaction with duplex DNA of a small library of structurally related complexes that all contain a d⁶‐metal ion coordinated to either the 2,2 ′ :4,4 ′′ :4 ′ ,4 ′′′ ‐quaterpyridyl ligand or its methylated derivative are reported. This library is made up of a mixture of newly synthesised and previously reported systems. Despite their structural similarities the complexes display an almost 20‐fold variation in binding affinities. Although effects due to the overall charge of the complexes are apparent, the differences in binding characteristics are deeper than this; indeed, in a number of cases, changes in overall charge have little effect on binding affinity. Intriguingly, despite interacting with DNA through unfused ring systems, although two of the complexes studied are groove binders, the majority are non‐classical intercalators. A rationale for these effects has been obtained through a combination of experimental and computational studies.     

An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells

Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six‐letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six‐letter DNA library to selectively bind liver cancer cells; and 2) in a six‐letter self‐assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer‐nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer‐targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.     

Spectroscopy and Dynamics of Cryptolepine in the Nanocavity of Cucurbit[7]uril and DNA

Herein, we explored the photophysical properties of the antimalarial, anticancer drug cryptolepine (CRYP) in the presence of the macrocyclic host cucurbit[7]uril (CB7) and DNA with the help of steady‐state and time‐resolved fluorescence techniques. Ground‐state and excited‐state calculations based on density functional theory were also performed to obtain insight into the shape, electron density distribution, and energetics of the molecular orbitals of CRYP. CRYP exists in two forms depending on the pH of the medium, namely, a cationic (charge transfer) form and a neutral form, which emit at λ=540 and 420 nm, respectively. In a buffer solution of pH 7, the drug exists in the cationic form, and upon encapsulation with CB7, it exhibits a huge enhancement in fluorescence intensity due to a decrement in nonradiative decay pathways of the emitting cryptolepine species. Furthermore, docking and quantum chemical calculations were employed to decipher the molecular orientation of the drug in the inclusion complex. Studies with natural DNA indicate that CRYP molecules intercalate into DNA, which leads to a huge quenching of the fluorescence of CRYP. Keeping this in mind, we studied the DNA‐assisted release of CRYP molecules from the nanocavity of CB7. Strikingly, DNA alone could not remove the drug from the nanocavity of CB7. However, an external stimulus such as acetylcholine chloride was able to displace CRYP from the nanocavity, and subsequently, the displaced drug could bind to DNA.     

Synthesis,Characterization, Crystal Structure,and Biological Activities of Transition Metal Complexes with 1‐Phenyl‐3‐methyl‐5‐hydroxypyrazole‐4‐methylene‐8′‐quinolineimine

The Schiff base ligand, 1‐phenyl‐3‐methyl‐5‐hydroxypyrazole‐4‐methylene‐8′‐quinolineimine, and its Cu^II, Zn^II, and Ni^II complexes were synthesized and characterized. The crystal structure of the Zn^II complex was determined by single‐crystal X‐ray diffraction, indicating that the metal ions and Schiff base ligand can form mononuclear six‐coordination complexes with 1:1 metal‐to‐ligand stoichiometry at the metal ions as centers. The binding mechanism and affinity of the ligand and its metal complexes to calf thymus DNA (CT DNA) were investigated by UV/Vis spectroscopy, fluorescence titration spectroscopy, EB displacement experiments, and viscosity measurements, indicating that the free ligand and its metal complexes can bind to DNA via an intercalation mode with the binding constants at the order of magnitude of 105–106 M ^–1, and the metal complexes can bind to DNA more strongly than the free ligand alone. In addition, antioxidant activities of the ligand and its metal complexes were investigated through scavenging effects for hydroxyl radical in vitro, indicating that the compounds show stronger antioxidant activities than some standard antioxidants, such as mannitol. The ligand and its metal complexes were subjected to cytotoxic tests, and experimental results indicated that the metal complexes show significant cytotoxic activity against lung cancer A 549 cells.     

Photo‐Cross‐Linking Probes for Trapping G‐Quadruplex DNA

We have developed a straightforward synthetic pathway to a set of six photoactivatable G‐quadruplex ligands with a validated G4‐binding motif (the bisquinolinium pyridodicarboxamide PDC‐360A) tethered through various spacers to two different photo‐cross‐linking groups: benzophenone and an aryl azide. The high quadruplex‐versus‐duplex selectivity of the PDC core was retained in the new derivatives and resulted in selective alkylation of two well‐known G‐quadruplexes (human telomeric G4 and oncogene promoter c‐myc G4) under conditions of harsh competition. The presence of two structurally different photoactivatable functions allowed the selective alkylation of G‐quadruplex structures at specific nucleobases and irreversible G4 binding. The topology and sequence of the quadruplex matrix appear to influence strongly the alkylation profile, which differs for the telomeric and c‐myc quadruplexes. The new compounds are photoactive in cells and thus provide new tools for studying G4 biology.     

Fluorescence‐Labeled Bis‐benzamidines as Fluorogenic DNA Minor‐Groove Binders: Photophysics and Binding Dynamics

In recent decades there has been great interest in the design of highly sensitive sequence‐specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis‐benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double‐stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.     

Control of Exchange Interactions in π Dimers of 6‐Oxophenalenoxyl Neutral π Radicals: Spin‐Density Distributions and Multicentered–Two‐Electron Bonding Governed by Topological Symmetry and Substitution at the 8‐Position

The tri‐tert‐butylphenalenyl (TBPLY) radical exists as a π dimer in the crystal form with perfect overlapping of the singly occupied molecular orbitals (SOMOs) causing strong antiferromagnetic exchange interactions. 2,5‐Di‐tert‐butyl‐6‐oxophenalenoxyl (6OPO) is a phenalenyl‐based air‐stable neutral π radical with extensive spin delocalization and is a counter analogue of phenalenyl in terms of the topological symmetry of the spin density distribution. X‐ray crystal structure analyses showed that 8‐tert‐butyl‐ and 8‐(p‐XC₆H₄)‐6OPOs (X=I, Br) also form π dimers in the crystalline state. The π‐dimeric structure of 8‐tert‐butyl‐6OPO is seemingly similar to that of TBPLY even though its SOMO–SOMO overlap is small compared with that of TBPLY. The 8‐(p‐XC₆H₄) derivatives form slipped stacking π dimers in which the SOMO–SOMO overlaps are greater than in 8‐tert‐butyl‐6OPO, but still smaller than in TBPLY. The solid‐state electronic spectra of the 6OPO derivatives show much weaker intradimer charge‐transfer bands, and SQUID measurements for 8‐(p‐BrC₆H₄)‐6OPO show a weak antiferromagnetic exchange interaction in the π dimer. These results demonstrate that the control of the spin distribution patterns of the phenalenyl skeleton switches the mode of exchange interaction within the phenalenyl‐based π dimer. The formation of the relevant multicenter–two‐electron bonds is discussed.     

Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole)

Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co²⁺, Ni²⁺, and Cu²⁺ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.     

Electrochemically‐controlled DNA Release under Physiological Conditions from a Monolayer‐modified Electrode

An indium tin oxide (ITO) electrode prepared on a flexible polymeric support was modified with an amino‐silane and then functionalized with trigonelline and 4‐carboxyphenylboronic acid covalently bound to the amino groups. The trigonelline species containing quarterized ammonium group produced positive charge on the electrode surface regardless of the pH value, while the phenylboronic acid species were neutral below pH 8 and negatively charged above pH 9 (note that their pK_a=8.4). The total charge on the monolayer‐modified electrode was positive at the neutral pH and negative at pH>9 (note that 4‐carboxyphenylboronic acid was attached to the electrode surface in excess to trigonelline, thus allowing the negative charge to dominate on the electrode surface at basic pH). Single‐stranded DNA molecules were loaded on the modified electrode at pH 7.0 due to their electrostatic attraction to the positively charged surface. By applying electrolysis at −1.0 V (vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase in the vicinity of the electrode surface. The process resulted in the transition to the total negative charge due to the negative charges formed on the phenylboronic acid species. This resulted in the electrostatic repulsion and release of the loaded DNA. The developed approach allowed the electrochemically‐triggered DNA release not only in the aqueous solutions, but also in human serum solution, thus giving promise for future biomedical applications.     

Synthesis and characterization of new α,β‐unsaturated γ‐lactones: Alkyl 3‐acetyl‐4‐hydroxy‐2‐methyl‐5‐oxo‐2,5‐dihydrofuran‐2‐ylcarbamates

A convenient procedure for the preparation of carbamate derivatives of 5‐oxo‐2,5‐dihydrofuran ( 3 ) was described. The method is based on the Michael type addition of three alkyl carbamates ( 2 ) with 4‐acetyl‐5‐methyl‐2,3‐dihydro‐2,3‐furandione ( 1 ). According to ¹H nmr spectra of compounds show tautomeric forms ( 3,4,5 ) in CDC1₃. In the solid state the synthesized compounds are enol forms ( 3 ). The products were characterized with molecular spectroscopic methods.     

Differences between G‐Protein‐Stabilized Agonist–GPCR Complexes and their Nanobody‐Stabilized Equivalents

Protein nanobodies have been used successfully as surrogates for unstable G‐proteins in order to crystallize G‐protein‐coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including metadynamics enhanced sampling, to investigate the similarities and differences between GPCR–agonist ternary complexes with the α‐subunits of the appropriate G‐proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist‐binding mode differs significantly between the two alternative ternary complexes. The ternary‐complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP‐specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.     

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

Paramagnetic metal ions deliver structural information both in EPR and solid‐state NMR experiments, offering a profitable synergetic approach to study bio‐macromolecules. We demonstrate the spectral consequences of Mg²⁺/ Mn²⁺ substitution and the resulting information contents for two different ATP:Mg²⁺‐fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.     

Electrophoretic behavior of DNA‐methyl‐CpG‐binding domain protein complexes revealed by capillary electrophoreses laser‐induced fluorescence

The free solution electrophoretic behavior of DNA‐protein complexes depends on their charge and mass in a certain experimental condition, which are two fundamental properties of DNA‐protein complexes in free solution. Here, we used CE LIF to study the free solution behavior of DNA‐methyl‐CpG‐binding domain protein (MBD2b) complexes through exploring the relationship between the mobilities, charge, and mass of DNA‐protein complexes. This method is based on the effective separation of free DNA and DNA‐protein complexes because of their different electrophoretic mobility in a certain electric field. In order to avoid protein adsorption, a polyacrylamide‐coated capillary was used. Based on the evaluation of the electrophoretic behavior of formed DNA‐MBD2b complexes, we found that the values of (μ₀/μ)‐1 were directly proportional to the charge‐to‐mass ratios of formed complexes, where the μ₀ and μ are the mobility of free DNA probe and DNA‐protein complex, respectively. The models were further validated by the complex mobilities of protein with various lengths of DNA probes. The deviation of experimental and calculated charge‐to‐mass ratios of formed complexes from the theoretical data was less than 10%, suggesting that our models are useful to analyze the DNA‐binding properties of the purified MBD2b protein and help to analyze other DNA‐protein complexes. Additionally, this study enhances the understanding of the influence of the charge‐to‐mass ratios of formed DNA‐protein complexes on their separation and electrophoretic behaviors.