Influence of metal coordination on the mismatch tolerance of ligand-modified PNA duplexes

Recent studies on metal incorporation in ligand-modified nucleic acids have focused on the effect of metal coordination on the stability of metal-containing duplexes or triplexes and on the metal binding selectivity but did not address the effect of the sequence of the nucleic acid in which the ligands are incorporated. We have introduced 8-hydroxyquinoline Q in 10-mer PNA strands with various sequences and have investigated the properties of the duplexes formed from these strands upon binding of Cu(2+). Variable-temperature UV-vis spectroscopy shows that, in the presence of Cu(2+), duplexes are formed even from ligand-modified Q-PNA strands that have a large number of mismatches. Spectrophotometric titrations demonstrate that at any temperature, one Cu(2+) ion binds a pair of Q-PNA strands that each contain one 8-hydroxyquinoline, but below the melting temperature, the PNA duplex exerts a supramolecular chelate effect, which prevents the transformation in the presence of excess Cu(2+) of the 1:2 Cu(2+):Q-PNA complexes into 1:1 complexes. EPR spectroscopy gives further support for the existence in the duplexes of [CuQ(2)] moieties that are similar to the corresponding square planar synthetic complex formed between Cu(2+) and 8-hydroxyquinoline. As PNA duplexes show a preferred handedness due to the chiral induction effect of a C-terminal l-lysine, which is transmitted through stacking interactions within the duplex, only if the metal-containing duplex has complementary strands, does it show a chiral excess measured by CD spectroscopy. The strong effect of the metal-ligand moiety is suggestive of an increased correlation length in PNA duplexes that contain such moieties. These results indicate that strong metal-ligand alternative base pairs significantly diminish the importance of Watson-Crick base pairing for the formation of a stable PNA duplex and lead to high mismatch tolerance, a principle that can be used in the construction of hybrid inorganic-nucleic acid nanostructures.     

Light-driven reversible handedness inversion in self-organized helical superstructures

We report here a fast-photon-mode reversible handedness inversion of a self-organized helical superstructure (i.e., a cholesteric liquid crystal phase) using photoisomerizable chiral cyclic dopants. The two light-driven cyclic azobenzenophanes with axial chirality show photochemically reversible trans to cis isomerization in solution without undergoing thermal or photoinduced racemization. As chiral inducing agents, they exhibit good solubility, high helical twisting power, and a large change in helical twisting power due to photoisomerization in three commercially available, structurally different achiral liquid crystal hosts. Therefore, we were able to reversibly tune the reflection colors from blue to near-IR by light irradiation from the induced helical superstructure. More interestingly, the different switching states of the two chiral cyclic dopants were found to be able to induce a helical superstructure of opposite handedness. In order to unambiguously determine the helical switching, we employed a new method that allowed us to directly determine the handedness of the long-pitched self-organized cholesteric phase.     

Coordination-driven self-assembly in a single pot

New multinuclear discrete heteroleptic complexes have been synthesized by mixing Pd(II), 2,2′-bipyridine and N,N′-(1,2-phenylene)diisonicotinamide in a single pot as a new approach. A dimeric molecular rhombus and a trimer in equilibrium are obtained where the dimer is the major product. Similar equilibrium is also observed when classical method is employed for the synthesis. The equilibrium is shifted exclusively in favour of the dimer upon addition of benzene. The complexes are characterized by NMR and ESI-MS methods. Crystal structure of the benzene encapsulated rhombus is presented.     

Coordination-driven self-assembly of predesigned supramolecular triangles

The design and self-assembly of three supramolecular triangles is described. A novel 60 degrees corner unit directs the exclusive formation of triangular assemblies that are not in detectable equilibrium with other macrocycles. The resulting triangles have sides ranging from 2.7 to 3.5 nm in length and molecular masses as high as 5396 amu. The crystal structure of one of the assemblies shows an approximately 1.4 nm cavity; the crystal packing forms open, triangular channels. The characterization of the supramolecular triangles by multinuclear NMR, elemental analysis, and electrospray mass spectrometry is also reported.     

Coordination-driven self-organization of switchable [2]rotaxane

A bistable porphyrin-containing [2]rotaxane is synthesized with a shuttling benzylic-amide macrocycle mechanically locked onto the thread subunit by formations of H-bonds with two potential stations. This macrocycle comprises two pyridine groups, which would be easily coordinated with zinc porphyrin. The Zn(II) coordination of porphyrin moiety on the thread subunit, immediately followed by the coordination with pyridine groups on the macrocycle, leads to an intermolecular axle-macrocycle-type nanostructure. Moreover, the self-assembly way shows great difference from the two states of the rotaxane monomer: The coordination-driven self-organization of the trans-state E2 leads to a network structure, whereas the cis-state Z2 gives birth to an irregular assembly.     

Quantifying interactions between cell receptors and adhesion ligand-modified polymers in solution

Specific interactions between cells and cell-interactive polymers in solution were investigated by the fluorescence resonance energy transfer (FRET) technique and rheological measurements. The green fluorescence emission was dramatically reduced when rhodamine-stained cells were mixed with a fluorescein-labeled RGD-alginate solution, compared with those mixed with no RGD-containing alginate solution, which indicated an occurrence of FRET and existence of specific interactions between the cells and the polymers in solution. Rheological measurements also confirmed the formation of ordered structures of cell/polymer mixtures, caused by specific cell-polymer interactions. The FRET method was able to provide a useful means of investigating cell-polymer interactions, both in a qualitative and quantitative manner, and this approach to monitoring and controlling specific interactions between cells and polymers could be useful in the design and tailoring of polymeric carriers for cells, as well as for biological drugs, especially for tissue engineering applications.     

Coordination-driven self-assembly of polyoxometalates into discrete supramolecular triangles

Pd(II)-directed self-assembly of a 3-pyridyl grafted Lindqvist hexavanadate led to the formation of a unique trimeric species, as confirmed by a variety of techniques, including pulsed-field gradient NMR spectroscopy and high-resolution ESI mass spectrometry.     

Coordination-driven face-directed self-assembly of trigonal prisms. Face-based conformational chirality

The coordination-driven self-assembly of four different trigonal prisms from 3 equiv of one of four different tetrapyridyl star connectors and 6 equiv of a platinum linker dication in nitromethane is presented. This face-directed approach affords high yields without template assistance. The prisms have been characterized by multinuclear and DOSY NMR and dual ESI-FT-ICR mass spectrometry. The use of a conformationally chiral star connector leads to a conformationally chiral prism when connector arm ends attached to a vertex have a strongly correlated twist sense and chirality is communicated across polyhedral faces, edges, and vertices. Molecular mechanics results suggest that in the smallest prism 3d collective effects dominate and the all-P and all-M conformers are strongly favored. NMR data prove that the two edges of the pyridine rings in the triflate salts of 3a-3d are distinct. An Eyring plot of rates obtained from line-shape analysis and 1-D EXCHSY NMR yields an activation enthalpy DeltaH(double dagger) of approximately 12 kcal/mol and activation entropy DeltaS(double dagger) of approximately -15 cal/mol x K for the edge interconversion process, compatible with pyridine rotation around the Pt-N bond. For 3c, this behavior is observed only up to approximately 318 K. At higher temperatures, the Eyring plot is again linear but follows a very different straight line, with a DeltaH(double dagger) of approximately 35 kcal/mol and DeltaS(double dagger) of approximately 60 cal/mol x K. This highly unusual result is further investigated and discussed in the following companion paper.     

Synthesis of pyrrolidinone PNA: a novel conformationally restricted PNA analogue

To preorganize PNA for duplex formation, a new cyclic pyrrolidinone PNA analogue has been designed. In this analogue the aminoethylglycine backbone and the methylenecarbonyl linker are connected, introducing two chiral centers compared to PNA. The four stereoisomers of the adenine analogue were synthesized, and the hybridization properties of PNA decamers containing one analogue were measured against complementary DNA, RNA, and PNA strands. The (3S,5R) isomer was shown to have the highest affinity toward RNA, and to recognize RNA and PNA better than DNA. The (3S,5R) isomer was used to prepare a fully modified decamer which bound to rU10 with only a small decrease in Tm (delta Tm/mod = 1 degree C) relative to aminoethylglycine PNA.     

Coordination-driven self-assembly of truncated tetrahedra capable of encapsulating 1,3,5-triphenylbenzene

The design and synthesis of coordinative truncated tetrahedra is described. The coordination-driven self-assembly of a truncated tetrahedron was achieved using 90° organoplatinum acceptors and a hexapyridyl ligand with six-fold symmetry under mild conditions. This tetrahedron can act as a host toward 1,3,5-triphenylbenzene. The truncated tetrahedral structures and the host-guest complex were identified using multinuclear ((31)P and (1)H) NMR spectroscopy, electrospray ionization mass spectrometry, X-ray crystallography, and pulsed-field-gradient spin-echo NMR, along with computational simulations.     

Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.     

Cyclobutyl-carbonyl substituted PNA: synthesis and study of a novel PNA derivative

A new, optically active, cyclobutyl-carbonyl substituted PNA monomer has been synthesized stereoselectively from a chiral amino acid prepared from (+)-α-pinene. A conformational search shows a lack of conformational bias for the monomer and incorporation of the monomer into a standard oligomer is tolerated without changing the binding affinity towards sequence complementary RNA, DNA or PNA targets.     

Synthesis of a ferrocenyl uracil PNA monomer for insertion into PNA sequences

The deprotection of the tert-butyl group of a ferrocenyl uracil Peptide Nucleic Acid (PNA) monomer, Fmoc-aeg(R)-O^tBu (1) was achieved using a two step synthesis involving hydrolysis in basic conditions to give first the zwitterion of ⁺NH₃-aeg(R)-O⁻ (7). Compound 7 was reacted in situ with N-(9-fluorenylmethoxycarbonyloxy)succinimide to obtain the expected compound Fmoc-aeg(R)-OH (2) (Abbreviations: Aeg = (2-aminoethyl)-glycine; Fmoc = 9-fluorenylmethoxycarbonyl; O^tBu = tert-butyl; R = 5-(N-ferroce-nylmethylbenzamido)uracyl).     

Synthesis and incorporation into PNA of fluorinated olefinic PNA (F-OPA) monomers

[structure: see text] A fluorinated OPA monomer containing the base thymine ((Z)-t-F-OPA) was synthesized in 12 steps, featuring a highly selective allylic over homoallylic Mitsunobu substitution for the introduction of the nucleobase. F-OPA modified PNA decamers were prepared by the MMTr/acyl protection strategy. The thermal stability of duplexes of PNA decamers containing (Z)-t-F-OPA units with antiparallel complementary DNA was measured. We found a strong dependence of stability from the sequential position of the (Z)-t-F-OPA units, ranging from DeltaT(m) of +2.4 to -8.1 degrees C/modification relative to unmodified PNA.     

Cyclopropane PNA: observable triplex melting in a PNA constrained with a 3-membered ring

The first peptide nucleic acid (PNA) with a cyclopropane in the backbone has been synthesized, and the effects of the ring on DNA/RNA binding properties of the PNA have been examined. Well-defined triplex to duplex melting transitions of PNA₂ DNA complexes is clearly observed by variable temperature UV absorbance with the cyclopropane-constrained PNA.     

Metal incorporation in modified PNA duplexes

Substitution of bipyridine for a nucleobase leads to modified peptide nucleic acid (PNA) single strands that are bridged in the presence of Ni2+ into a duplex containing a combination of hydrogen and coordinative bonds. CD experiments demonstrate that the duplex adopts a structure similar to that of an unmodified 10-bp PNA duplex, and UV melting experiments show a very sensitive dependence of the duplex stability on the substitution of a nucleobase pair with a pair of ligands or a metal-ligand alternative base pair.     

Coordination-driven self-assembly of metallodendrimers possessing well-defined and controllable cavities as cores

The design and self-assembly of novel cavity-cored metallodendrimers via noncovalent interactions are described. By employing [G0]-[G3] 120 degrees ditopic donor linkers substituted with Fréchet-type dendrons and appropriate rigid di-Pt(II) acceptor subunits, [G0]-[G3]-rhomboidal metallodendrimers and [G0]-[G3]-hexagonal, "snowflake-shaped" metallodendrimers with well-defined shape and size were prepared under mild conditions in high yields. The assemblies were characterized with multinuclear NMR ((1)H and (31)P), mass spectrometry (ESI-MS and ESI-FT-ICR-MS), and elemental analysis. Isotopically resolved mass spectrometry data support the existence of the metallodendrimers with rhomboidal and hexagonal cavities, and NMR data are consistent with the formation of all ensembles. The structures of [G0]- and [G1]-rhomboidal metallodendrimers were unambiguously confirmed via single-crystal X-ray crystallography. The shape and size of two [G3]-hexagonal metallodendrimers were investigated with MM2 force-field modeling.     

Coordination-driven self-assembly of supramolecular cages: heteroatom-containing and complementary trigonal prisms

The self-assembly of three nanoscopic prisms of approximate size 1 x 4 nm is reported. Tetrahedral carbon, silicon, and phosphorus were used as structure-defining elements in these coordination-based cages. A carbon-based assembly completes a pair of nanoscopic complementary 3-D structures. The formation of the structures is supported by multinuclear NMR, ESI FT-ICR mass spectrometry, and elemental analysis data.     

Coordination-driven assembly of molecular rectangles via an organometallic "clip"

The combination of linear dipyridyl ligands with a new type of modular building unit, based upon a 1,8-platinum-functionalized anthracene, leads to the self-organization of rectangular frameworks. X-ray crystallography confirms the cyclic structure of the supramolecular cationic complexes. Spectral assignments were provided by 2D NOESY (1)H NMR experiments.     

Dynamic covalent chemistry on self-templating PNA oligomers: formation of a bimolecular PNA quadruplex

The tetramolecular PNA quadruplex motif has been probed using a dynamic covalent chemistry (DCC) approach to create and characterize a bimolecular PNA quadruplex.