Ferrocene-bis(thymine/uracil) conjugates: base pairing directed, spacer dependent self-assembly and supramolecular packing

X-ray crystallographic studies of methylene linked Ferrocene-bis(thymine/uracil) conjugates Fc(T:T)(M) and Fc(U:U)(M) reveal base dependent 2-D supramolecular assemblies generated via wobble self-pairing for bis-thymine and reverse wobble self-pairing for bis-uracil conjugates, differing in architecture from the corresponding butylene spacer linked conjugates.     

DNA base stacking: The stacked uracil/uracil and thymine/thymine minima

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)‐corrected M06‐2X/6‐31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4‐dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center‐of‐mass, whereas the other monomer remained still. Both face‐to‐back (one molecule exactly on top of the other) and face‐to‐face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas‐phase M06‐2X/6‐31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. © 2012 Wiley Periodicals, Inc.     

Micelles of lipid-oligonucleotide conjugates: implications for membrane anchoring and base pairing

This report examines the organization properties of new fluorescent DNA-lipids, either alone in water or in interaction with 1-octyl-beta-d-glucopyranoside micelles or egg phosphatidylcholine vesicles. We first describe the design and the syntheses of the conjugates. Then, we use UV-Vis absorption, steady-state fluorescence emission, electron microscopy, and fluorescence correlation spectroscopy after two-photon excitation to show that these DNA-lipids form spherical micelles in aqueous solution and incorporate much better in micelles than in vesicles. We also investigate the significance of the lipophilic chains of these DNA-lipids on the melting behavior of the double-stranded hybrids: in water melting curves are broadened whereas in amphiphilic assemblies duplexes melt as the unconjugated controls. This work is expected to be useful for improving the rational design of antisense medicines.     

The benzoylation of uracil and thymine

Uracil and thymine react with benzoyl chloride in acetonitrile-pyridine solution at room temperature to give first their 1-$\text{N}$-benzoyl (2b and 3b) and then their 1-$\text{N}$, 3-$\text{N}$-dibenzoyl derivatives (4a and 4b, respectively); the latter compounds are converted into the corresponding 3-$\text{N}$-benzoyl derivatives (5a and 6a) under mild conditions of basic hydrolysis.     

Thermochemistry of uracil and thymine revisited

Thermochemical properties of uracil and thymine have been evaluated using additional experiments. Standard (p⁰ = 0.1 MPa) molar enthalpies of formation in the gas phase at T = 298.15 K for uracil −(298.1 ± 0.6) and for thymine −(337.6 ± 0.9) kJ · mol⁻¹ have been derived from energies of combustion measured by static bomb combustion calorimetry and molar enthalpies of sublimation determined using the transpiration method. The G3 and G4 quantum-chemical methods were used for calculations of theoretical gaseous enthalpies of formation being in very good agreement with the re-measured experimental values.     

Homopairing possibilities of the DNA base thymine and the RNA base uracil: an ab initio density functional theory study

All planar homopairings of the DNA base thymine and the RNA base uracil are reported for the first time in this study. Using the idea of binding sites discussed in our previous work (Kelly et al. J. Phys. Chem. B 2005, 109, 11933; J. Phys. Chem. B 2005, 109, 22045) and ab initio density functional theory, we predict and relax 10 thymine and 10 uracil homopairs. The stabilization energies of the homopairs vary from just below zero to -0.82 eV. The results on the pair geometry and energetics are compared with those available in the literature. The collected data on all planar thymine and uracil homopairs can be used to construct the thymine and uracil superstructures seen experimentally on various surfaces.     

The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs

Uracil DNA glycosylase (UNG) locates uracil and its structural congener thymine in the context of duplex DNA using a base flipping mechanism. NMR imino proton exchange measurements were performed on free and UNG-bound DNA duplexes in which a single thymine (T) was paired with a series of adenine analogues (X) capable of forming one, two, or three hydrogen bonds. The base pair opening equilibrium for the free DNA increased 55-fold as the number of hydrogen bonds decreased, but the opening rate constants were nearly the same in the absence and presence of UNG. In contrast, UNG was found to slow the base pair closing rate constants (kcl) compared to each free duplex by a factor of 3- to 23-fold. These findings indicate that regardless of the inherent thermodynamic stability of the TX pair, UNG does not alter the spontaneous opening rate. Instead, the enzyme holds the spontaneously expelled thymine (or uracil) in a transient extrahelical sieving site where it may partition forward into the enzyme active site (uracil) or back into the DNA base stack (thymine).     

Vibrational Feshbach resonances in uracil and thymine

Sharp peaks in the dissociative electron attachment (DEA) cross sections of uracil and thymine at energies below 3 eV are assigned to vibrational Feshbach resonances (VFRs) arising from coupling between the dipole bound state and the temporary anion state associated with occupation of the lowest sigma* orbital. Three distinct vibrational modes are identified, and their presence as VFRs is consistent with the amplitudes and bonding characteristics of the sigma* orbital wave function. A deconvolution method is also employed to yield higher effective energy resolution in the DEA spectra. The site dependence of DEA cross sections is evaluated using methyl substituted uracil and thymine to block H atom loss selectively. Implications for the broader issue of DNA damage are briefly discussed.     

Virus-like supramolecular assemblies formed by cooperation of base pairing interaction and peptidic association

A peptide nucleic acid(PNA)-peptide conjugated molecule, T′_3(AKAE)_2, was designed to have both a PNA segment for oligonucleotide binding and an ionic self-complementary peptide sequence for self-association. T′_3(AKAE)_2 could co-assemble with oligoadenines(d(A)_x) to form virus-like supramolecular structures whose morphology showed dependence on the chain length and rigidity of the d(A)_x molecules. Smaller nanospheres with diameters of 13.0±2.0 nm were produced in the case of d(A)_6. Wormlike aggregates with lengths of 20–50 nm and diameters of 15.0±2.5 nm were found in the cases of d(A)_(12), d(A)_(18), d(A)_(24) and d(A)_(30). And larger spherical aggregates with diameters of 18±5 nm came into presence in the cases of d(A)_(36) and d(A)_(42). These nanostructures were suggested to be formed under a cooperative effect of base pair recognition and peptidic association. The study provides insights into the programmed assembly of a multi-components system as well as control of the size and shape of the co-assembled structures, which is of great significance in developing gene/drug delivery systems.     

Fullerene self-assembly and supramolecular nanostructures

This review presents a summary of the recent research progresses on fullerene self-assembly and supramolecular nanostructures. Fullerene nanospheres, one-dimensional nanowires/nanotubes, and two-dimensional layers were studied with various microscopic techniques such as the scanning tunneling microscopy, scanning electronic microscopy, and the transmission electron microscopy etc. It was revealed that the fullerene self-assembling structures were determined by both the fullerene intermolecular interactions and the fullerene–substrate interaction, therefore, different fullerene supramolecular nanostructures and morphologies could be obtained through controlling experimental conditions, e.g., the chemical modification of fullerenes by different chemical groups, the treatment of substrates, or the adopting of solvents etc.     

Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a Gd^III ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU–Gd^III–dcaU pair significantly stabilized the DNA duplex containing one dcaU–dcaU mismatch (ΔT_m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU–A pair was destabilized in the presence of Gd^III (ΔT_m = −3.5 °C). The Gd^III-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of Gd^III ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.

A novel N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleobase was found to form both a hydrogen-bonded dcaU–A and a metal-mediated dcaU–Gd^III–dcaU base pair. The hybridization partner of the dcaU-containing DNA was altered in response to Gd^III ions.     

Quantum-chemical study on uracil and thymine nitrosonium complexes

Quantum-chemical calculations at the RI-MP2/L1 level of theory showed that the most energetically favorable complexes of uracil and thymine with nitrosonium cation are those of n-type with NO⁺ coordination at the nitrogen or oxygen atom. A correlation was found between the experimental and calculated affinities of the dioxo tautomer of thymine for nitrosonium ion ( $ A_{NO^ + } $ ). A linear relation was revealed between $ A_{NO^ + } $ values for structurally similar tautomers of uracil and thymine.     

Polymerization of cyclic derivatives of uracil and thymine

Cyclic derivatives of uracil and thymine were synthesized from their corresponding 1-(2′-chloroethyl) derivatives by dehydrochlorination. These compounds were found to undergo a variety of reactions, giving many valuable derivatives of uracil and thymine. The cyclic derivatives, as monomers, were polymerized with a cationic initiator by a unique ring-opening process. The polymerization proceeded by ring opening with isomerization of the pyrimidine ring to give a polymer in which pyrimidine rings were connected with ethylene between N-1 and N-3 or O-4 in the pyrimidine ring. The structure of these polymers was determined by nuclear magnetic resonance (NMR), ultraviolet (UV), infrared (IR), and mass spectra. The structure was affected by polymerization temperature.     

Helical supramolecular self-assembly by prolamide thymidine/uridine analogues

This report describes the syntheses of rationally designed non-sugar nucleoside as prolamide nucleosides which contain prolyl ring and pyrimidine nucleobases (uracil/thymine) via acetamide bonds. These nucleosides have propensity to form distinctive self-assembly supramolecular helical structures ubiquitously through Watson-Crick/reverse type of hydrogen bonding with nucleobases. Moreover, the prolyl acetamide backbone groups- carbonyl (-C = O) and hydroxyl (-OH) group, are also involved in strengthening of self-assembled helical structures. Importantly, both prolamide thymidine and prolamide uridine have shown two distinctive helical structural patterns, in spite of containing the same backbone. Hence thymine and uracil moieties of prolamide nucleosides are responsible for unique supramolecular helical structural architectures.     

Synthesis of bifunctionally modified hexofuranosides of thymine and uracil

The glycosylation of bis(trimethylsilyl) derivatives of uracil and thymine by bifunctionally modified derivatives of D-glucofuranose in the presence of SnCl₄ as the condensing agent was studied. It is shown that the anomers of D-glucofuranose derivatives with a 1,2-trans orientation of the OAc groups undergo condensation more readily than the anomers. Both anomers give a mixture of and nucleosides with significant preponderance of the latter due to the primary formation of a 1,2-acetoxonium ion. It is assumed that the formation of nucleosides is due to the competitive coparticipation of other groups and/or more remote acetyl groups.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 542–548, April, 1982.     

Size of supramolecular SNARE complex: membrane-directed self-assembly

Full length v-SNARE protein in lipid vesicles when exposed to t-SNARE-reconstituted lipid membrane results in the self-assembly of a t-/v-SNARE complex in a ring pattern, forming pores, and establishing continuity between the opposing bilayers. It is known that smaller vesicles fuse more efficiently than larger ones, and hence the curvature of secretory vesicles may dictate the potency and efficacy of their fusion at the cell plasma membrane. The diameter of t- and v-SNARE vesicles may, therefore, reflect the size of the t-/v-SNARE complex formed. In the present study, this hypothesis was tested, and results from the study demonstrate that the size of the t-/v-SNARE complex is directly proportional to the vesicle diameter (R2 = 0.9725).