DNA-nanotube artificial ion channels

There is considerable interest in developing chemical devices that mimic the function of biological ion channels. We recently described such a device, which consisted of a single conically shaped gold nanotube embedded within a polymeric membrane. This device mimicked one of the key functions of voltage-gated ion channels: the ability to strongly rectify the ionic current flowing through it. The data obtained were interpreted using a simple electrostatic model. While the details are still being debated, it is clear that ion-current-rectification in biological ion channels is more complicated and involves physical movement of an ionically charged portion of the channel in response to a change in the transmembrane potential. We report here artificial ion channels that rectify the ion current flowing through them via this "electromechanical" mechanism. These artificial channels are also based on conical gold nanotubes, but with the critical electromechanical response provided by single-stranded DNA molecules attached to the nanotube walls.     

Protein biosensors based on biofunctionalized conical gold nanotubes

There is increasing interest in the concept of using nanopores as the sensing elements in biosensors. The nanopore most often used is the alpha-hemolysin protein channel, and the sensor consists of a single channel embedded within a lipid bilayer membrane. An ionic current is passed through the channel, and analyte species are detected as transient blocks in this current associated with translocation of the analyte through the channel-stochastic sensing. While this is an extremely promising sensing paradigm, it would be advantageous to eliminate the very fragile lipid bilayer membrane and perhaps to replace the biological nanopore with an abiotic equivalent. We describe here a new family of protein biosensors that are based on conically shaped gold nanotubes embedded within a mechanical and chemically robust polymeric membrane. While these sensors also function by passing an ion current through the nanotube, the sensing paradigm is different from the previous devices in that a transient change in the current is not observed. Instead, the protein analyte binds to a biochemical molecular-recognition agent at the mouth of the conical nanotube, resulting in complete blockage of the ion current. Three different molecular-recognition agents, and correspondingly three different protein analytes, were investigated: (i) biotin/streptavidin, (ii) protein-G/immunoglobulin, and (iii) an antibody to the protein ricin with ricin as the analyte.     

Oligonucleosides with a nucleobase-including backbone; synthesis and self-association of novel dinucleotide analogues

The synthesis and self-association of protected oxymethylene-bridged UA analogues are described.     

Kinetics of the simultaneous oxidation of nickel(II) and sulfur(IV) by oxygen in alkaline medium in Ni(II)–sulfur(IV)–O2 system

In the Ni(II)–S(IV)–O₂ system in the region of pH > 8.4, both Ni(II) and S(IV) are simultaneously autoxidized, and when sulfur is consumed fully NiOOH precipitates. At pH > 8.4, ethanol has no effect on the rate, whereas ammonia strongly inhibits the reaction when pH > 7.0. The kinetics of the reaction, in both the presence and the absence of ethanol, is defined by the rate law where k is the rate constant, K_O is the equilibrium constant for the adsorption of O₂ on ? Ni(OH)₂ particle surface. In ammonia buffer, the factor F is defined by where K, K_OH, K₁, K₂, K₃, and K₄ are the stability constants of NiSO₃, NiOH⁺, Ni(NH₃)²⁺, Ni(NH₃), Ni(NH₃), and Ni(NH₃), respectively. In unbuffered medium, the factor F reduces to The values of k and K^sp were found to be (1.3 ± 0.08) × 10^?1 s^?1 and (4.2 ± 3.5) × 10^?16, respectively, at 30°C. A nonradical mechanism that assumes the adsorption of both SO₃^2? and O₂ on the ? Ni(OH)₂ particle surface has been proposed. At pH ≤ 8.2, Ni(II) displays no catalytic activity for sulfur(IV)‐autoxidation and it is also not oxidized to NiOOH. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 464–478, 2010     

Structural characterization of pseudo-binary semiconducting alloys using molecular simulations

Monte Carlo simulations with the Keating model have been performed to predict the lattice constant and bond length variations with composition for pseudo-binary semiconducting alloys. In general, it is observed that the deviations of the lattice constants from Vegard's law predictions are larger as the lattice mismatch between the constituent binaries increases. Further, it is noted that these alloys have partial virtual crystal model characteristics and tend to be more towards the flexible (floppy) crystal limit as compared to the rigid crystal limit. The topological rigidity parameters are bond-type dependent. The angular deviations from perfect tetrahedral structure are also measured.     

Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA

We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 ?) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.     

Inhibition of Ras Signaling by Blocking Ras–Effector Interactions with Cyclic Peptides

Ras genes are frequently activated in human cancers, but the mutant Ras proteins remain largely “undruggable” through the conventional small‐molecule approach owing to the absence of any obvious binding pockets on their surfaces. By screening a combinatorial peptide library, followed by structure–activity relationship (SAR) analysis, we discovered a family of cyclic peptides possessing both Ras‐binding and cell‐penetrating properties. These cell‐permeable cyclic peptides inhibit Ras signaling by binding to Ras‐GTP and blocking its interaction with downstream proteins and they induce apoptosis of cancer cells. Our results demonstrate the feasibility of developing cyclic peptides for the inhibition of intracellular protein–protein interactions and of direct Ras inhibitors as a novel class of anticancer agents.     

Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs

Combining the structural elements of the second generation 2'-O-methoxyethyl (MOE) and locked nucleic acid (LNA) antisense oligonucleotide (AON) modifications yielded the highly nuclease resistant 2',4'-constrained MOE and ethyl bicyclic nucleic acids (cMOE and cEt BNA, respectively). Crystal structures of DNAs with cMOE or cEt BNA residues reveal their conformational preferences. Comparisons with MOE and LNA structures allow insights into their favourable properties for AON applications.