Length-based encoding of binary data in DNA

We developed a system to encode digital information in DNA polymers based on the partial restriction digest (PRD). Our encoding method relies on the length of the fragments obtained by the PRD rather than the actual content of the nucleotide sequence, thus eliminating the need for expensive sequencing machinery. In this letter, we report on the encoding of 12 bits of data in a DNA fragment of 110 nucleotides and the process of recovering the data.     

Pyridine-tert-nitrogen-phenol ligands: N,N,O-Type tripodal chelates for the [M(CO)3]+ core (M = Re, Tc)

The design rationale, synthesis, and preliminary radiolabeling evaluation of new N,N,O-type pyridyl- tert-nitrogen-phenol ligands for the [M(CO) 3] (+) core, where M = (99m)Tc or Re, are described. The capability of the ligands to bind this technetium core is initially demonstrated by using the cold surrogate [Re(CO) 3] (+). NMR studies of the relevant rhenium tricarbonyl complexes indicate the formation of either a monomeric or a possible dimeric complex with each phenolic O atom bridging between two metal centers. Labeling with [ (99m)Tc(CO) 3] (+) provided further insight into the differences in complex formation on the dilute, no carrier added, level compared to the macroscopic scale at which the Re (I) counterparts were made. These new tridentate, monoanionic ligands are competent chelates in binding the [ (99m)Tc(CO) 3] (+) core because radiolabeling yields ranged from 85 to 99% and the resulting complexes were stable to cysteine and histidine challenges for as long as 24 h.     

Protonation‐Driven Membrane Insertion of a pH‐Low Insertion Peptide

The pH‐low insertion peptide (pHLIP) inserts into membranes and forms a transmembrane (TM) α‐helix in response to slight acidity, and has shown great potential for cancer diagnosis and treatment. As a lead, pHLIP is challenging to optimize because the mechanism of its pH‐dependent membrane interactions is not completely understood. Within pHLIP there are multiple D/E residues which could sense the pH change, the particular role played by each of them in the protonation‐driven insertion process is not clear. The precise location of the TM helix within the pHLIP sequence is also unknown. In this work, solid‐state NMR spectroscopy is used to address these central questions. Tracing backbone conformations revealed that the TM helix spans from A10 to D33 with a break at T19 to P20. Residue‐specific pK_a values of D31, D33, D25, and D14 were determined to be 6.5, 6.3, 6.1, and 5.8, respectively, and define the sequence of protonations which lead to insertion. Furthermore, possible intermediate states which disrupt membranes at pH 6.4 were proposed based on tryptophan fluorescence quenching and NMR data.     

Phosphate Assisted Proton Transfer in Water and Sugar Glasses: A Study Using Fluorescence of Pyrene-1-carboxylate and IR Spectroscopy

The role of water’s H-bond percolation network in acid-assisted proton transfer was studied in water and glycerol solutions and in sugar glasses. Proton transfer rates were determined by the fluorescence of pyrene-1-carboxylate, a compound with a higher pK in its excited state relative to the ground state. Excitation of pyrene-1-COO⁻ produces fluorescence from pyrene-1-COOH when a proton is accepted during the excited singlet state lifetime of pyrene-1-COO⁻. The presence of glycerol as an aqueous cosolvent decreases proton transfer rates from phosphoric and acetic acid in a manner that does not follow the Stokes relationship on viscosity. In sugar glass composed of trehalose and sucrose, proton transfer occurs when phosphate is incorporated in the glass. Sugar glass containing phosphate retains water and it is suggested that proton transfer requires this water. The infrared (IR) frequency of water bending mode in sugar glass and in aqueous solution is affected by the presence of phosphate and the IR spectral bands of all phosphate species in water are temperature dependent; both results are consistent with H-bonding between water and phosphate. The fluorescence results, which studied the effect of cosolvent, highlight the role of water in assisting proton transfer in reactions involving biological acids, and the IR results, which give spectroscopic evidence for H-bonding between water and phosphate, are consistent with a mechanism of proton transfer involving H-bonding. The possibility that the phosphate-rich surface of membranes assists in proton equilibration in cells is discussed.     

Non-destructive assay technique for the determination of <Superscript>238</Superscript>U/<Superscript>232</Superscript>Th ratio in the mixed oxides of uranium and thorium using prompt gamma-ray neutron activation

A non-destructive assay technique based on prompt gamma-ray neutron activation analysis for the determination of ²³⁸U to ²³²Th ratio in the mixed oxide fuel materials has been established. The method uses closely spaced high energy gamma-rays in the region of 4000 keV to 4150 keV enabling it to be applied for samples of any geometry and thickness without having any correction for gamma-ray attenuations and detection efficiencies.     

Optical, redox, and NLO properties of tricyanovinyl oligothiophenes: comparisons between symmetric and asymmetric substitution patterns

A series of tricyanovinyl (TCV)-substituted oligothiophenes was synthesized and investigated with a number of physical methods including UV/Vis, IR, and Raman spectroscopy, nonlinear optical (NLO) measurements, X-ray diffraction, and cyclic voltammetry. Mono- or disubstituted oligomers were prepared by the reaction of tetracyanoethylene with mono- or dilithiated oligomers. The comparative effects of the symmetric and asymmetric substitutions in the electronic and molecular properties have been addressed. These oligomers display dramatic reductions in both their optical and electrochemical band gaps in comparison with unsubstituted molecules. The analysis of the electronic properties of the molecules was assisted by density functional theory calculations, which are in excellent agreement with the experimental data. TCV substitution influences the energies of the frontier orbitals, especially with respect to the stabilization of LUMO orbitals. X-ray structural characterization of a monosubstituted oligomer exhibits pi-stacking with favorable intermolecular interactions. NLO results agree with the role of the intramolecular charge-transfer feature in the asymmetric samples. These results furthermore exalt the role of conformational flexibility in the disubstituted compounds and reveal an unexpected nonlinear optical activity for symmetric molecules. Regarding the electronic structure, the interpretation of the vibrational data reflects the balanced interplay between aromatic and quinoid forms, finely tuned by the chain length and substitution pattern. The electronic and structural properties are consistent with the semiconducting properties exhibited by these materials in thin film transistors (TFTs).     

Two bonding configurations of acetylene on Si(001)-(2 x 1): a combined high-resolution electron energy loss spectroscopy and density functional theory study

Two coexisting adsorption states of molecularly adsorbed acetylene on the Si(001)-(2 x 1) surface have been identified by a combined study based on the high-resolution electron energy loss spectroscopy and density functional computations. Seven possible adsorbate-substrate structures are considered theoretically including their full vibrational analysis. Based on a significantly enhanced experimental resolution, the assignment of 15 C2H2- and C2D2-derived vibrational modes identifies a dominant di-sigma bonded molecule adsorbed on top of a single Si-Si dimer. Additionally there is clear evidence for a second minority species which is di-sigma bonded between two Si-Si dimers within the same dimer row (end-bridge geometry). The possible symmetries of the adsorbate complexes are discussed based on the specular and off-specular vibrational measurements. They suggest lower than ideal C(2v) and C(s) symmetries for on-top and end-bridge species, respectively. At low coverages the symmetry reductions might be lifted.     

Submicron streptavidin patterns for protein assembly

Micron and submicron-scale features of aldehyde functionality were fabricated in polymer films by photolithography to develop a platform for protein immobilization and assembly at a biologically relevant scale. Films containing the pH-reactive polymer poly(3,3'-diethoxypropyl methacrylate) and a photoacid generator (PAG) were patterned from 500 nm to 40 mum by exposure to 365 nm (i-line) light. Upon PAG activation and hydrolysis of acetals, aldehyde groups formed. After the films were incubated with a biotinylated aldehyde reactive probe, the X-ray photoelectron spectroscopy results were consistent with biotin being attached to the surface. The background was subsequently passivated by flood exposure and incubation with an aminooxy-terminated poly(ethylene glycol), resulting in a 98% reduction in nonspecific protein adsorption. Protein patterning and assembly was demonstrated using streptavidin, biotinylated anthrax toxin receptor-1, and the protective antigen moiety of anthrax toxin and confirmed by fluorescence microscopy and atomic force microscopy (AFM). AFM demonstrated that 500 nm protein features were achieved. Because of the abundance of biotinylated proteins, this methodology provides a platform for protein immobilization and assembly for various applications in biotechnology.