Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

A Biosilification Fusion Protein for a ‘Self‐immobilising’ Sarcosine Oxidase Amperometric Enzyme Biosensor

Monomeric sarcosine oxidase (mSOx) fusion with the silaffin peptide, R5, designed previously for easy protein production in low resource areas, was used in a biosilification process to form an enzyme layer electrode biosensor. mSOx is a low activity enzyme (10–20 U/mg) requiring high amounts of enzyme to obtain an amperometric biosensor signal, in the clinically useful range <1 mM sarcosine, especially since the K_m is >10 mM. An amperometric biosensor model was fitted to experimental data to investigate dynamic range. mSOx constructs were designed with 6H (6×histidine) and R5 (silaffin) peptide tags and compared with native mSOx. Glutaraldehyde (GA) cross‐linked proteins retained ～5 % activity for mSOx and mSOx‐6H and only 0.5 % for mSOx‐R5. In contrast R5 catalysed biosilification on (3‐mercaptopropyl) trimethoxysilane (MPTMS) and tetramethyl orthosilicate (TMOS) particles created a ‘self‐immobilisation’ matrix retaining 40 % and 76 % activity respectively. The TMOS matrix produced a thick layer (>500 μm) on a glassy carbon electrode with a mediated current due to sarcosine in the clinical range for sarcosinemia (0–1 mM). The mSOx‐R5 fusion protein was also used to catalyse biosilification in the presence of creatinase and creatininase, entrapping all three enzymes. A mediated GC enzyme linked current was obtained with dynamic range available for creatinine determination of 0.1–2 mM for an enzyme layer ～800 nm.     

Functionalized Silver-Ion-Mediated α-dC/β-dC Hybrid Base Pairs with Exceptional Stability: α-d-5-Iodo-2′-Deoxycytidine and Its Octadiynyl Derivative in Metal DNA

Silver-mediated α-dC–Ag⁺–β-dC hybrid base pairs decorated with 5-iodo- or 5-octadiynyl residues are well accommodated in duplex DNA. A strong T_m increase and favorable thermodynamic data for duplex DNA were observed after addition of silver ions. The phenomenon is particularly obvious when both nucleobases of the base pairs are functionalized. Neither the position of the base pair, nor the type of 5-substituent had a negative influence. On the contrary, functionalization of conventional silver-mediated β-dC–Ag⁺–β-dC homo base pairs showed a negative impact induced by the bulky substituents. To this end, cytosine modified 12-mer oligodeoxynucleotides were prepared by solid-phase synthesis employing new α-anomeric 2′-deoxycytidine phosphoramidites. A multigram scale synthesis was developed for 5-iodo-α-d -2′-deoxycytidine ( 1 ) employing the direct glycosylation of cytosine with Hoffer's α-d -halogenose followed by separation of anomeric DMT nucleosides. Regarding base-pair stability and functionalization silver-mediated α/β-dC hybrid base pairs were found to be superior to β/β-dC homo pairs. According to their extraordinary properties, they might find applications in DNA diagnostics, material science, or nanotechnology.     

Transition‐Metal‐Free Trifluoromethylthiolation of N‐Heteroarenes

A general and efficient methodology for the direct transition metal free trifluoromethylthiolation of a broad range of biologically relevant N‐heteroarenes is reported employing abundant sodium chloride as the catalyst. This method is operationally simple, exhibits high functional group tolerance, and does not require protecting groups.     

Heterogeneous photobleaching in confocal microscopy

Photobleaching was studied during recording of confocal scanning laser microscopy. Studies on fluorescent gels of FITC-labeled dextran were used to evaluate differential bleaching along thez-axis. Differential bleaching along the z-axis was observed and it was seen that this was related to the numerical aperture of the objective in use. This points to the conclusion that photon energy flux density is an important parameter in photobleaching. To check if photon energy flux density heterogeneity is affected by local variation in the refractive index of the sample, photobleaching rates were calculated for different fluorescent objects (sections of seeds, animal cells stained with nuclear stains, immunocytochemistry preparations) and a pronounced similarity was found between photobleaching rates and DIC images.     

N7-DNA: Synthesis and Base Pairing of Oligonucleotides containing 7-(2-Deoxy-β -D-erythro-pentofuranosyl)adenine (N7Ad)

The synthesis of oligonucleotides containing 7-(2-deoxy-β -D -erythro-pentofuranosyl)adenine (N⁷A_d; 1 ) is described. Compound 1 was obtained from the precursor 4-amino-1H -imidazole-5-carbonitrile 2-deoxyribonucleoside 6 and was found to be much more labile than A_d. The N⁶-benzoyl protecting group (see 8 ) destabilized the N-glycosylic bond further and was difficult to remove by NH₃-catalyzed hydrolysis. Therefore, a (dimethyl-amino)methylidene residue was introduced (→ 9 ). Amidine 9 was blocked at OH? C(5′) with the dimethoxytrityl residue ((MeO)₂Tr), and phosphonate 4 as well as phosphoramidite 5 were prepared under standard conditions. Phosphonate 4 was employed in solid-phase oligonucleotide synthesis. Homooligonucleotides as well as self-complementary oligonucleotides were prepared. The oligomer d[(N⁷A)₁₁-A] ( 11 ) formed a duplex with d(T₁₂) ( 13 ). Antiparallel chain polarity and reverse Watson-Crick base pairing was deduced from duplex formation of the self-complementary d[(N⁷A)₈-T₈] ( 14 ).