Designer ribozymes: programming the tRNA specificity into flexizyme

Fx3 is an artificial ribozyme with the ability to aminoacylate various tRNAs with phenylalanine and its nonnatural derivatives. Herein we report a simple strategy to build tRNA specificity into the generic Fx3, by appending to its 3'-end a tRNA-specific sequence (TSS), which is complementary to the acceptor stem of the cognate tRNA. This new designer ribozyme, referred to as Fx10, is able to recognize its cognate tRNA via a 10-base-pair interaction that is formed after the invasion of the tRNA acceptor stem by the TSS. We have demonstrated that Fx10 can aminoacylate its cognate tRNA with a high degree of specificity and also discriminate against the noncognate tRNAs. Because the tRNA specificity can be easily programmed into Fx10, it is a custom-made catalyst to generate nonnatural aminoacyl-tRNAs.     

Probing the conformational features of a phage display polypeptide sequence directed against single-walled carbon nanohorn surfaces

Single-walled carbon nanohorns (SWNHs) are interesting carbon nanostructures that have applications to science and technology. Using M13 phage display technology, polypeptides directed again SWNHs surfaces have been created for a number of nanotechnology and pharmaceutical purposes, yet the molecular mechanism of polypeptide sequence interaction and binding to SWNHs surfaces is not known. Recently, we identified a linear 12-AA M13 phage pIII sequence, NH-12-5-2 (DYFSSPYYEQLF), that binds with high affinity to SWNHs surfaces. To probe the structure of this pIII tail polypeptide further, we investigated the conformation of a model peptide representing the 12 AA NH-12-5-2 sequence. At neutral pH, the NH-12-5-2 model polypeptide is conformationally labile and exhibits two-state conformational exchange involving the D1-S5 N-terminal segment. Simultaneous with this conformational exchange process is the observation that the P6 residue exhibits imido ring conformational variation. In the presence of the structure-stabilizing solvent, TFE, or at pH 2.5, both the exchange process and Pro ring motion phenomena disappear, indicating that the structure of this peptide sequence can be stabilized by extrinsic factors. Interestingly, we observe NMR parameters (ROEs, (3)J coupling constants) for NH-12-5-2 in 90% v/v TFE that are consistent with the presence of a partial helical structure, similar to what was observed at low pH in our earlier CD experiments. We conclude that the NH-12-5-2 model polypeptide sequence possesses an inherent conformational instability that involves the D1-S5 sequence segment and the P6 residue but that this instability can be offset by extrinsic factors (e.g., charge neutralization, imido ring interconversion, and hydrophobic-hydrophobic interactions). These nonbonding interactions may play a role in the recognition and binding of this phage sequence region to SWNHs surfaces.     

Synthesis,Structure, Optical,and Electrochemical Properties of Triple‐ and Quadruple‐Decker Co‐facial Tetrathiafulvalene Arrays

Understanding the details of the electronic structure in face‐to‐face arranged tetrathiafulvalenes (TTFs) is very important for the design of supramolecular functional materials and superior conductive organic materials. This article is a comprehensive study of the interactions among columnar stacked TTFs using trimeric (trimer) and tetrameric (tetramer) TTFs linked by alkylenedithio groups (‐S(CH₂)_nS‐, n=1–4) as models of triple‐ and quadruple‐decker TTF arrays. Single‐crystal X‐ray analyses of neutral trimeric TTFs revealed that the three TTF moieties are oriented in a zigzag arrangement. Cyclic voltammetry measurements (CV) reveal that the trimer and tetramer exhibited diverse reversible redox processes with multi‐electron transfers, depending on the length of the ‐S(CH₂)_nS‐ units and substituents. The electronic spectra of the radical cations, prepared by electrochemical oxidation, showed charge resonance (CR) bands in the NIR/IR region (1630–1850 nm), attributed to a mixed valence (MV) state of the triple‐ and quadruple‐decker TTF arrays. In the trimeric systems, the dicationic state (+2; 0.66 cation per TTF unit) was found to be a stable state, whereas the monocationic state (+1) was not observed in the electronic spectra. In the tetrameric system, substituent‐dependent redox processes were observed. Moreover, π‐trimers and π‐tetramers, which show a significant Davydov blueshift in the spectra, are formed in the tricationic (trimer) and tetracationic (tetramer) state. In addition, these attractive interactions are strongly dependent on the length of the linkage unit.     

Structural properties of an artificial protein that regulates the nucleation of inorganic and organic crystals

Technological advances have facilitated the generation of artificial proteins that possess the capabilities of recognizing and binding to inorganic solids and/or controlling nucleation processes that form inorganic solids. However, very little is known regarding the structure of these interesting polypeptides and how their structure contributes to functionality. To address this deficiency, we report structural investigations of an artificial protein, p288, that self-assembles and controls the nucleation of simple salts and organic compounds into dendrite-like crystals. Under aqueous conditions at low pH and in the presence of high salt, p288 is conformationally labile and exists primarily as a random coil conformer in equilibrium with other undefined secondary structures, including polyproline type II and beta turn. We note that p288 can fold into either a partial beta strand (at neutral pH) or a predominantly alpha helical (in the presence of TFE) conformation. Solid-state 13C-15N NMR experiments also reveal that p288 in the lyophilized, hydrated state possesses some degree of nonrandom coil structure. These results indicate that p288 is conformationally labile but can undergo conformational transitions to a more stable structure when water solvent loss/displacement occurs and protein concentrations increase. We believe that conformational instability and the ability to adopt different structures as a function of different environmental conditions represent important molecular features that impact p288 supramolecular assembly and crystal nucleation processes.     

Chemical structure of escherichia coli lipid A

The chemical structure of E. coli lipid A was elucidated to be $\text{2}$ by determination of the nature of the individual acyl groups bound to the two hydroxyl groups in positions 3,3′ and the two amino groups of the D-glucosamine disaccharide phosphate backbone.     

Synthesis of bulgecinine: a new amino acid in bulgecins

Bulgecinine, a new proline type amino acid in bulgecins, was synthesized stereospecifically by use of D-glucose as a chiral precursor.     

Partial degradation and biological activities of an antitumor polysaccharide from rice bran.

A rice bran polysaccharide designated RON was subjected either to partial hydrolysis with formic acid or to partial degradation by ultrasonic irradiation. A significant change in the molecular size was also observed during simple chromatography of RON on a strongly acidic ion exchange resin, although the apparent molecular weight of RON had been assumed to be more than 1 x 10(6) daltons (Da). This fact indicates that RON exists as molecular aggregates, presumably mediated by metal cations. Degradation products with average molecular weights above ca. 1 x 10(4) Da which were obtained by any of the three methods still retained the following activities of RON: in vivo antitumor activity against Meth-A fibrosarcoma in mice by oral administration, and in vitro macrophage stimulatory effects to induce tumoricidal activity and interleukin 1 production. This molecular size was proven to be the minimum requisite for these activities because smaller fragments were scarcely active. The aggregation was characteristic of RON but not essential for its antitumor activity because definite, though slightly reduced, activity was exhibited even by the smaller fragments obtained after the ion exchange resin treatment.     

Synthesis and biological activities of analogs of a lipid A biosynthetic precursor: 1-O-phosphonooxyethyl-4'-O-phosphono-disaccharides with (R)-3-hydroxytetradecanoyl or tetradecanoyl groups at positions 2, 3, 2' and 3'.

Two novel analogs of a biosynthetic precursor of lipid A (2) were synthesized. The one analog (3) has acyl groups identical to those of 2, and the other (4) has tetradecanoyl groups in place of the (R)-3-hydroxytetradecanoyl groups of 2. Both 3 and 4 possess an alpha-glycosidically-bound phosphonooxyethyl group in place of the alpha-glycosyl phosphate group of 2. Compounds 3 and 4 exhibited definite antitumor activity against Meth A fibrosarcoma and low toxicity in rabbits, as the original compound 2 does. The replacement of the hydroxytetradecanoyl groups with tetradecanoyl groups barely affected the antitumor activity, but slightly enhanced the toxicity in rabbits.     

Singular values of some modular functions

For an integer N greater than 5 and a triple \({\mathfrak{a}}=[a_{1},a_{2},a_{3}]\) of integers with the properties 0<a _i ≤N/2 and a _i ≠a _j for i≠j, we consider a modular function \(W_{\mathfrak{a}}(\tau)=\frac{\wp (a_{1}/N;L_{\tau})-\wp (a_{3}/N;L_{\tau})}{\wp (a_{2}/N;L_{\tau})-\wp(a_{3}/N;L_{\tau})}\) for the modular group Γ ₁(N), where ?(z;L _τ ) is the Weierstrass ?-function relative to the lattice L _τ generated by 1 and a complex number τ with positive imaginary part. For a pair of such triples \({\mathfrak{A}}=[{\mathfrak{a}},{\mathfrak{b}}]\) and a pair of non-negative integers F=[m,n], we define a modular function \(T_{{\mathfrak{A}},F}\) for the group Γ ₀(N) as the trace of the product \(W_{\mathfrak{a}}^{m}W_{\mathfrak{b}}^{n}\) to the modular function field of Γ ₀(N). In this article, we study the integrality of singular values of the functions \(W_{\mathfrak{a}}\) and \(T_{{\mathfrak{A}},F}\) by using their modular equations. We prove that the functions \(T_{{\mathfrak{A}},F}\) for suitably chosen \({\mathfrak{A}}\) and F generate the modular function field of Γ ₀(N), and from Shimura reciprocity and Gee–Stevenhagen method we obtain that singular values \(T_{{\mathfrak{A}},F}(\tau)\) for suitably chosen \({\mathfrak{A}}\) and F generate ring class fields. Further, we study the class polynomial of \(T_{{\mathfrak{A}},F}\) for Schertz N-system.     

Lithium isotope separation by laser

A lithium isotope separation was performed using a laser isotope separation method. It was found that the lithium atoms with a natural isotopic abundance enhanced its⁶Li concentration up to over 90% by tuning the laser wavelength to the² P _1/2 of⁶Li. Too high power, however, leads to a loss of enrichment due to the power broadening effect which was analysed by the equation of motion of density matrices.