Home About us Contact
|
Home About us Contact | ||
|
|
||
Internal Loop (internal + loop)
Selected AbstractsMeasurement of mass transfer coefficient in an airlift reactor with internal loop using coalescent and non-coalescent liquid mediaJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 12 2004M Bla Abstract In this work the sulfite oxidation (SOM), dynamic pressure-step (DPM) and gassing-out (GOM) methods were compared for volumetric mass transfer coefficient measurement in an airlift reactor with internal loop. As a liquid phase both, non-coalescent and coalescent media were used. Among the methods discussed here, the mass transfer coefficient (kLa) values obtained by the DPM appear as the most reliable as they were found to be independent of oxygen concentration in the inlet gas, which confirmed the physical correctness of this method. The difference between data measured using air and oxygen was not higher than 10%, which was comparable to the scatter of experimental data. It has been found that the sulfite oxidation method yielded kLa values only a little higher than those obtained by the DPM and the difference did not exceed 10%. Up to an inlet gas velocity (UGC) of ,0.03 m s,1 the GOM using oxygen as a gas medium gave kLa values in fact identical with those obtained by the DPM. At higher flows of the inlet gas, the GOM yielded kLa values as much as 15% lower. The enhancement in oxygen mass transfer rate determined in non-coalescent media was estimated to be up to +15%, when compared with a coalescent batch. The experimental dependence of kLa vs the overall gas hold-up was described by an empirical correlation.1 Copyright © 2004 Society of Chemical Industry [source] Binding of Helix-Threading Peptides to E. coli 16S Ribosomal RNA and Inhibition of the S15,16S ComplexCHEMBIOCHEM, Issue 12 2005Barry D. Gooch Abstract Helix-threading peptides (HTPs) constitute a new class of small molecules that bind selectively to duplex RNA structures adjacent to helix defects and project peptide functionality into the dissimilar duplex grooves. To further explore and develop the capabilities of the HTP design for binding RNA selectively, we identified helix 22 of the prokaryotic ribosomal RNA 16S as a target. This helix is a component of the binding site for the ribosomal protein S15. In addition, the S15,16S RNA interaction is important for the ordered assembly of the bacterial ribosome. Here we present the synthesis and characterization of helix-threading peptides that bind selectively to helix 22 of E. coli 16S RNA. These compounds bind helix 22 by threading intercalation placing the N termini in the minor groove and the C termini in the major groove. Binding is dependent on the presence of a highly conserved purine-rich internal loop in the RNA, whereas removal of the loop minimally affects binding of the classical intercalators ethidium bromide and methidiumpropyl,EDTA,Fe (MPE,Fe). Moreover, binding selectivity translates into selective inhibition of formation of the S15,16S complex. [source] The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switchACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2007Jiro Kondo In previous studies, it was reported that DNA fragments with the sequence d(gcGXYAgc) (where X = A or G and Y = A, T or G) form a stable base-intercalated duplex (Bi-duplex) in which the central X and Y residues are not involved in any base-pair interactions but are alternately stacked on each other between the two strands. To investigate the structural stability of the Bi-duplex, the crystal structure of d(gcGAACgc) with a point mutation at the sixth residue of the sequence, d(gcGAAAgc), has been determined. The two strands are associated in an antiparallel fashion to form two types of bulge-containing duplexes (Bc-duplexes), I and II, both of which are quite different from the Bi-duplex of the parent sequence. In both Bc-duplexes, three Watson,Crick G·C base pairs constitute the stem regions at the two ends. The A4 residues are bulged in to form a pair with the corresponding A4 residue of the opposite strand in either duplex. The A4·A4* pair formation is correlated to the orientations of the adjacent A5 residues. A remarkable difference between the two Bc-duplexes is seen at the A5 residue. In Bc-duplex I, it is flipped out and comes back to interact with the G3 residue. In Bc-duplex II, the A5 residue extends outwards to interact with the G7 residue of the neighbouring Bc-duplex I. These results indicate that trans sugar-edge/Hoogsteen (sheared-type) G3·A6* base pairs are essential in the formation of a Bi-duplex of d(gcGXYAgc). On the other hand, the alternative conformations of the internal loops containing two consecutive bulged A residues suggest molecular switching. [source] The Role of Flexibility in the Rational Design of Modularly Assembled Ligands Targeting the RNAs that Cause the Myotonic DystrophiesCHEMBIOCHEM, Issue 3 2010Matthew D. Disney Prof. Abstract Modularly assembled ligands were designed to target the RNAs that cause two currently untreatable neuromuscular disorders, myotonic dystrophy types 1 (DM1) and 2 (DM2). DM1 is caused by an expanded repeating sequence of CUG, and DM2 is caused by expanded CCUG repeats. Both are present in noncoding regions and fold into hairpins with either repeating 1×1 nucleotide UU (DM1) or 2×2 nucleotide 5,-CU/3,-UC (DM2) internal loops separated by two GC pairs. The repeats are toxic because they sequester the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Rational design of ligands targeting these RNAs was enabled by a database of RNA motif,ligand partners compiled by using two-dimensional combinatorial screening (2DCS). One 2DCS study found that the 6,,-azido-kanamycin A module binds internal loops similar to those found in DM1 and DM2. In order to further enhance affinity and specificity, the ligand was assembled on a peptoid backbone to precisely control valency and the distance between ligand modules. Designed compounds are more potent and specific binders to the toxic RNAs than MBNL1 and inhibit the formation of the RNA,protein complexes with nanomolar IC50 values. This study shows that three important factors govern potent inhibition: 1) the surface area sequestered by the assembled ligands; 2) the spacing between ligand modules since a longer distance is required to target DM2 RNAs than DM1 RNAs; and 3) flexibility in the modular assembly scaffold used to display the RNA-binding module. These results have impacts on the general design of assembled ligands targeting RNAs present in genomic sequence. [source] | ||||||||||