A porphycene-DNA hybrid and its DNA-templated interactions with a porphyrin

2012 ◽  
Vol 16 (05n06) ◽  
pp. 545-555 ◽  
Author(s):  
Rüdiger Haug ◽  
Clemens Richert
Keyword(s):  
Solid Phase ◽  
Functional Materials ◽  
Side Chain ◽  
Template Strand ◽  
Target Strand ◽  
Close Proximity ◽  
Complementary Region ◽  
Dna Strand ◽  
Duplex Formation ◽  
Uv Melting

A porphycene with a hydroxyethyl side chain was coupled to the 3′-terminus of an oligodeoxynucleotide via solid-phase synthesis. The resulting porphycene-DNA hybrid binds to a complementary region of a DNA target strand with greater affinity than the unmodified control oligonucleotide, resulting in an increase of the UV-melting point of 12.7 °C. Duplex formation is accompanied by an increase in porphycene fluorescence at 640 nm by 18%. When a tetrakis(p-hydroxyphenyl)porphyrin appended to the 5′-terminus of another DNA-strand is brought into close proximity of the porphycene by hybridizing it to the downstream-region of the template strand, 94% of the porphycene fluorescence is quenched. By quenching each others fluorescence to different degrees, porphycene and porphyrin, together, report on local DNA structure in a fashion reminiscent of that of molecular beacons. The introduction of porphycenes and the porphycene-porphyrin "two hybrid system'' to DNA-based structuring may open up new avenues to designed functional materials.

Comparison of the Potency of 8-L-Arginine, 8-D-Arginine and 8-D-Homoarginine Vasopressin Analogs with Substituted Phenylalanine in Position 2

1994 ◽  
Vol 59 (6) ◽  
pp. 1439-1450 ◽  
Author(s):  
Miroslava Žertová ◽  
Jiřina Slaninová ◽  
Zdenko Procházka
Keyword(s):  
Amino Acid ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Basic Amino Acid ◽  
The Other ◽  
Side Chain ◽  
Inhibitory Potency ◽  
Phase Synthesis ◽  
Other Hand ◽  
Order Of Magnitude

An analysis of the uterotonic potencies of all analogs having substituted L- or D-tyrosine or -phenylalanine in position 2 and L-arginine, D-arginine or D-homoarginine in position 8 was made. The series of analogs already published was completed by the solid phase synthesis of ten new analogs having L- or D-Phe, L- or D-Phe(2-Et), L- or D-Phe(2,4,6-triMe) or D-Tyr(Me) in position 2 and either L- or D-arginine in position 8. All newly synthesized analogs were found to be uterotonic inhibitors. Deamination increases both the agonistic and antagonistic potency. In the case of phenylalanine analogs the change of configuration from L to D in position 2 enhances the uterotonic inhibition for more than 1 order of magnitude. The L to D change in position 8 enhances the inhibitory potency negligibly. Prolongation of the side chain of the D-basic amino acid in position 8 seems to decrease slightly the inhibitory potency if there is L-substituted amino acid in position 2. On the other hand there is a tendency to the increase of the inhibitory potency if there is D-substituted amino acid in position 2.

Fmoc Solid Phase Peptide Synthesis

1999 ◽  
Keyword(s):  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Peptide Chain ◽  
Standard Approach ◽  
Side Chain ◽  
Complex Structures ◽  
Protein Conjugation ◽  
Chemoselective Ligation ◽  
Routine Production

In the years since the publication of Atherton and Sheppard's volume, the technique of Fmoc solid-phase peptide synthesis has matured considerably and is now the standard approach for the routine production of peptides. The basic problems outstanding at the time of publication of this earlier work have now been, for the most part, solved. As a result, innovators in the field have focussed their efforts to develop methodologies and chemistry for the synthesis of more complex structures. The focus of this new volume is much broader, and covers not only the essential procedures for the production of linear peptides but also more advanced techniques for preparing cyclic, side-chain modified, phospho- and glycopeptides. Many other methods also deserving attention have been included: convergent peptide synthesis; peptide-protein conjugation; chemoselective ligation; and chemoselective purification. The difficult preparation of cysteine and methionine-containing peptides is also covered, as well as methods for overcoming aggregation during peptide chain assembly and a survey of available automated instrumentation.

scholarly journals Pyrrole-Mediated Peptide Cyclization Identified through Genetically Reprogrammed Peptide Synthesis

Biomedicines ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 99 ◽  
Author(s):  
Klaas Decoene ◽  
Willem Vannecke ◽  
Toby Passioura ◽  
Hiroaki Suga ◽  
Annemieke Madder
Keyword(s):  
Peptide Synthesis ◽  
Cyclic Peptide ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Screening Method ◽  
In Vitro Translation ◽  
Side Chain ◽  
One Pot ◽  
Depth Analysis

Flexible in vitro translation (FIT) was used as a screening method to uncover a new methodology for peptide constraining based on the attack of a nucleophilic side-chain functionality onto an oxidized furylalanine side chain. A set of template peptides, each containing furylalanine as furan-modified amino acid and a nucleophilic residue (Cys, His, Lys, Arg, Ser, or Tyr), was produced through FIT. The translation mixtures were treated with N-bromosuccinimide (NBS) to achieve selective furan oxidation and subsequent MALDI analysis demonstrated Lys and Ser as promising residues for cyclisation. Solid-phase peptide synthesis (SPPS) was used to synthesize suitable amounts of material for further in-depth analysis and characterisation. It was found that in the case of the peptide containing lysine next to a furylalanine residue, a one-pot oxidation and reduction reaction leads to the generation of a cyclic peptide featuring a pyrrole moiety as cyclisation motif, resulting from the attack of the lysine side chain onto the oxidized furylalanine side chain. Structural evidence was provided via NMR and the generality of the methodology was explored. We hereby expand the scope of our previously developed furan-based peptide labeling and crosslinking strategy.

scholarly journals The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Philipp K Zuber ◽  
Irina Artsimovitch ◽  
Monali NandyMazumdar ◽  
Zhaokun Liu ◽  
Yuri Nedialkov ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Complex Structure ◽  
Transcription Regulator ◽  
Transcription Bubble ◽  
Template Strand ◽  
Domains Of Life ◽  
Dna Strand ◽  
Functional Analyses ◽  
Template Dna

RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.

scholarly journals Apoptotic endonuclease EndoG regulates alternative splicing of human telomerase catalytic subunit hTERT

2016 ◽  
Vol 62 (5) ◽  
pp. 544-554 ◽  
Author(s):  
D.D. Zhdanov ◽  
D.A. Vasina ◽  
E.V. Orlova ◽  
V.S. Orlova ◽  
M.V. Pokrovskaya ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Telomerase Activity ◽  
Catalytic Subunit ◽  
Over Expression ◽  
Htert Gene ◽  
Template Strand ◽  
Non Coding Rna ◽  
Dna Strand ◽  
Human Telomerase ◽  
Long Non Coding Rna

Human telomerase catalytic subunit hTERT is subjected to alternative splicing results in loss of its function and leads to decrease of telomerase activity. However, very little is known about the mechanism of hTERT pre-mRNA alternative splicing. Apoptotic endonuclease EndoG is known to participate this process. The aim of this study was to determine the role of EndoG in regulation of hTERT alternative splicing. Increased expression of b-deletion splice variant was determined during EndoG over-expression in CaCo-2 cell line, after EndoG treatment of cell cytoplasm and nuclei and after nuclei incubation with EndoG digested cell RNA. hTERT alternative splicing was induced by 47-mer RNA oligonucleotide in naked nuclei and in cells after transfection. Identified long non-coding RNA, that is the precursor of 47-mer RNA oligonucleotide. Its size is 1754 nucleotides. Based on the results the following mechanism was proposed. hTERT pre-mRNA is transcribed from coding DNA strand while long non-coding RNA is transcribed from template strand of hTERT gene. EndoG digests long non-coding RNA and produces 47-mer RNA oligonucleotide complementary to hTERT pre-mRNA exon 8 and intron 8 junction place. Interaction of 47-mer RNA oligonucleotide and hTERT pre-mRNA causes alternative splicing.

scholarly journals Microstructure features of the BST/(Mg, Ln)-ceramic

2021 ◽  
pp. 2160005
Author(s):  
K. P. Andryushin ◽  
A. V. Nagaenko ◽  
S. V. Khasbulatov ◽  
L. A. Shilkina ◽  
E. V. Glazunova ◽  
...  
Keyword(s):  
Solid Solutions ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Functional Materials ◽  
Ceramic Technology ◽  
Phase Synthesis ◽  
Fine Grained ◽  
Average Grain Size ◽  
Crystallite Sizes ◽  
Fine Grained Structure

Solid solutions of the composition Ba[Formula: see text](Mg, Ln)[Formula: see text]Sr[Formula: see text]TiO3 ([Formula: see text] = 0.01; 0.025; 0.04; [Formula: see text] = 0.20; 0.50; 0.80; Ln = La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tu, Yb) were prepared by two-stage solid-phase synthesis followed by sintering using conventional ceramic technology. The influence of rare-earth elements on the microstructure of the prepared ceramic samples was investigated. It was found that regardless of the type of modifiers introduced, the grain landscape of the studied solid solutions with different amounts of SrTiO3 is refined (in the initial system, the average grain size, [Formula: see text], at [Formula: see text] = 0.20 is 6 [Formula: see text]m; at [Formula: see text] = 0.50 is 4 [Formula: see text]m; at [Formula: see text] = 0.80 is 18 [Formula: see text]m) to crystallite sizes not exceeding (2–3) [Formula: see text]m, and compacted. The using of mechanical activation procedures leads to an even greater decrease in the size and an increase in the density of ceramics. The increasing in the concentration of modifiers in each group (within the considered range of dopant variation) against the background of such a fine-grained structure has little effect on the dynamics of changes in [Formula: see text]. It is concluded that it is advisable to use the data obtained in the development of functional materials based on BST/(Mg, Ln) and devices with the participation of these compositions.

scholarly journals Mechanism of R-loop formation and conformational activation of Cas9

2021 ◽  
Author(s):  
Martin Pacesa ◽  
Martin Jinek
Keyword(s):  
Dna Cleavage ◽  
Structural Basis ◽  
Seed Region ◽  
Loop Formation ◽  
Base Pairs ◽  
Guide Rna ◽  
Target Strand ◽  
Target Dna ◽  
Dna Strand ◽  
Dna Substrate

Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage. The programmable activity of Cas9 has been widely utilized for genome editing applications. Despite extensive studies, the precise mechanism of target DNA binding and on-/off-target discrimination remains incompletely understood. Here we report cryo-EM structures of intermediate binding states of Streptococcus pyogenes Cas9 that reveal domain rearrangements induced by R-loop propagation and PAM-distal duplex positioning. At early stages of binding, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the PAM-distal duplex of the DNA substrate. Target hybridisation past the seed region positions the guide-target heteroduplex into the central binding channel and results in a conformational rearrangement of the REC lobe. Extension of the R-loop to 16 base pairs triggers the relocation of the HNH domain towards the target DNA strand in a catalytically incompetent conformation. The structures indicate that incomplete target strand pairing fails to induce the conformational displacements necessary for nuclease domain activation. Our results establish a structural basis for target DNA-dependent activation of Cas9 that advances our understanding of its off-target activity and will facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.

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