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Triple Helices (triple + helice)
Selected AbstractsSynthesis and Triple-Helix-Stabilization Properties of Branched Oligonucleotides Carrying 8-Aminoadenine MoietiesHELVETICA CHIMICA ACTA, Issue 2 2004Anna Aviño The synthesis of several branched oligonucleotides, i.e., of the parallel hairpins 5,8 and the Y-shaped 9 is described, together with their use in the formation of pyrimidine,pyrimidine,purine triple helices. Special attention was paid to the optimization of the assembly of the second strand from asymmetric branching molecules. The presence of 8-aminoadenine moieties in the WatsonCrick purine strand and 2,- O -methyl-RNA in the Hoogsteen pyrimidine strand produced strong stabilization of the triplex. [source] Collagen-like triple helix formation of synthetic (Pro-Pro-Gly)10 analogues: (4(S)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10, (4(R)-hydroxyprolyl-4(R)-hydroxyprolyl-Gly)10 and (4(S)-fluoroprolyl-4(R)-fluoroprolyl-Gly)10JOURNAL OF PEPTIDE SCIENCE, Issue 10 2005Masamitsu Doi Abstract For the rational design of a stable collagen triple helix according to the conventional rule that the pyrrolidine puckerings of Pro, 4-hydroxyproline (Hyp) and 4-fluoroproline (fPro) should be down at the X-position and up at the Y-position in the X-Y-Gly repeated sequence for enhancing the triple helix propensities of collagen model peptides, a series of peptides were prepared in which X- and Y-positions were altogether occupied by HypR, HypS, fProR or fProS. Contrary to our presumption that inducing the X-Y residues to adopt a down-up conformation would result in an increase in the thermal stability of peptides, the triple helices of (HypS -HypR -Gly)10 and (fProS -fProR -Gly)10 were less stable than those of (Pro-HypR -Gly)10 and (Pro-fProR -Gly)10, respectively. As reported by Bächinger's and Zagari's groups, (HypR -HypR -Gly)10 which could have an up-up conformation unfavorable for the triple helix, formed a triple helix that has a high thermal stability close to that of (Pro-HypR -Gly)10. These results clearly show that the empirical rule based on the conformational preference of pyrrolidine ring at each of X and Y residues should not be regarded as still valid, at least for predicting the stability of collagen models in which both X and Y residues have electronegative groups at the 4-position. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Supramolecular assembly of collagen triblock peptidesBIOPOLYMERS, Issue 4 2003Raquel Martin Abstract The relationship between primary sequence and collagen triple-helix formation is relatively well characterized, while higher levels of structural assembly from these sequences is poorly understood. To address this gap, a new collagen-like triblock peptide design was used to study the relationship between amino acid sequence and supramolecular assembly. Four collagen-like peptides with the sequence (Glu)5(Gly,Xaa,Hyp,Gly,Pro,Hyp)6(Glu)5 and corresponding to Xaa = alanine, proline, serine, or valine, and an analogous peptide without the glutamic acid end blocks, were solubilized in water at high concentrations (20,150 mg/mL) and analyzed in optical polarizing microscopy and transmission electron microscopy. Some of the peptides self-assembled into supramolecular structures, the nature of which was determined by the core collagen-like sequence. The globular end blocks appeared necessary for these short triple-helix-forming peptides to spontaneously organize into supramolecular structures in solution and also provided enhanced thermal stability based on CD analysis. The results indicate a strong dependence of the peptide triblock assembly behavior on the identity of the guest residue Xaa; nematic order when Xaa was valine, no organization when Xaa was serine, and banded spherulites displaying a cholesteric-like twist when Xaa was proline or alanine. According to these results, the identity of the amino acid in position Xaa of the triplet Gly,Xaa,Yaa dramatically determined the type of supramolecular assembly formed by short triple helices based on collagen-triblock like sequences. Moreover, the structural organization observed for these collagen-triblock peptides was analogous to some assemblies observed for native collagen in vivo and in vitro. The amino acid sequence in the native collagen proteins may therefore be a direct determinant of the different supramolecular architectures found in connective tissues. © 2003 Wiley Periodicals, Inc. Biopolymers 70:435,444, 2003 [source] Optimization of Triple-Helix-Directed DNA Cleavage by Benzoquinoquinoxaline,Ethylenediaminetetraacetic Acid ConjugatesCHEMBIOCHEM, Issue 9 2003Rula Zain Dr. Abstract The formation of triple-helical structures of DNA is based on sequence-specific recognition of oligopyrimidine,oligopurine stretches of double-helical DNA. Triple-helical structures can be stabilized by DNA-binding ligands. Benzoquinoquinoxaline (BQQ) derivatives are among the most potent intercalating-type agents known to stabilize DNA triple-helical structures. We previously reported the conversion of BQQ into a triplex-directed DNA cleaving agent, namely BQQ,ethylenediaminetetraacetic acid (EDTA), by coupling of 6-(3-aminopropylamino)BQQ to a suitable ethylenediaminetetraacetic acid derivative, and we demonstrated the ability of this conjugate to cause double-stranded cleavage of DNA at the triplex site. However, this prototype derivative BQQ,EDTA conjugate showed lower affinity towards triplex DNA than BQQ itself. In the light of this observation, and guided by molecular modeling studies, we synthesized a second generation of BQQ,EDTA conjugates based on 6-[bis(2-aminoethyl)amino]- and 6-(3,3,-diamino- N -methyldipropylamino),BQQ derivatives. We confirmed by DNA melting experiments that the new conjugates displayed an increased specific affinity towards triple helices when compared to the previously synthesized BQQ,EDTA. In addition, the efficiency of these new agents in triplex-specific binding and cleavage was demonstrated by triplex-directed double-stranded cleavage of plasmid DNA. [source] |