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DNA Backbone (dna + backbone)
Selected AbstractsPolyfluorophores on a DNA Backbone: Sensors of Small Molecules in the Vapor Phase,ANGEWANDTE CHEMIE, Issue 39 2010Dr. Florent Samain Immer die richtige Antwort: An Polyethylenglycol-Polystyrol-Kügelchen konjugierte Oligodesoxyfluoroside (ODFs) wurden als Fluoreszenzsensoren für organische Dämpfe genutzt (siehe Bild). Die ODFs , DNA-artige Oligomere, in denen Fluorophor-, Spacer- und Quencher-Einheiten die DNA-Basen ersetzen , waren ausreichend elektronisch verschieden, um deutlich unterschiedlich auf chemisch verschiedene flüchtige organische Verbindungen zu reagieren. [source] Realistic simulations of combined DNA electrophoretic flow and EOF in nano-fluidic devicesELECTROPHORESIS, Issue 24 2008Duc Duong-Hong Abstract We present a three-dimensional dissipative particle dynamics model of DNA electrophoretic flow that captures both DNA stochastic motion and hydrodynamics without requiring expensive molecular dynamics calculations. This model enables us to efficiently and simultaneously simulate DNA electrophoretic flow and local EOF (generated by counterions near the DNA backbone), in mesoscale (,,m) fluidic devices. Our model is used to study the electrophoretic separation of long DNA chains under entropic trapping conditions [Han and Craighead, Science 2000, 288, 1026,1029]. Our simulation results are in good agreement with experimental data for realistic geometries (tapered walls) and reveal that wall tapering in entropic traps has a profound impact in the DNA trapping behavior, an effect which was largely ignored in previous modeling. [source] Missense mutations of human homeoboxes: A reviewHUMAN MUTATION, Issue 5 2001Angela V. D'Elia Abstract The homeodomain (encoded by the homeobox) is the DNA-binding domain of a large variety of transcriptional regulators involved in controlling cell fate decisions and development. Mutations of homeobox-containing genes cause several diseases in humans. A variety of missense mutations giving rise to human diseases have been described. These mutations are an excellent model to better understand homeodomain molecular functions. To this end, homeobox missense mutations giving rise to human diseases are reviewed. Seventy-four independent homeobox mutations have been observed in 17 different genes. In the same genes, 30 missense mutations outside the homeobox have been observed, indicating that the homeodomain is more easily affected by single amino acids changes than the rest of the protein. Most missense mutations have dominant effects. Several data indicate that dominance is mostly due to haploinsufficiency. Among proteins having the homeodomain as the only DNA-binding domain, three "hot spot" regions can be delineated: 1) at codon encoding for Arg5; 2) at codon encoding for Arg31; and 3) at codons encoding for amino acids of recognition helix. In the latter, mutations at codons encoding for Arg residues at positions 52 and 53 are prevalent. In the recognition helix, Arg residues at positions 52 and 53 establish contacts with phosphates in the DNA backbone. Missense mutations of amino acids that contribute to sequence discrimination (such as those at positions 50 and 54) are present only in a minority of cases. Similar data have been obtained when missense mutations of proteins possessing an additional DNA-binding domain have been analyzed. The only exception is observed in the POU1F1 (PIT1) homeodomain, in which Arg58 is a "hot spot" for mutations, but is not involved in DNA recognition. Hum Mutat 18:361,374, 2001. © 2001 Wiley-Liss, Inc. [source] A solid-state 23Na NMR study of monovalent cation binding to double-stranded DNA at low relative humidityMAGNETIC RESONANCE IN CHEMISTRY, Issue 4 2008Alan Wong Abstract We report a solid-state 23Na NMR study of monovalent cation (Li+, Na+, K+, Rb+, Cs+ and NH4+) binding to double-stranded calf thymus DNA (CT DNA) at low relative humidity, ca 0,10%. Results from 23Na31P rotational echo double resonance (REDOR) NMR experiments firmly establish that, at low relative humidity, monovalent cations are directly bound to the phosphate group of CT DNA and are partially dehydrated. On the basis of solid-state 23Na NMR titration experiments, we obtain quantitative thermodynamic parameters concerning the cation-binding affinity for the phosphate group of CT DNA. The free energy difference (,G° ) between M+ and Na+ ions is as follows: Li+ (,1.0 kcal mol,1), K+ (7.2 kcal mol,1), NH4+ (1.0 kcal mol,1), Rb+ (4.5 kcal mol,1) and Cs+ (1.5 kcal mol,1). These results suggest that, at low relative humidity, the binding affinity of monovalent cations for the phosphate group of CT DNA follows the order: Li+ > Na+ > NH4+ > Cs+ > Rb+ > K+. This sequence is drastically different from that observed for CT DNA in solution. This discrepancy is attributed to the different modes of cation binding in dry and wet states of DNA. In the wet state of DNA, cations are fully hydrated. Our results suggest that the free energy balance between direct cation,phosphate contact and dehydration interactions is important. The reported experimental results on relative ion-binding affinity for the DNA backbone may be used for testing theoretical treatment of cation-phosphate interactions in DNA. Copyright © 2008 John Wiley & Sons, Ltd. [source] DNA minor groove binders as potential antitumor and antimicrobial agentsMEDICINAL RESEARCH REVIEWS, Issue 4 2004Pier Giovanni Baraldi Abstract DNA minor groove binders constitute an important class of derivatives in anticancer therapy. Some of these compounds form noncovalent complexes with DNA (e.g., distamycin A, Hoechst 33258, and pentamidine) while others DNA-binding compounds (such as CC-1065) cause cleavages in the DNA backbone. In this article, we have reviewed the minor groove binders currently in preclinical evaluation in the last years. Diarylamidines such as DAPI, berenil, and pentamidine; bis-benzimidazoles such as Hoechst 33258; ecteinascidins, pyrrololo [2,1- c]-[1,4]-benzodiazepines (PBDs), CC-1065, and distamycins are the classes discussed in this review article. A special section has been dedicated to hybrid molecules resulted by the combination of two minor groove binders, especially for derivatives of naturally occurring antitumor agents, such as anthramycin or the alkylating unit of the antibiotic CC-1065, and distamycin frames. © 2004 Wiley Periodicals, Inc. Med Res Rev, 24, No. 4, 475,528, 2004 [source] Acridizinium Salts as a Novel Class of DNA-binding and Site-selective DNA-photodamaging Chromophores,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2001Heiko Ihmels ABSTRACT It was demonstrated that the interaction of the aminoacridizinium salts 2a,2d with DNA depends on the substitution pattern of the chromophore. Spectrophotometric and fluorometric titrations of the acridizinium salts 2a,2d with natural and synthetic polynucleotides reveal that the degree of interaction of the acridizinium salts 2a,2d with the nucleic acid differs significantly. The binding mode of the dyes with DNA was evaluated by circular dichroism and linear dichroism spectroscopy and compared with the parent system 2c. Whereas the 9-aminoacridizinium (2a) mainly intercalates into DNA, the salts 2b,c show a higher degree of association to the DNA backbone. The intercalated aminoacridizinium 2a caused few strand breaks upon UVA exposure, whereas the salts 2b,2d exhibit relatively efficient DNA-damaging properties. All acridizinium salts showed a sequence-selective strand cleavage for guanine-rich DNA regions. [source] Tunable DNA Cleavage by Intercalating PeptidoconjugatesCHEMBIOCHEM, Issue 5 2006Kerry P. Mahon Jr. Abstract The properties of a novel family of peptide-based DNA-cleavage agents are described. Examination of the DNA-cleavage activities of a systematic series of peptide,intercalator conjugates revealed trends that show a strong dependence on peptide sequence. Conjugates differing by a single residue displayed reactivities that varied over a wide range. The cleavage activity was modulated by the electrostatic or steric qualities of individual amino acids. Isomeric conjugates that differed in the position of the tether also exhibited different reactivities. The mechanism of DNA cleavage for these compounds was also probed and was determined to involve hydrogen-atom abstraction from the DNA backbone. Previous studies of these compounds indicated that amino acid peroxides were the active agents in the cleavage reaction; in this report, the chemistry underlying the reaction is characterized. The results reported provide insight into how peptide sequences can be manipulated to produce biomimetic compounds. [source] | |||||||||||||