Search results for: single-stranded dna binding domain
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublicationBiałka wiążące się do jednoniciowego DNA (SSB) odgrywają ważną rolę w replikacji, rekombinacji i naprawie DNA u bakterii, archea i eukariota. Ostatnio wzrosło zainteresowanie białkami SSB jako przydatnymi narzędziami w metodach badawczych biologii molekularnej, analitycznych i diagnostycznych. Większość znanych prokariotycznych białek SSB zbudowanych jest z czterech podjednostek (homotetramer) z jedną domeną wiążąca (OB) jednoniciowe...
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublicationDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Identification and properties of the Deinococcus grandis andDeinococcus proteolyticus single-stranded DNA binding proteins (SSB)
PublicationW celu poznania właściwości biochemicznych białek SSB pochodzących z Deinococcus grandis (DgrSSB) i Deinococcus proteolyticus (DprSSB) sklonowano zaamplifikowane w reakcji PCR geny ssb w systemie ekspresyjnym Escherichia coli. Geny składają się z 891(DgrSSB) i 876 (DprSSB) nukleotydów kodujących odpowiednio 296 i 291 reszt aminokwasowych o teoretycznie wyznaczonej masie cząsteczkowej dla białek, równej 32,29 i 31,33 kDa. Sekwencja...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublicationOkreślono molekularne właściwości białek SSB-podobnych z Thermus thermophi-lus i T. aquaticus. Zbadano aktywność białek oraz termostabilność. Ponadto, dowiedziono homodimeryczność obu białek i ustalono minimalną sekwencję wiążącą ssDNA.
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublicationSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublicationZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea psychrophila, Flavobacterium psychrophilum, Psychrobacter arcticus, Psychrobacter cryohalolentis, Psychromonas ingrahamii, Psychroflexus torquis, and Photobacterium profundum
PublicationBackground: Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in Bacteria, Archaea and Eukarya. In recent years, there has been an increasing interest in SSBs, since they find numerous applications in diverse molecular biology and analytical methods. Results: We report the characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria Desulfotalea...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Benzonaza(R): możliwości praktycznych zastosowań.
PublicationBenzonaza znajduje zastosowanie w efektywnym obniżaniu lepkości i usuwaniu kwasów nukleinowych z roztworów białkowych. Zbadano w praktyce jej możliwości aplikacyjne w oczyszczaniu białek rekombinantowych wiążących jednoniciowe DNA (ang. SSB - single stranded DNA binding protein).
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Białka prokariotycznego systemu MMR: rola oraz interakcje
PublicationUszkodzenia komórkowego DNA w postaci błędnie sparowanych lub niesparowanych zasad azotowych są wynikiem niewłaściwie zachodzących procesów metabolizmu DNA, takich jak replikacja, rekombinacja oraz naprawa DNA. Utrwalenie tego rodzaju zmian prowadzi do powstania mutacji. System MMR (ang. DNA mismatch repair) usuwa te uszkodzenia przyczyniając się do zwiększenia wierności replikacji DNA oraz utrzymania stabilności genomu komórki....
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Conservation and diversity of MutS proteins
PublicationThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Novel anticancer strategy aimed at targeting shelterin complexes by the induction of structural changes in telomeric DNA: hitting two birds with one stone.
PublicationThe ends of chromosomes in mammals are composed of telomeric DNA containing TTAGGG repeats, which bind specific proteins called shelterins. This telomeric DNA together with shelterins form a cap that protects the ends of chromosomes from being recognized as sites of DNA damage and from chromosomal fusions. Many very successful antitumor drugs used in the treatment of cancer patients bind to DNA, some of them with a prominent sequence...
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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublicationMembers of a novel class of anticancer compounds, exhibiting high antitumor activity, i.e. the unsymmetrical bisacridines (UAs), consist of two heteroaromatic ring systems. One of the ring systems is an imidazoacridinone moiety, with the skeleton identical to the structural base of Symadex. The second one is a 1-nitroacridine moiety, hence it may be regarded as Nitracrine’s structural basis. These monoacridine units are connected...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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MutS3: a MutS homologue of unknown biological function
PublicationThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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Taq DNA polymerase fused with DNA binding protein with increased resistance to inhibitors from clinical samples
PublicationNowadays PCR method is commonly used in molecular diagnostic. However, in many cases PCR is limited, by the presence of inhibitory substances in biological, soil or food samples Efficiency and fidelity of amplification is strongly connected with DNA polymerase and reaction conditions. To meet the requirements of modern diagnostic methods it is essential to seeking for new DNA polymerases with better properties useful in these field....
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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
PublicationWe present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...
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Synthesis, structure, DNA binding and anticancer activity of mixed ligand ruthenium(II) complex
PublicationIn order to obtain a potential chemotherapeutic which is not affected on the normal BALB/3T3 cell line, a new arene ruthenium(II) complex {[RuCl(L1)(η6-p-cymene)]PF6}2 · H2O has been synthesized by a direct reaction of precursor, [{(η6-p-cymene)Ru(μ-Cl)}2Cl2], with N,N-chelating ligand (L1 - 2,2′-bis(4,5-dimethylimidazole). The compound has been fully characterized by elemental analysis, X-ray diffraction, IR, UV–Vis and 1H, 13C...
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Electroanalytical and spectroscopic procedures for examination of interactions between double stranded DNA and intercalating drugs
PublicationPrzedstawiono metodę elektrochemicznego opisu oddziaływań dsDNA ze związkiem biologicznie czynnym w warunkach, w których zarówno badany związek jak i cząsteczka DNA są w roztworze elektrolitu. Opracowano warunki pomiaru, gdzie ani związek, ani DNA nie adsorbuje na elektrodzie. Wykazano, podobnie jak podczas badania innymi metodami, że oddziaływania są dwojakiego rodzaju: elektrostatyczne i poporzez interkalację.
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Syntheses and DNA binding of new cationic porphyrin–tetrapeptide conjugates
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Optimising DNA binding to carbon nanotubes by non-covalent methods
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublicationPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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Induced circularly polarized luminescence for revealing DNA binding with fluorescent dyes
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Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Selective Cytostatic and Cytotoxic Anticancer Effects of Bisfunctional Agents: A Strategy for the Design of DNA Binding Agents
PublicationVarious agents have been synthesized and proved useful for the National Cancer Institute's anticancer testing as potential new drugs, but most agents suffer side effects from their limited selectivity against cancer cells over healthy ones. Therefore, this paper attempts to describe drugs in terms of the level of tumor cell selectivity which they possess to define the features of mols. that are essential for useful cytotoxicity....
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Quantification of Radiation-Induced Single-Strand Breaks in Plasmid DNA using a TUNEL/ELISA-Based Assay
PublicationWprowadzono nową metodę służącą do oznaczania in vitro pojedynczych pęknięć nici DNA powstałych pod wpływem naświetlań. Porównano wyniki otrzymane z nowej metody z modelem teoretycznym. Porównano wyniki z szeroko używaną metodą elektroforezy żelowej. Pokazano, że poziom pojedynczych pęknięć powstających w niciach DNA pod wpływem promieniowania VUV jest wyższy niż zakładany na podstawie wyników otrzymywanych metodami standardowymi.
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Antitumor Activity of Triazine Mimic Antibiotics for DNA-binding Implications (Impressive Activity in Vitro Against a Variety of Tumor Types in the NCI-60 Screen): NSC 710607 To Fight HCT-116 Human Colon Carcinoma Cell Lines in Vivo Using the Hollow Fiber Assay and Xenograft Mouse Models
PublicationPurpose Successful clinical applications of DNA-directed selective cytotoxic agents disrupt the vital replication/transcription processes and ultimately lead to cancer cell death. This study aimed to examine the growth screen of two lead triazine compounds in a number of cell lines and xenografts and to develop anticancer agents with noncovalent binding affinity bringing fewer side effects. Methods The NCI initial hollow...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Jaroslaw Spychala dr
PeopleOprócz bardzo dobrego wykształcenia osoba posiada również wieloletnie doświadczenie zawodowe, które jest poświadczeniem tego, że potrafi wykorzystać swoją wiedzę teoretyczną w praktycznych działaniach. Doświadczenie zawodowe jest bardzo bogate i rozbudowane. Ze względu na nabyte całkiem nowe umiejętności zwiększa się atrakcyjność doświadczonego pracownika. Są to między innymi kreatywne myślenie, zorientowanie na cel, odporność...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublicationBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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Data on solutions of Hes1 system
Open Research DataHes1 protein (hairy and enhancer of split 1) belongs to the helix-loop-helix (bHLH) family of transcription proteins, i.e. DNA-binding proteins in the promoter region or in another region where regulation of transcription processes occurs. The database collects data on solutions of the Hes1 systems with multiple binding sites and the dimer formation...
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Sequences of large subunit ribosomal RNA gene, partial sequence encoding D1/D2 domain of psychrotolerant pigment-producing yeast-like fungi
Open Research DataDNA fragments encoding D1/D2 domain of large subunit ribosomal RNA of psychrotolerant pigment-producing yeast-like fungi named Red, Pink and Black were PCR amplified using NL1 5’ GCATATCAATAAGCGGAGGAAAAG 3’ and NL4 5’ GGTCCGTGTTTCAAGACGG 3’ primers and sequenced by Sanger method using the same primers.
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Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.
PublicationThe crystal structure of the esterase EstA from the cold-adapted bacteriumPseudoalteromonas sp. 643A was determined in a covalently inhibited form at aresolution of 1.35 A˚. The enzyme has a typical SGNH hydrolase structureconsisting of a single domain containing a five-stranded beta-sheet, with threehelices at the convex side and two helices at the concave side of the sheet, and isornamented with a couple of very short helices...
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublicationOchratoxin A (OTA) is a hazardous contaminant of a large variety of plant and animal originated food. Herein, we report an interaction of OTA with calf thymus DNA (ct DNA) on the nanodiamond surface. We employed multispectroscopic techniques to elucidate the binding mechanism of OTA with ct DNA. The fluorescence and UV–Vis spectroscopy results show that OTA binds to ds ct DNA and forms complexes. We obtained the binding constants...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand-dsDNA complexes of various types of binding : an electrochemical study.
PublicationSeveral medicinally important compounds that bind to dsDNA strands via intercalation (C-1311, C-1305, EtBr), major groove binding (Hoechst 33258) and covalent binding (cis-Pt) were examined. The obtained results suggest that both the transfer of conformation B to C and the denaturation process, for the ligand-dsDNA complexes, except for covalently bound cis-Pt, took place at higher temperatures compared to the unbound helix. Furthermore,...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublicationThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models
PublicationOxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Experience Based Clinical Decision Support Systems: An Overview and Case Studies
PublicationThis chapter briefly overviews the evolution of the application of the Decisional DNA and the Set of Experience Knowledge Structure (SOEKS) in the medical domain and in particular in the specific case of the experience-based decision support systems. Decisional DNA, as a knowledge representation structure, offers great possibilities on gathering explicit knowledge of formal decision events as well as a tool for decision making...
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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublicationDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublicationNumerous antitumor and carcinogenic compounds are able to modify DNA by forming covalent bonds with its constituents, while some anticarcinogenic compounds are known to prevent such a modification. All these processes are of vital biological import_ance, though deeper inside into factors influencing formation of DNA adducts is difficult due to the low level of their occurrence. 32P-Postlabelling approach ensures very sensitive...
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Ruthenium(II) and Iridium(III) Complexes as Tested Materials for New Anticancer Agents
PublicationThe oncological use of cisplatin is hindered by its severe side eects and a very important resistance problem. To overcome these problems, scientists have attempted to design new generation transition-metal anticancer complexes. In this study, we present new complexes, ruthenium(II) [(6-p-cymene)RuCl(py2CO)]PF6 (1), iridium(III) [(5-Cp)IrCl(py2CO)]PF6 (2), and NH4[IrCl4(py2CO)]H2O (3), based on di-2-pyridylketone (py2CO). The prepared...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Experience based knowledge representation for Internet of Things and Cyber Physical Systems with case studies
PublicationCyber Physical Systems and Internet of Things have grown significant attention from industry and academia during the past decade. The main reason behind this interest is the capabilities of such technologies to revolutionize human life since they appear as seamlessly integrating classical networks, networked objects and people to create more efficient environments. However, enhancing these technologies with intelligent skills becomes...
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A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies
PublicationTriazoloacridinone C-1305, a potent antitumor agent recommended for Phase I clinical trials, exhibits high activity towards a wide range of experimental colon carcinomas, in many cases associated with complete tumor regression. C-1305 is a well-established dsDNA intercalator, yet no information on its mode of binding into DNA is available to date. Herein, we present the NMR-driven and MD-refined reconstruction of the 3D structures...
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Molecular basis for the DNA damage induction and anticancer activity of asymmetrically substituted anthrapyridazone PDZ-7
Publicationnthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another...
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Genotoxic properties of glucosinolates and isothiocyanates present in Brassica vegetables
PublicationThe bioactive phytochemicals found in Brassica vegetables, in this number glucosinolates (GLS), as well as products of their degradation such as isothiocyanates (ITC) and indoles, are regarded as the most promising chemopreventive compounds. These secondary metabolites display stron antibiological activity and constitute defence system preventing the development of agrophages attacking Brassica plants. Such properties suggest...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Stable nanoconjugates of transferrin with alloyed quaternary nanocrystals Ag–In–Zn–S as a biological entity for tumor recognition
PublicationOne way to limit the negative effects of anti-tumor drugs on healthy cells is targeted therapy employing functionalized drug carriers. Here we present a biocompatible and stable nanoconjugate of transferrin anchored to Ag-In-Zn-S quantum dots modified with 11-mercaptoundecanoic acid (Tf-QD) as a drug carrier versus typical anticancer drug, doxorubicin. Detailed investigations of Tf-QD nanoconjugates without and with doxorubicin...
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The Usefulness of Cyclic Diamidines with Different Core-substituents as Antitumor Agents
PublicationA series of related polycationic compds. has been screened for potential antitumor activity by the NCI's in vitro testing (one dose primary anticancer assay and the NCI-60 full panel screening). The GI50 values of triazines 3 and 4 are on av. 1.9 μM and 2.4 μM, resp. Furan 8 deserves mention too (1.9 μM). The biol. test results showed that carbazole 10 possessed cytotoxic activity in the nanomolar range, much better than...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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The Decisional DNA-Based Smart Bike for Internet of Things
PublicationIn this paper, we introduce a novel application of the Internet of Things, the Decisional DNAbased Smart Bike. The Decisional DNA is a domain-independent, flexible and standard knowledge representation structure; it allows its domains to acquire and store experiential knowledge and formal decision events in an explicit way. By using Decisional DNA, the sensor-equipped bicycle is able to learn its user’s weight, riding habits, etc....
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Sound signals generated during lapping of technical ceramics using electroplated tools with diamond grains
Open Research DataData contains the recordings of sound generated during single-sided lapping with the use of electroplated diamond tools. This relationship was examined with the use of spectral analysis of the sound signal in the frequency domain with a focus on the Ra parameter of the surface roughness. The estimated sound coefficient increased as the surface roughness...
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Applying Decisional DNA to Internet of Things: The Concept and Initial Case Study
PublicationIn this article, we present a novel approach utilizing Decisional DNA to help the Internet of Things capture decisional events and reuse them for decision making in future operations. The Decisional DNA is a domain-independent, standard and flexible knowledge representation structure that allows its domains to acquire, store, and share experiential knowledge and formal decision events in an explicit way. We apply this approach...
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Magnetism from fundamentals to spintronics 22/23
e-Learning Courses1. Basic magnetic quantities2. Magnetism of atoms and molecules, atoms in external magnetic fields3. Solid state magnetism, types of magnetic materials (dia-, para-, and ferromagnetism)4. Ferromagnetism and domain structures5. Magnetism of small particles, single domain particles (StonerWohlfarth model), thin films6. Experimental techniques of magnetic properties and magnetisation state determination. Domain structurevisualisation...
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A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublicationThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
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Gaining knowledge through experience: developing decisional DNA applications in robotics
PublicationOmówiono nowatorskie podejscie do zastosowania wiedzy opartej na doświadczeniu i budowie decyzyjnego DNA w obszarach związanych z robotyką.In this article, we explore an approach that integrates Decisional DNA, a domain-independent, flexible, and standard knowledge representation structure, with robots in order to test the usability and suitability of this novel knowledge representation structure. Core issues in using this Decisional...
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Experience-Oriented Knowledge Management for Internet of Things
PublicationIn this paper, we propose a novel approach for knowledge management in Internet of Things. By utilizing Decisional DNA and deep learning technologies, our approach enables Internet of Things of experiential knowledge discovery, representation, reuse, and sharing among each other. Rather than using traditional machine learning and knowledge discovery methods, this approach focuses on capturing domain’s decisional events via Decisional...
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Copper(I) halide cluster-based coordination polymers modulated by chiral ditopic dithiodianthranilide ligands: synthesis, crystal structure and photoluminescence
PublicationReaction of copper(I) halides with chiral dithiodianthranilidesmdtaandbdtaafforded polymeric complexeswhere polynuclear CuX clusters were linked together by ditopic bridging ligands into 1D chains or 2D layerstructures. In the case of racemic ligands double stranded chain polymers were formed where the Cu4X4(X = I or Br) cores are connected by enantiomeric pairs of the ditopic ligands. In contrast, a homochiralmdtaligand created...
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Loop-mediated isothermal amplification (LAMP) as a diagnostic tool in detection of infectious diseases
PublicationLoop-mediated isothermal amplification (LAMP) is a gene amplification method which amplifies DNA with high specificity and efficiency under isothermal conditions. Because of its rapidity and simplicity, it is a valuable diagnostic tool in the early detection and identification of infectious diseases. LAMP method is based on the use of a set of four to six specially designed primers spanning six to eight distinct sequences on the...
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Changes in gene methylation patterns in neonatal murine hearts: Implications for the regenerative potential
PublicationBackground The neonatal murine heart is able to regenerate after severe injury; this capacity however, quickly diminishes and it is lost within the first week of life. DNA methylation is an epigenetic mechanism which plays a crucial role in development and gene expression regulation. Under investigation here are the changes in DNA methylation and gene expression patterns which accompany the loss of regenerative potential. Results The...
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Cloning, expression in Komagataella phaffii, and biochemical characterization of recombinant sequence variants of Pseudomonas sp. S9 GDSL-esterase
PublicationTwo recombinant Komagataella phaffii (formerly Pichia pastoris) yeast strains for production of two sequential variants of EstS9 esterase from psychrotolerant bacterium Pseudomonas sp. S9, i.e. αEstS9N (a two-domain enzyme consisting of a catalytic domain and an autotransporter domain) and αEstS9Δ (a single-domain esterase) were constructed. However, only one of recombinant K. phaffii strains, namely Komagataella phaffii X-33/pPICZαestS9Δ,...
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EASY ACCESS TOOL FOR SMALL INTERFERING RNA (siRNA) DATA
PublicationFor many decades it was an accepted dogma of molecular genetics that the expression of genes is a “one-way-road” leading only in one direction from DNA to RNA to proteins. Recent discoveries in modern molecular genetics have challenged this dogma showing that specific RNA molecules play a central role in controlling the activity of genes by changing the structure of DNA sequences, targeting other RNAs for degradation or blocking...
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Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains
PublicationAims We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. Materials and Methods Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver, heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. Results and conclusion A number of differentially methylated regions distinguishing between...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Chromatographic analyses of Lavandula angustifolia and Rosmarinus officinalis extracts and their biological effects in mammalian cells and cell-free systems
PublicationKnowledge of biological properties of natural compounds allows to understand their therapeutic value, efficacy and security. We investigated: composition of Lavandula angustifolia (LA) and Rosmarinus officinalis (RO) extracts, their antioxidant capacity, cytotoxicity and genotoxicity, their DNA-protective potential against DNA damage induced in hamster V79 cells by several genotoxins or in plasmid DNA by Fe2+ ions and activity...
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...