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Wyniki wyszukiwania dla: DNA-PROTEIN INTERACTIONS
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Interplay of hydrogen bonding and aryl-perfluoroaryl interactions in construction of supramolecular aggregates
PublikacjaThe stacking between aryl and perfluoroaryl units is an important class of the aromatic – aromatic interactions that has attracted rapidly growing interest in recent years. Continuing interest of our group in this subject it had been prepared three new complexes of pentafluorobenzoic acid with benzyl alcohol, 4-methylbenzyl alcohol and 4-tert-butylbenzyl alcohol and in the next step investigated their self-assembly modes by...
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublikacjaMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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Examining Government-Citizen Interactions on Twitter using Visual and Sentiment Analysis
PublikacjaThe goal of this paper is to propose a methodology comprising a range of visualization techniques to analyze the interactions between government and citizens on the issues of public concern taking place on Twitter, mainly through the official government or ministry accounts. The methodology addresses: 1) the level of government activity in different countries and sectors; 2) the topics that are addressed through such activities;...
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Intermolecular Hydrogen Bonding Directed by Aryl–Perfluoroaryl π–π Stacking Interactions
PublikacjaThe crystal structures of five compounds capable of forming self-complementary hydrogen bonds but crystallizing as catemers or creating more complex crystal structures were compared with their complexes prepared by cocrystallization with perfluoroaryl compounds. The results of X-ray diffraction revealed that in all the cases the π–π stacking interactions caused reorganization of hydrogen bonds and induced creation of the expected...
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H2AX phosphorylation, its role in DNA damage response and cancer therapy
PublikacjaDouble-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may have severe consequences for cell survival, as they lead to chromosome aberrations, genomic instability, or cell death. Various physical, chemical, and biological factors are involved in DSB induction. Cells respond to DNA damage by activating the so-called DNA damage response (DDR), a complex molecular mechanism developed to detect...
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Analysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
PublikacjaAnalysis of hull, propeller and engine interactions in regular waves by a combination of experiment and simulation
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Analysis of odor interactions in ternary gas mixtures using electronic nose
PublikacjaIn recent years there has been a noticeable increase in interest in the use of electronic noses in analytical chemistry. These devices perform a holistic analysis of the gas mixtures composition, without the separation and identification of its individual components. For this reason e-noses are increasingly replacing the conventional olfactometers, due to the significantly shorter analysis time and possible automation. In the work...
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DNA AND CELL BIOLOGY
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublikacjaThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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Applying Decisional DNA to Internet of Things: The Concept and Initial Case Study
PublikacjaIn 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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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublikacjaAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Radiosensitization of DNA in presence of Pt(II)-based compounds
PublikacjaX-ray irradiation of plasmid DNA in presence of platinum (II)-based compounds was carried out in order to assess the radiosensitization capabilities of these drugs. In present investigations pBR322 plasmid DNA was used to monitor the effectiveness of chosen compounds in inducing strand breaks. Samples were incubated in the presence of potential radiosensitisers: platinum (II) bromide and cis-diamminedibromoplatinum (II). The results...
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Decisional DNA, reflexive ontologies, and security: developing decisional trust
PublikacjaOmowiono model osiagania zaufania decyzjnego opartego na decyzyjnym DNA, refleksyjnych ontologiach oraz na bezpieczenstwie technologicznym.
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Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex
PublikacjaZa pomocą metod chemi obliczeniowej badano właściwości molekularne kompleksu telomerowego białka TEBP z Oxytricha nova w kompleksie trójskkładnikowym z DNA o sekwencji telomerowej. Wyliczone wartości energii kompleksowania wskazują specyficznie na jedną z dróg tworzenia kompleksu, gdzie wpierw podjednostka alfa łaczy się z DNA a następnie podjednostka beta dołącza się do takiego dwuskładnikowego kompleksu. Policzone rozkłady molekularnego...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublikacjaThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Artificial DNA: PNA and XNA
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Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series
PublikacjaIntermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublikacjaThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation
PublikacjaHypoxia—a hallmark of solid tumors—makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublikacjaThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Isolation and structure of a covalent cross-link adduct between mitomycin C and DNA
PublikacjaA DNA cross-link adduct of the antitumor agent mitomycin C (MC) to DNA has been isolated and characterized; the results provide direct proof for bifunctional alkylation of DNA by MC. Exposure of MC to Micrococcus luteus DNA under reductive conditions and subsequent nuclease digestion yielded adducts formed between MC and deoxyguanosine residues. In addition to the two known monoadducts, a bisadduct was obtained. Reductive MC activation...
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Obrazy akustyczne dna morskiego w wybranych akwenach Bałtyku
PublikacjaMetody akustyczne obserwacji obszarów podwodnych mórz i oceanów stosowane są od początku XX wieku. Początkowo były to echosondy nawigacyjne najczęściej składające się z pojedynczych przetworników. Następnie zaczęto stosować sonary do wykrywania obiektów stanowiących przeszkody nawigacyjne pod woda, które miały głównie zastosowanie w marynarce wojennej. W drugiej połowie XX wieku rozpoczęto konstruowanie urządzeń akustycznych, których...
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Gaining knowledge through experience: developing decisional DNA applications in robotics
PublikacjaOmówiono 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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Modyfikacje polimeraz DNA jako rozwiązania problemów w reakcjach PCR
PublikacjaReakcja PCR już od wielu lat jest podstawowym narzędziem stosowanym w biotechnologii molekularnej. Nadal napotykamy jednak liczne problemy podczas jej przeprowadzania związane z trudnymi matrycami, obecnością inhibitorów itp. Optymalizacja reakcji PCR jest więc niezbędna w celu poprawy wyników. Jednym z rozwiązań tych problemów może być modyfikowanie polimeraz DNA. W powyższym artykule opisano problemy i rozwiązania zależne polimerazy...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions
PublikacjaExperiments were carried out to determine the dependence of the physical form of supercoiled DNA films on the initial temperature of the substrate. Such films are often used in irradiation experiments involving low energy particles, like electrons or photons. In order to obtain absolute values for cross sections for such experiments, the spatial distribution of the sample in the film has to be well estimated. These investigations...
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Development of novel optoelectronic sensory structures utilising colour centres in nanodiamonds and their interactions with analytes
PublikacjaThe goal of this dissertation was to develop and assess surface modifications of fluorescent nanodiamonds (NDs) for optical sensing. Three modification routes were tested, each aimed at a different application. Modification with poly-L-lysine (pLys) was verified for optical sensing of pH via an interrelationship between electrically negative (NV¯) and neutral (NV0) nitrogen-vacancy centres. Immobilisation of Ochratoxin A (OTA),...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublikacjaFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Interactions of dissolved dsDNA with intercalating drug by anodic voltammetry and spectroscopy. Influence of pH
PublikacjaOddziaływanie związku przeciwnowotworowego C-1305 z DNA było badane przy pomocy impulsowej voltametrii różnicowej oraz spektroskopii UV/Vis. Triazoloakrydon C-1305 oddziałuje z DNA na dwóch drogach: przez interkalacje pomiedzy pary zasad oraz przez wiązanie sie w małym rowku helisy. W fizjologicznym pH (7,4) stałe wiązania wynoszą: K1=3,36E+5 i K2=0,18E+5 [1/M] a wielkość miejsca wiązania: n1=2,5 i n2=4,0, odpowiednio dla pierwszego...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublikacjaSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublikacjaApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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DNA restriction analysis as a supportive tool in mechanistic studies carried out by 32P-postlabelling
PublikacjaNumerous 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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Radio- and photosensitization of DNA with compounds containing platinum and bromine atoms
Publikacja. Irradiations of plasmid DNA by both X-rays and UV light in the presence and absence of compounds containing platinum and bromine atoms were performed in order to asses the sensitization potential of these compounds. Plasmid DNA pBR322 was incubated with platinum (II) bromide, hydrogen hexabromoplatinate (IV), hydrogen hexahydroxyplatinate (IV) and sodium hexahydroxyplatinate (IV). Incubation was followed by X-ray or UV irradiations....
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Toward Intelligent Vehicle Intrusion Detection Using the Neural Knowledge DNA
PublikacjaIn this paper, we propose a novel intrusion detection approach using past driving experience and the neural knowledge DNA for in-vehicle information system security. The neural knowledge DNA is a novel knowledge representation method designed to support discovering, storing, reusing, improving, and sharing knowledge among machines and computing systems. We examine our approach for classifying malicious vehicle control commands...
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Smart innovation process enhancement using SOEKS and decisional DNA
PublikacjaProduct innovation always requires a foundation based on both knowledge and experience. The production and innovation process of products is very similar to the evolution process of humans. The genetic information of humans is stored in genes, chromosomes and DNA. Similarly, the information about the products can be stored in a system having virtual genes, chromosomes and decisional DNA (DDNA). The present paper proposes...
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The Protein Folding Problem
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A proposal for knowledge sharing in the e-Decisional community using Decisional DNA
PublikacjaZaproponowano model platformy wspomagającej wymianę wiedzy w społeczeństwie decyzyjnym opartym na decyzyjnym DNA.
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublikacjaThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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The interaction of antitumor 1-nitroacridines with DNA in cell-free systems
PublikacjaUzyskano nowe pochodne 1-nitro i 3-nitroakrydyny wykazujące zdolność do specyficznego cięcia DNA w miejscach bezzasadowych. Z użyciem oligonukleotydu z indukowanym miejscem bezzasadowym potwierdzono taką aktywność u obu otrzymanych pochodnych.
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Zastosowanie immobilizowanego białka MutS do wychwytywania fragmentów DNA zawierających niesparowane zasady
PublikacjaBiałko MutS wiąże DNA zawierające błędnie sparowane oraz niesparowane zasady w DNA. Podjęto szereg prób wykorzystania tego białka jako narzędzia do detekcji nieznanych mutacji lub zagęszczania frakcji DNA z niesparowaną zasadą. Dotychczas żadna z metod oparta na użyciu białka MutS nie została wdrożona powszechnie do praktyki laboratoryjnej. Głównym powodem takiego stanu rzeczy jest stosunkowo silne powinowactwo MutS do DNA w pełni...
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Justification of quasi-stationary approximation in models of gene expression of a self-regulating protein
PublikacjaWe analyse a model of Hes1 gene transcription and protein synthesis with a negative feedback loop. The effect of multiple binding sites in the Hes1 promoter as well as the dimer formation process are taken into account. We consider three, possibly different, time scales connected with: (i) the process of binding to/dissolving from a binding site, (ii) formation and dissociation of dimers, (iii) production and degradation of Hes1...
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Multi-mode vibronic interactions in the five lowest electronic states of the fluorobenzene radical cation
PublikacjaThe multi-mode vibronic interactions between the five lowest electronic states of the fluorobenzene radical cation are investigated theoretically, based on ab initio electronic structure data, and employing the linear vibronic coupling model. Low-energy conical intersections, and strong vibronic couplings are found to prevail within the set of X-A and B-C-D cationic states, while the interactions between these two sets of states...
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PROTEIN AND PEPTIDE LETTERS
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Preparation of DNA films for studies under vacuum conditions. The influence of cations in buffer solutions
PublikacjaBadania zostały przeprowadzone w celu określenia optymalnych warunków wymaganych do przygotowania jednolitych filmów superskręconego plazmidowego DNA do wykorzystania w doświadczeniach napromieniowania w warunkach wysokiej próżni. Badania pokazują, że znaczne szkody w DNA powstają w wyniku odpompowywania filmów DNA z roztworów zawierających jedynie czysta wodę.
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Interactions of selected mono- and disaccharides with precipitated calcium carbonate particles
PublikacjaCalcium carbonate is a widespread compound in nature and it can be produced by living organisms in the biomineralization process. Calcite, aragonite and vaterite are anhydrous polymorphic forms of calcium carbonate, wherein the calcite is the most thermodynamically stable. Vaterite is the metastable crystalline phase, which can be a precursor of calcite and aragonite, because it can easily transformed by dissolution and re crystallization...
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Structure and Interactions in Chitosan Composites
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Interactions of Quinones with Thioredoxin Reductase
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Beyond Antioxidant Activity: Redox Properties of Catechins May Affect Changes in the DNA Methylation Profile—The Example of SRXN1 Gene
PublikacjaThe role of catechins in the epigenetic regulation of gene expression has been widely studied; however, if and how this phenomenon relates to the redox properties of these polyphenols remains unknown. Our earlier study demonstrated that exposure of the human colon adenocarcinoma HT29 cell line to these antioxidants affects the expression of redox-related genes. In particular, treatment with (−)-epigallocatechin (EGC) downregulated...
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Interactions of PDA tetramers with the Au surfaces
Dane BadawczeThis dataset contains electrostatic difference potential (EDP) maps, density of states (DOS) spectra, and adsorption geometries of cyclic tetramers on the Au surface. The real polydopamine was modelled either as the cyclic tetramers in the oxidised (indolequinone, IQ) and reduced (dihydroxyindole, DHI) chemistries with all units being the same - either...
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Single-stranded DNA-binding proteins (SSBs) - sources and applicationsin molecular biology
PublikacjaBiałka 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...