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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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Structural, spectral and magnetic properties of Ni(II), Co(II) and Cd(II) compounds with imidazole derivatives and silanethiolate ligands
PublikacjaA series of new metal heteroleptic complexes have been obtained in simple reactions of 1-(3-aminopropyl)-imidazole (api) and 1,4-bis(imidazol-1-yl)-butane (bbi) ligands with metal silanethiolates or acetylacetonates. The obtained complexes are the coordination polymers [Ni{SSi(tBuO)3}2(μ-api)]n1, [Co{SSi(tBuO)3}2(μ-api)]n2, [Cd{SSi(tBuO)3}2(μ-api)·2CH3OH]n3, [Cd{SSi(tBuO)3}2(μ-bbi)·CHCl3]n4 and the dimer [Co{SSi(tBuO)3}2(μ-bbi)·3CH3OH]25....
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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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Novel tetrahedral cobalt(II) silanethiolates: structures and magnetism
PublikacjaThree heteroleptic complexes of Co(II) tri-tert-butoxysilanethiolates have been synthesized with piperidine [Co{SSi(OtBu)3}2(ppd)2] 1, piperazine [Co{SSi(OtBu)3}2(NH3)]2(μ-ppz)·2CH3CN 2, and N-ethylimidazole [Co{SSi(OtBu)3}2(etim)2] 3. The complexes have been characterized by a single-crystal X-ray, revealing their tetrahedral geometry on Co(II) coordinated by two nitrogen and two sulfur atoms. Complexes 1 and 3 are mononuclear,...
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Quantitative fluorescent determination of DNA – Ochratoxin a interactions supported by nitrogen-vacancy rich nanodiamonds
PublikacjaOchratoxin 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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Spectroscopic and cytotoxic characteristics of (p-cymene)Ru(II) complexes with bidentate coumarins and density functional theory comparison with selected Pd(II) complexes
PublikacjaThis paper presents the synthesis of two new (p-cymene)-ruthenium(II) complexes with the bidentate coumarin ligands. Both complexes were characterized by FTIR spectroscopy, 1H NMR, 13C NMR, MS, elemental analysis and DFT calculations. The X-ray structure of complex 3a was also solved. The cytotoxic properties of both complexes were examined on human leukemia NALM-6 and HL-60 cells and melanoma WM-115 cells. The complexes possess...
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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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Lower rim substituted tert-butylcalix[4]arenes. Part 10. New Pb(II)-selective electrodes based on tetrasubstituted calix[4]arenes amides
PublikacjaOpracowano elektrody selektywne na jony Pb(II) oparte na lipofilowych tetrapodstawionych amidowych pochodnych kaliks[4] arenu. Charakterystyki elektrod mają nachylenie nernstowskie w szerokim zakresie stężeń 10 (-1.3) do 10 (-7.2).
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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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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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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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Zn(II) and Cd(II) coordination polymers with tri-tert-butoxysilanethiol and bipyridines. Synthesis, crystal structure and spectroscopy
PublikacjaTrzy nowe silanotiolany cynku(II) I kadmu(II) [Zn{SSi(OtBu)3}2(μ-bpea) •CH3CN]n 1, [Cd{SSi(OtBu)3}2(μ -bpea) •2CHCl3]n 2 oraz [Cd{SSi(OtBu)3}2(μ -bpey)•C7H8]n 3 otrzymane z użyciem pochodnych bipirydylu [bpea = 1,2-bis(4-pyridyl)etan and bpey = 1,2-bis(4-pyridyl)etylen] zostały zsyntetyzowane i strutkualnie scharakteryzowane przy użyciu rentgenografii strukturalnej XRD. Ich budowa krystaliczna została dodatkowo potwierdzona przy...
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Lead(II)-selective ionophores for ion-selective electrodes: A review
PublikacjaIn potentiometry, high selectivity of the ion-selective membranes must be assured in order to reliably measure various analytes in clinical, industrial and environmental samples. Due to the toxic nature of lead(II) it is important to monitor Pb2+ distribution in natural waters. This may be achieved by implementation of ion-selective electrodes (ISEs) with high selectivity towards lead(II) and low detection limit. A great number...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-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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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublikacjaSingle-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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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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(4-Hydroxymethyl-1H-imidazole-κN3)bis(tri-tert-butoxysilanethiolato-κ2O,S)cadmium(II)
PublikacjaAtom kadmu w tytułowym kompleksie jest koordynowany przez pięć atomów: 2 atomy tlenu i dwa atomy siarki z chelatujących ligandów silanotiolanowych oraz atom azotu pochodnej imidazolu. Kompleks ten jest izostrukturalny z opisanym wcześniej analogicznym związkiem cynku.
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Tri-tert-butoxysilanethiolate complexes of manganese(II) with chelating heterocyclic bases - Structure of compounds with a MnN2O2S2 or MnN2OS2 kernel and MeOH within the coordination sphere
PublikacjaNieliczna, do tej pory, grupa tiolanowych kompleksów manganu (II) wzbogaciła się o układy wywodzące się z tri-tert-butoksysilanotiolu jako źródła liganda. Połączenia te można ustabilizować wprowadzając N-donorowe ligandy chelatujące takie jak 2,2'-bipirydyl (bipy), 1,10-fenantrolina (phen) czy też 2,9-dimetylo-1,10-fenantrolina (neo).Skład związków[(tBuO)3SiS]2Mn(bipy) (2), [(tBuO)3SiS]2Mn(phen)(MeOH)] (3), [(tBuO)3SiS]2Mn(phen)]...
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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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Ruthenium(II) and Iridium(III) Complexes as Tested Materials for New Anticancer Agents
PublikacjaThe 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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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...
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Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method
PublikacjaApplications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers –...
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres
PublikacjaTelomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified...
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Introducing the concept of Decisional DNA-Based web content mining
PublikacjaPrzedstawiono koncepcje zastosowania struktury reprezentacji wiedzy opartej na decyzyjnym DNA w procesie wyszukiwania informacji w internecie. Dokonano analizy eksperymentow tak wspomaganego wyszukiwania oraz sformulowano wnioski na temat przyszlych badan prowadzacych do dalszej integracji procesu wyszukiwania z doswiadczeniami zdobytymi w trakcie tego wyszukiwania.
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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublikacjaMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublikacjaThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Evolutionary algorithm and decisional DNA for multiple travelling salesman problem
PublikacjaIn the real world, it is common to face optimization problems that have two or more objectives that must be optimized at the same time, that are typically explained in different units, and are in conflict with one another. This paper presents a hybrid structure that combines set of experience knowledge structures (SOEKS) and evolutionary algorithms, NSGA-II (Non-dominated Sorting Genetic Algorithm II), to solve multiple optimization...
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cis-Dichloro(di-tert-butylphosphine-kappa-P)(triphenylphosphine-kappa-P)platinum(II) tetrahydrofuran hemisolvate
PublikacjaTytułowy związek, [cis-(t-Bu2PH)(Ph3P)PtCl2] został otrzymany w reakcji (Ph3P)2PtCl2 z 1,1,3,3-tetra-tert-butylo-2-trimetylosililotrifosfanem. Widmo 31P{1H} NMR wskazuje na tworzenie się tytułowego związku razem ze znacznymi ilościami Ph3P oraz 1,1,3,3-tetra-tert-butylotrifosfanu.
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Thermal decomposition of some aromatic azomonoethers. Part II. Non-isothermal study of three liquid crystals in dynamic air atmosphere
PublikacjaW ramach pracy zweryfikowano stabilność termiczną trzech barwników azowych o właściwościach ciekłokrystalicznych - potencjalnych prekursorów do otrzymywania warstw stosowanych w optyce nieliniowej. Zarejestrowano przebiegi TG, DTG, DTA oraz DSC jak również analizowano skład gazów powstających podczas rozpadu za pomocą przystawki FTIR. Przeprowadzono analizę kinetyki rozkładu, wyznaczając energię aktywacji procesu.
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Covalent DNA modification by products of myrosinase catalysed glucosinolate degradation in cell-free system
PublikacjaThe bioactive phytochemicals found in Brassica vegetables belonging to glucosinolates (GLS) and especially the products of their degradation isothiocyanates (ITC) and indoles are regarded as the most promising cancer chemopreventive compounds. These secondary metabolites constitute defence system repelling or preventing the development of agrophages attacking brassica plants. The antibiological properties of these compounds suggest...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublikacjaAn 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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Set of Experience and Decisional DNA: Toward Brains for Cyber-physical Systems and Industry of the Future
PublikacjaThe concept of Decisional DNA is decade old. This article introduces the initial idea of Set of Experience Knowledge Structure, its advancement into Decisional DNA, and its potential for real life applications in divers domains. The most current and future research steps into Industry 4.0 are also presented and discussed
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Prediction based on integration of Decisional DNA and a feature selection algorithm Relief-F
PublikacjaThe paper presents prediction model based on Decisional DNA and Set of experienced integrated with Relief_F algorithm for feature selection
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublikacjaMy 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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Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor
PublikacjaRolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line...
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Decisional DNA based intelligent knowledge model for flexible manufacturing system
PublikacjaModeling an effective mechanism for design and control strategies for the implementation of a flexible manufacturing system (FMS) has been a challenge. Consequently, to overcome this issue various techniques have applied in the past but most of these models are effective only for some specific situation or an element of FMS. In this study, the knowledge representation technique of Decisional DNA (DDNA) is applied to FMS to develop...
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Simple colorimetric copper(II) sensor – spectral characterization and possible applications
PublikacjaNew o-hydroxyazocompound L bearing pyrrole residue was obtained in the simple synthetic protocol. The structure of L was confirmed and analyzed by X-ray diffraction. It was found that new chemosensor can be successfully used as copper(II) selective spectrophotometric regent in solution and can be also applied for the preparation of sensing materials generating selective color signal upon interaction with copper(II). Selective colorimetric...
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Novel Diazocrowns with Pyrrole Residue as Lead(II) Colorimetric Probes
PublikacjaNovel 18- and 23-membered diazomacrocycles were obtained with satisfactory yields by diazocoupling of aromatic diamines with pyrrole in reactions carried under high dilution conditions. X-ray structure of macrocycle bearing five carbon atoms linkage was determined and described. Compounds were characterized as chromogenic heavy metal ions receptors. Selective color and spectral response for lead(II) was found in acetonitrile and...
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Filozofia społeczna Jana Pawła II (krótkie wprowadzenie)
PublikacjaW artykule przedstawiono zarys antropologii filozoficznej oraz główne tezy filozofii społecznej Jana Pawła II wyłożone w encyklikach: ''Redemptor hominis'', ''Laborem exercens'', ''Sollicitudo rei socialis'' i ''Centesimus annus''.
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Pyrrole bearing diazocrowns: Selective chromoionophores for lead(II) optical sensing
PublikacjaDiazocrowns of 18-, 21- and 23-membered rings with pyrrole residue as a part of macrocycle were for the first time used as chromoionophores in lead(II) selective optodes. Sensing properties of optodes depend on the type of macrocycle, namely its size and the type of linker: oligoether or hydrocarbon chain. The best results were obtained for optode bearing 18-membered crown with oligoether linker showing linear response range of...
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(-4,4'-Bipyridyl-2N:N')bis[bis(tri-tert-butoxysilanethiolato-2S,O)cadmium(II)] toluene disolvate
PublikacjaW strukturze tytułowego kompleksu znajdują się oddzielne cząsteczki, w których każdy atom kadmu jest koordynowany przez dwa atomy siarki, dwa atomy tlenu i jeden atom azotu. Geometria każdego z atomów kadmu jest pośrednia pomiędzy piramidą o podstawie kwadratu a bipiramidą trygonalną. Dwie jednostki tri-tert-butoksysilanotiolanu kadmu są połączone cząsteczką 4,4'-bipirydylu. Dodatkowo w strukturze kompleksu znajduje się cząsteczka...
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Aplikacja wspomagająca przetwarzanie sekwencji dna: moduł dopasowań
PublikacjaBiologia molekularna jest obecnie bardzo dynamicznie rozwijającą się dziedziną nauki. Wzrost mocy obliczeniowej komputerów pozwala na coraz szybszą i dokładniejszą analizę wielocząsteczkowych biologicznych polimerów. Poniższy artykuł przedstawia jeden z modułów programu AlignGator - modułowego systemu przeznaczonego do analizy DNA. Omawiany moduł pozwala na tworzenie, oraz edycję wielodopasowań. W początkowej części artykułu opisane...
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Macrocyclic derivatives of imidazole as chromoionophores for bismuth(III)/lead(II) pair
Publikacja18-membered diazomacrocycles with imidazole or 4-methylimidazole residue as a part of macrocycle were used as chromoionophores in bismuth(III) and lead(II) dual selective optodes for the first time. Cellulose triacetate membranes doped with macrocyclic chromoionophores are bismuth(III) and lead(II) selective with color change from orange/red to different shades of blue and violet, respectively. Results obtained for model and real...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated 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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Heteroleptic cadmium(II) complex, potential precursor for semiconducting CdS layers. Thermal stability and non-isothermal decomposition kinetics
PublikacjaW ramach pracy zweryfikowano stabilność termiczną [Cd{SSi(OBut)3}(S2CNEt2)]2 - potencjalnego prekursora do otrzymywania warstw półprzewodnikowych CdS. Równocześnie przeprowadzono analizę kinetyki rozkładu za pomocą różnych metod izokonwersyjnych zaproponowanych przez Flynn-Wall-Ozawa, Kissinger-Akahira-Sunose i Friedmanna w wyniku czego wyznaczono całkowity tryplet kinetyczny dla omawianego kompleksu.
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Badania spektroskopowe wybranych silanotiolanów kobaltu(II)
PublikacjaPodjęto próby otrzymania i scharakteryzowania tri-tert-butoksysilanotiolanowych kompleksów kobaltu(II), mogących spełnić rolę biomimetyków dla centrów katalitycznych wybranych metaloprotein. Przedstawiono wyniki analizy strukturalnej otrzymanych kompleksów uzyskanych z wykorzystaniem metod spektroskopii UV-vis i FT-IR zarówno dla roztworów jak i w ciele stałym. Skonfrontowano je z danymi uzyskanymi metodą analizy rentgenostrukturalnej...
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Decisional DNA with embedded Relief-F linear regression for knowledge and experience management
PublikacjaOmowiono zastowania Decyzyjnego DNA, regresji liniowej oraz funkcji RELIEF-F w procesach formalnego modelowania i wspomagania zarzadzania wiedza oraz zarzadzania doswiadczeniem.
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DNA repair is responsible for the presence of oxidatively damaged DNA lesions in urine
Publikacja -
Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties
PublikacjaPyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure...
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Mono- and polynuclear Co(II) silanethiolates with aliphatic diamines
PublikacjaFour Co(II) complexes, [Co{SSi(OtBu)3}2(dmpda)] 1, [Co{SSi(OtBu)3}2(bda)2]n2 [Co{SSi(OtBu)3}2(pda)2]n3 and [Co{SSi(OtBu)3}2(hda)2]n4 [dmpda = 3-(dimethylamino)-1-propylamine; bda = 1.4-butanediamine; pda = 1.5-pentanediamine; had = 1.6-hexanediamine] have been synthesized and characterized using X-ray diffraction. Complex 1 is mononuclear and contains Co(II) coordinated by dmpda molecule in chelating mode, whereas compounds 3 and...