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Wyniki wyszukiwania dla: SSDNA
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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.
PublikacjaSeveral 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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Spectrofotometric titration of dsDNA by nitroacridines - chemometrics approach
PublikacjaW pracy zastosowano podejście chemometryczne do analizy zestawów widm absorpcyjnych w obszarze widzialnym, uzyskanych podczas miareczkowania spektrofotometrycznego nitroakrydyn o potencjalnej aktywności przeciwnowotworowej przy pomocy DNA.Zastosowanie analizy głównych składowych (PCA) wykazało, że podczas miareczkowania 1-nitroakrydyn powstają dwa typy kompleksów, podczas gdy w przypadku 3-nitroakrydyn tylko jeden. Iteracyjna procedura...
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublikacjaPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus - expression and purification
PublikacjaBiałka SSB są niezbędne do życia każdemu organizmowi. W tej pracy prezentujemy wyniki otrzymania i oczyszczania białek SSB Thermus thermophilus i T. aquaticus. Dotąd były znane białka SSB jedynie o budowie homotetrameru lub heterotrimeru. Białka SSB Thermus thermophilus i T. aquaticus stanowią nową klasę białek SSB - białek homodimerycznych. Ponadto dowiedziono, iż białka te są użyteczne w reakcji PCR.
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Novel thermostable ssDNA-binding proteins from Thermus thermophilus and T. aquaticus-expression and purification
PublikacjaSklonowano w system ekspresyjny pET-30LIC Escherichia coli gen kodujący białka SSB-podobne Thermus thermophilus i T. aquaticus. Oczyszczono do homogenności białka SSB-podobne, a uzyskane preparaty umożliwiają wykonanie badań strukturalnych w/w białek.
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublikacjaRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Electrooxidation of dissolved dsDNA backed by in situ UV-Vis spectroscopy
PublikacjaPrzeprowadzono badania elektrochemicznego utleniania dsDNA stosując metody cyklowoltametryczne na elektrodzie weglowej, platynowej, platynowej w formie siatki oraz z siatki platynowej osadzonej na węglu. Otrzymane wyniki analizy spektroelektrochemicznej wykazały, że wraz ze wzrostem potencjału i piku prądowego absorpcja roztworu dsDNA wzrasta w sposób zależny od typu elektrody. Jednak położenie maksimum absorpcji nie zmieniało...
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CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
PublikacjaOverexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression...
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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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RecA Proteins from Deinococcus geothermalis and Deinococcus murrayi - Cloning, Purification and Biochemical Characterisation
PublikacjaEscherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS response and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in gamma-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA...
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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
PublikacjaBackground 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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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
PublikacjaTriazoloacridinone 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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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublikacjaSingle-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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Multisine impedimetric probing of biocatalytic reactions for label-free detection of DEFB1 gene: How to verify that your dog is not human?
PublikacjaAlbert is a dog (Canis familiaris), but he does not realize this. Albert loves human food (and beer), watching movies on the internet, sleeping in bed, and more. But he should not do all these things. To convince him that, we have desinged a test procedure. The DEFB1 gene is unique to human species. Detecting its presence from saliva and in short periods may offer an advantage in the field of forensic medicine, and influence Albert’s...
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Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
PublikacjaOkreślono 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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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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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublikacjaWe 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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Recombinant !ermostable AP Exonuclease from Thermoanaerobacter tengcongensis: Cloning, Expression, Purification, Properties and PCR Application
PublikacjaApurinic/apyrimidinic (AP) sites in DNA are considered to be highly mutagenic and must be corrected to preserve genetic integrity, especially at high temperatures. !e gene encoding a homologue of AP exonuclease was cloned from the thermophilic anaerobic bacterium Thermoanaerobacter tengcongensis and transformed into Escherichia coli. The protein product showed high identity (80%) to human Ape1 nuclease, whereas to E. coli exonuclease...
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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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The interactions of monomeric acridines and unsymmetrical bisacridines (UAs) with DNA duplexes: an insight provided by NMR and MD studies
PublikacjaMembers 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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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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Electroanalytical and spectroscopic procedures for examination of interactions between double stranded DNA and intercalating drugs
PublikacjaPrzedstawiono 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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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
PublikacjaMatrix 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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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublikacjaWe 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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Design, synthesis and high antitumor potential of new unsymmetrical bisacridine derivatives towards human solid tumors, specifically pancreatic cancers and their unique ability to stabilize DNA G-quadruplexes
PublikacjaNew promising unsymmetrical bisacridine derivatives (UAs), have been developed. Three groupsincluding 36 compounds were synthesized by the condensation of 4-nitro or 4-methylacridinone, imi-dazoacridinone and triazoloacridinone derivatives with 1-nitroacridine compounds linked with anaminoalkyl chain. Cytotoxicity screening revealed the high potency of these compounds against severaltumor cell lines. Particularly, imidazoacridinone-1-nitroacridine...
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Synthesis of green benzamide-decorated UiO-66-NH2 for biomedical applications
PublikacjaMetal-organic frameworks (MOFs) biocompatible systems can host enzymes/bacteria/viruses. Herein we synthesized a series of fatty acid amide hydrolase (FAAH)-decorated UiO-66-NH2 based on Citrus tangerine leaf extract for drug delivery and biosensor applications. Five chemically manipulated FAAH-like benzamides were localized on the UiO-66-NH2 surface with physical interactions. Comprehensive cellular and molecular analyses were...
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Identification and properties of the Deinococcus grandis andDeinococcus proteolyticus single-stranded DNA binding proteins (SSB)
PublikacjaW 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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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublikacjaBACKGROUND: 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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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
PublikacjaBackground: 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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c-Myc Protein Level Affected by Unsymmetrical Bisacridines Influences Apoptosis and Senescence Induced in HCT116 Colorectal and H460 Lung Cancer Cells
PublikacjaUnsymmetrical bisacridines (UAs) are highly active antitumor compounds. They contain in their structure the drugs previously synthesized in our Department: C-1311 and C-1748. UAs exhibit different properties than their monomer components. They do not intercalate to dsDNA but stabilize the G-quadruplex structures, particularly those of the MYC and KRAS genes. Since MYC and KRAS are often mutated and constitutively expressed in cancer...
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JAKOŚ(Ć) ? : Dwa lata Regionalnej Biblioteki Nanotechnologii Politechniki Gdańskiej
PublikacjaArtykuł, na przykładzie Regionalnej Biblioteki Nanotechnologii, opisuje w jaki sposób biblioteka jako organizacja radzi sobie w obliczu ciągłych zmian. Przedstawienie RBN oraz umieszczenie jej w otoczeniu zewnętrznym (bliższym i dalszym) i wewnętrznym pokazuje, że dzisiejsze biblioteki muszą wciąż dostosowywać się do zmian. Artykuł stawia również pytanie - jak społeczeństwo wiedzy (jako nowy typ społeczeństwa) ma tą wiedzą zarządzać?...