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    Wyświetlanie 1-9 z 9
    Tytuł:
    Molecular dynamic simulations of large RNA molecules: the yeast tRNA^{Phe}
    Autorzy:
    Pliszka, B.
    Ołodziej, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954518.pdf
    Data publikacji:
    1999
    Wydawca:
    Politechnika Gdańska
    Tematy:
    tRNA Phe
    molecular dynamics
    modified bases
    nucleic acids
    electrostatic interaction
    Opis:
    Molecular dynamics trajectories (700 ps) of the solvated and neutralized 75-residue yeast tRNA Phe were generated using the AMBER 5.0 molecular dynamics software package. The cut-off scheme was used to treat electrostatic interactions; consequently, all long-range interactions beyond 12 angstroms were neglected. The equilibration procedure and conditions during simulations led to a dynamically stable model of the tRNA molecule. During the simulations all base-base interactions (which determine the secondary and the tertiary structure of the molecule) were well preserved. Consequently, the global shape of the molecule was preserved well and the RMS deviation calculated between the starting x-ray structure and the final structure after 700 ps of simulations was 3.25 angstroms. The biggest deviation is observed in the region of the anticodon hairpin loop; this high mobility is associated with the presence of a very unusual Y-base and a binding site of a magnesium ion in this region.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1999, 3, 3; 333-342
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Modyfikowane oligodeoksyrybonukleotydy zawierające w wiązaniu internukleotydowym w pozycji mostkowej atom azotu
    Modified oligodeoxyribonucleotides containing nitrogen at a bridging position of an internucleotide bond
    Autorzy:
    Radzikowska, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/172442.pdf
    Data publikacji:
    2013
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    analogi kwasów nukleinowych
    modyfikacje wiązania internukleotydowego
    oligodeoksyrybonukleozydo-(P3’→N5’)amidofosforany
    oligodeoksyrybonukleozydo-(N3’→P5’)amido(tio)fosforany
    strategia antysensowa
    telomeraza
    reakcja Athertona-Todda
    nucleic acids analogues internucleotide linkage modifications
    oligodeoxyribonucleoside-(P3’→N5’)phosphoramidates
    oligodeoxyribonucleoside-
    (N3’→P5’)(thio)phosphoramidates antisense strategy
    telomerase
    Atherton-Todd reaction
    Opis:
    Synthetic oligonucleotides (ONs) constitute an important class of compounds which exhibit biological activity. As potential drugs ONs are employed in the antisense strategy [1]. The antisense therapeutic agent acts on the pathogenic mRNA causing inactivation of the target. Ideal antisense agent should be resistant to exo and/or endonucleases, have a suitable pharmacological and pharmacokinetic profile and high affinity for the target. To improve some properties of antisense oligonucleotides plethora of chemical modifications introduced within both sugar unit and internucleotides linkage were investigated. Among numerous ONs modified in internucleotide phosphodiester bond, one of the most interesting are oligonucleotide phosphoramidates (NP-oligos) in which one of the bridging oxygens is replaced by nitrogen atom (at 3’ or 5’ position). Hence, two classes of compounds are formed: oligonucleotide-(N5’→P3’)phosphoramidates and oligonucleotide(N3’→P5’)-phosphoramidates. These compounds, similar to native DNA and RNA, possess an achiral phosphorous atom and all internucleotides bonds are negatively charged. Additionally, NP-oligo shows good resistance to nucleolytic degradation and can bind to the target DNA or RNA with high affinity [12]. In literature several synthetic strategies concerning both (N5’→P3’) and (N3’→P5’) NP-oligos have been described. Some of them allowed to obtain only corresponding dimers. In the light of recent discoveries the most promising candidates for therapeutic and diagnostic applications are oligonucleotide-(N3’→P5’)thiophosphoramidates. Gryaznov et al. have found that such compounds can act as potent and selective telomerase inhibitors [29]. Human telomerase (TA) is a reverse transcriptase ribonucleoprotein that synthesizes de novo d-(TTAGGG)n repeats at chromosomal DNA ends. Whereas activity of this enzyme is observed in ~85% of all human tumors, most of normal somatic cells either lack TA activity or express it only at low levels. For these reasons TA constitute an attractive and nearly universal anticancer target for rational drug development.
    Źródło:
    Wiadomości Chemiczne; 2013, 67, 11-12; 1003-1025
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Oligonukleotydy DNA jako warstwy receptorowe sensorów elektrochemicznych
    DNA oligonucleotides as receptor layers of electrochemical sensors
    Autorzy:
    Górski, Ł.
    Ziółkowski, R.
    Bala, A.
    Jarczewska, M.
    Malinowska, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/171556.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    biosensor
    metale ciężkie
    kwasy nukleinowe
    samoorganizujące się monowarstwy
    woltamperometria
    znaczniki redoks
    biosensors
    heavy metals
    nucleic acids
    self-assembled monolayers
    voltammetry
    redox indicators
    Opis:
    The need for elaboration of analytical devices of small dimensions and the accessibility of novel nanomaterials caused the increase in the number of publications referring to the development of biosensors. DNA-based biosensors are of special interest and they were primarily used for the determination of a specific sequence which is crucial in the detection of cancer, genetic mutations, pathogens, as well as analysis of modified food. Interestingly, they could be also applied for the detection of other analytes including heavy metal ions, especially in connection with electrochemical techniques. It should be noted that the design of DNA biosensor concerns not only the development of transducer, but also careful preparation of sensing layer and the choice of the method of analytical signal generation. Selectivity is one of the essential parameter of the biosensor that determines its utility, particularly in real samples of complex matrices. In case of DNA sensors dedicated for the detection of complementary sequence, high selectivity is provided by the hybridization process. A pronounced specificity of sensing layer-analyte interaction can be also achieved with the use of functional nucleic acids - aptamers, which change their conformation upon binding an analyte. Herein, DNA-modified electrodes were firstly used for the detection of uranyl ions, as they exhibit high affinity towards phosphate moieties of nuclec acids. It was shown that UO2 2+ interacts with sensing layer independently from the chosen oligonucleotide sequence. Moreover, the influence of Pb2+ was reduced by elimination of adenine, which strongly interacts with lead ions. Another oligonucleotide-based sensor was developed for detection of mercury ions. The results indicate that Hg2+ concentration can be determined only with the use of sequence containing 100% thymine residues. Oligonucleotide-based sensor with receptor layer containing aptamers was elaborated for the detection of Pb2+ ions. In the presence of lead cations, an aptamer probe forms a G-quadruplex structure, a proposed biosensor could be characterized with selectivity towards Pb2+ The performance of DNA-based sensors for UO2 2+, Hg2+ and Pb2+ ions was optimized and addressed the choice of the manner of analytical signal generation, the influence of electrode modification with blocking agent, sensitivity dependence on the oligonucleotide sequence and the possibility of regeneration of sensing layer. Finally, the utility of proposed DNA sensors was tested by analysis in real samples.
    Źródło:
    Wiadomości Chemiczne; 2015, 69, 5-6; 325-336
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Functional investigation of MiR92b-3p for diagnosis and miRNA-based cure in chemically induced liver injury in fish: a project description
    Autorzy:
    Brzuzan, P.
    Woźny, M.
    Florczyk, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/363176.pdf
    Data publikacji:
    2016
    Wydawca:
    Uniwersytet Warmińsko-Mazurski w Olsztynie
    Tematy:
    hepatotoxicity mechanism
    liver regeneration
    Locked Nucleic Acids
    microcystin
    RNA interference
    toxicogenomics
    whitefish
    Opis:
    The continued lack of knowledge concerning the molecular background of adverse effects caused by microcystin-LR (MC-LR) is surprising. This toxin requires additional attention, not only for its ability to cause acute poisoning, but also for its ability to initiate cancer in acute doses, and potentially, to promote cancer via chronic exposure to low concentrations in drinking water. Our recent studies on whitefish (Coregonus lavaretus) revealed that long-term exposure to MC-LR resulted in severe liver injury, followed by regeneration of the liver and its unexpected resilience to further toxin uptake. These effects were accompanied by perturbations of hepatic microRNAs (miRNAs) that have target genes involved in cytoskeletal remodeling, cell metabolism, cell cycle regulation, and apoptosis. Among the most pronounced individual alterations, the reduction of MiR92b-3p expression was the most remarkable, and we suggest roles for the miRNA in the aberrant processes of liver cells. This project addresses potential involvement of MiR92b-3p in the as yet unknown regulatory network of MC-induced hepatotoxicity in fish. After a suite of biochemical, physiological, anatomical, and transcriptomic analyses in vitro and in vivo, we will show how MiR92b-3p works in a damaged liver and which processes it targets. Finally, the research will confirm if and how MiR92b-3p can be targeted therapeutically. We expect it to be shown effective enough to pave a way for its use as a tool for treatment of liver damage in fish. What is more, the RNA-based silencing technique that will be used should yield exciting data for our understanding of the system-level biology of vertebrates.
    Źródło:
    Environmental Biotechnology; 2016, 12, 2; 40-42
    1734-4964
    Pojawia się w:
    Environmental Biotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Overview of the RNA G-quadruplex structures
    Autorzy:
    Malgowska, Magdalena
    Czajczynska, Karolina
    Gudanis, Dorota
    Tworak, Aleksander
    Gdaniec, Zofia
    Powiązania:
    https://bibliotekanauki.pl/articles/1038712.pdf
    Data publikacji:
    2016
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    G-tetrad
    U-tetrad
    RNA G-quadruplex
    NMR
    crystallography
    nucleic acids structure
    Opis:
    G-quadruplexes are non-canonical secondary structures which may be formed by guanine rich sequences, both in vitro and in living cells. The number of biological functions assigned to these structural motifs has grown rapidly since the discovery of their involvement in the telomere maintenance. Knowledge of the G-quadruplexes' three-dimensional structures plays an important role in understanding of their conformational diversity, physiological functions, and in the design of novel drugs targeting the G-quadruplexes. In the last decades, structural studies have been mainly focused on the DNA G-quadruplexes. Their RNA counterparts gained an increased interest along with a still-emerging recognition of the central role of RNA in multiple cellular processes. In this review we focus on structural properties of the RNA G-quadruplexes, based on high-resolution structures available in the RCSB PDB data base and on structural models. In addition, we point out the current challenges in this field of research.
    Źródło:
    Acta Biochimica Polonica; 2016, 63, 4; 609-621
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Receptory rozpoznające wirusowe kwasy nukleinowe w odpowiedzi przeciwwirusowej ryb
    Receptors recognizing viral nucleic acids during immune response of fish
    Autorzy:
    Rakus, Krzysztof
    Chadzińska, Magdalena
    Powiązania:
    https://bibliotekanauki.pl/articles/1034001.pdf
    Data publikacji:
    2017
    Wydawca:
    Polskie Towarzystwo Przyrodników im. Kopernika
    Tematy:
    interferons
    nucleic acids
    innate immunity
    pattern recognition receptors
    RLR
    TLR
    viral infection
    interferony
    kwasy nukleinowe
    odporność wrodzona
    receptory rozpoznające wzorce molekularne
    zakażenia wirusowe
    Opis:
    Kluczowym etapem nieswoistej reakcji odpornościowej organizmu na zakażenie wirusowe jest szybkie wykrycie obecności wirusów w komórce i aktywacja syntezy interferonów (IFN) typu I. Wirusowe kwasy nukleinowe (DNA i RNA) są głównymi strukturami pochodzenia wirusowego rozpoznawanymi przez receptory wrodzonego układu odpornościowego. Wśród receptorów rozpoznających te struktury bardzo istotną rolę odgrywają receptory Toll-podobne (TLR) i RIG-I-podobne (RLR). Wiele z tych receptorów opisanych u ssaków występuje także u ryb, chociaż z drugiej strony ryby posiadają także receptory, które nie zostały zidentyfikowane u ssaków. Ryby, które są pierwszymi kręgowcami z pełni rozwiniętym układem odpornościowym wrodzonym i nabytym, stanowią doskonały model do badania ewolucji mechanizmów odporności u kręgowców. W pracy przedstawiono receptory rozpoznające wirusowe kwasy nukleinowe opisane u ryb oraz główne białka adaptorowe biorące udział w przekazywaniu sygnału wewnątrzkomórkowego w celu aktywacji syntezy IFN typu I i cytokin prozapalnych.
    Recognition of the non-self signature of invading viruses is a crucial step for the initiation of the anti-viral innate immune defense mechanisms including interferon (IFN) type I production. Viral nucleic acids occur the main virus-derived structures to be recognized by the receptors of the innate immune system. There are a number of receptors that recognize viral nucleic acids among which the most important are Toll-like receptors (TLR) and RIG-I-like receptors (RLR). Many of those receptors described in mammals have been also found in fish, although fish possess some specific receptors which have not been characterized in mammals. Teleost fish represent a relevant model for the study of the core immune mechanisms activated by viral infections. In this work we review the current knowledge about the fish receptors for viral nucleic acids and the main adaptor proteins involved in signaling pathways for the activation IFN type I and pro-inflammatory cytokine synthesis.
    Źródło:
    Kosmos; 2017, 66, 4; 609-621
    0023-4249
    Pojawia się w:
    Kosmos
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Evolution and application of new genetic techniques - from nucleic acids via microarrays to CRISPR
    Autorzy:
    Kocki, J.
    Bogucka-Kocka, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/283868.pdf
    Data publikacji:
    2018
    Wydawca:
    Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Polskie Towarzystwo Biominerałów
    Tematy:
    nucleic acids
    microarrays
    CRISPR
    Źródło:
    Engineering of Biomaterials; 2018, 21, 148; 80
    1429-7248
    Pojawia się w:
    Engineering of Biomaterials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Sesquicentennial of the discovery of DNA. Forgotten Professor Richard Altmann from Iława
    Autorzy:
    Zubek, Aniela
    Belter, Agnieszka
    Naskręt-Barciszewska, Mirosława Z.
    Stefan, Jurga
    Markiewicz, Wojciech T.
    Barciszewski, Jan
    Powiązania:
    https://bibliotekanauki.pl/articles/704410.pdf
    Data publikacji:
    2019
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Richard Altmann
    DNA
    nucleic acids
    mitochondria
    Opis:
    This year we are celebrating 150 anniversary of the discovery of DNA by Friedrich Miescher. His finding initiated a series of discoveries that allowed to depicts life's most famous molecule with novel features with considerable biological interest. In this article we recall the biggest mile stones of 150-year history of DNA and present the context and meaning of several key observations that have brought us closer to understanding DNA. 150 years ago, people had no idea that DNA existed, and they certainly hadn’t heard of DNA structure and sequencing. We now know that DNA is a dynamic, tortuous coil, constantly shuffling and unwinding. Today DNA is all around us, in a physical sense and in a cultural sense. It is really part of our culture. We will discuss also the little known facts, often overlooked in similar discussions. We will focus particularly on Professor Richard Altmann's from Iława, whose contribution to knowledge about nucleic acids is significant, although not well recognized so far.
    Źródło:
    Nauka; 2019, 1
    1231-8515
    Pojawia się w:
    Nauka
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Chemia bioortogonalna – użyteczne narzędzie badania procesów wewnątrzkomórkowych
    Bioortogonal chemistry - a useful tool for studying intercellular processes
    Autorzy:
    Latos, Krystian
    Powiązania:
    https://bibliotekanauki.pl/articles/2200602.pdf
    Data publikacji:
    2022
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    chemia bioortogonalna
    bioortogonalna ligacja
    kwasy nukleinowe
    białka
    sacharydy
    bioorthogonal chemistry
    bioorthogonal ligation
    nucleic acids
    proteins
    saccharides
    Opis:
    Bioorthogonal chemistry is a rapidly developing field of science operating on the border of chemistry and biology. Its initial goal was to study metabolism and imaging using fluorescently labelled compounds. Due to recent advances, bioorthogonal chemistry can also be used to engineer therapeutic bioconjugates. By using a combination of bioconjugation and advanced omics techniques, it is possible to study and modify complex interactions inside living cells. In the relatively short time since its introduction, bioorthogonal chemistry has found many applications. In nucleic acid research, it is used for labelling, e.g. with biotin, to facilitate detection, immobilization, and purification. Additionally, thanks to the use of fluorescent nucleoside analogues, it can be used to study the interaction and dynamics of nucleic acids. For the study of proteins, bioorthogonal chemistry is an invaluable tool for studying conformation, as well as intramolecular and intermolecular interactions. Using techniques such as PET and FRET it is possible to take a closer look at the structure of proteins, which has a significant impact on their functionality. By using biarsenical dyes, interactions between proteins are tracked. This is used in the study of protein aggregation in diseases such as Alzheimer's, Huntington's, and prion diseases. Thanks to this, it becomes possible to understand the mechanism and pathology of these diseases. In biosensing, the elements of bioorthogonal chemistry have been used in a variety of tests and imaging methods. In the end, methods for testing glycan are presented. The advantage of bioorthogonal methods is that they allow labelling on the whole cell or lysate. This application in glycoproteomics is extremely important due to the fact that changes in glycosylation occur during disease states.
    Źródło:
    Wiadomości Chemiczne; 2022, 76, 1-2; 79-95
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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