Wyniki wyszukiwania - BazTech

1

Chromatograficzna analiza związków budujących kwasy nukleinowe

Studzińska S., Rola R., Łobodziński F., Krzemińska K.

Wiadomości Chemiczne

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2016

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[Z] 70, 9-10

633--656

EN

Understanding the characteristics, role and structure of nucleic acids allowed to answer questions about the disease processes. Today, nucleic acids and their constituents are tools, which are used by molecular biology in medicine and biotechnology. Antisense and gene therapy are intensively developing methods for possible treating or preventing disease. They use short fragments of DNA or RNA - oligonucleotides to silence the genes expression. They are not the only ones that allow analytical chemists to obtain information about the state of our body. Determination of modified nucleoside allows detection of cancer, while analysis of nucleotides allows the estimation of strengthening the immune system. There is a great need of sensitive, selective and precise methods of separation of nucleosides, nucleotides and oligonucleotides and their qualitative and quantitative analysis. Consequently liquid chromatography (LC) is the most commonly used for analysis of nucleic acid constituents. The most widely used modes of LC include Ion Exchange Chromatography (IEC) and Reversed Phase High Performance Liquid Chromatography (RP HPLC). Both techniques have their advantages and disadvantages in the analysis of nucleosides, nucleotides and oligonucleotides. In the case of IEC it is necessary to use high concentrations of the salt in the mobile phase or concentration gradients, which considerably limits the possibility of using MS detection. RP HPLC can be coupled with MS detection but only when volatile salts are mobile phase components. On the other hand there is a significant problem is the lack of sufficient selectivity for the most polar nucleosides and nucleotides. RP HPLC MS is still most often used in the determination of nucleosides and nucleotides, due to its high sensitivity and a comprehensive qualitative analysis. Another system used for the HPLC analysis of oligonucleotides is Ion Pair Reversed Phase High Performance Liquid Chromatography (IP RP HPLC). These compounds can not be analyzed by RP HPLC due to their high polarity. The advantage of IP RP HPLC is selectivity, achieved by a suitable choice of mobile phase composition and the possibility of using MS. A disadvantage of IP RP HPLC in the analysis of oligonucleotides is however lower sensitivity compared to RP HPLC. During the last few years Hydrophilic Interaction Liquid Chromatography (HILIC) was applied for the separation of mixtures of nucleosides, nucleotides, oligonucleotides extracted from a biological or food samples. The presented results demonstrate the usefulness of this method, however, the resolving power is limited due to the asymmetric peak shape. On the other hand proper selection of the mobile and stationary phase can lead to a high selectivity in the analysis of the most polar nucleosides, nucleotides and oligonucleotides, which can not be separated by RP HPLC.

2

Techniki sekwencjonowania jako nowej generacji analityka w omice

Szymańska S., Studzińska S., Pareek Ch. S., Buszewski B.

Analityka : nauka i praktyka

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2012

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nr 3

27--36

PL

Sekwencjonowanie pozwala na ustalenie kolejności nukleotydów i wymaga dalszych analiz dających możliwości wyciągania inspirujących wniosków pozwalających na odkrycia mogące mieć kluczowe znaczenie podczas walki z chorobami cywilizacyjnymi ludzkości.

3

Wykorzystanie spektrometrii mas do analizy modyfikacji nukleotydów i adduktów DNA

Hanus J., Jelonek K., Pietrowska M.

Wiadomości Chemiczne

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2011

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[Z] 65, 3-4

191-205

EN

Chemically modified nucleotides, which are not normally present in genetic material, are called DN A adducts. This type of DN A modifications (damage) is directly related to processes of mutagenesis and carcinogenesis. Elevated levels of DN A adducts present in genetic material reflect exposure of humans to carcinogenic factors and are markers of increased risk of cancer [1]. For this reason different methods useful for quantitative and qualitative analyses of DN A adducts are used in the field of cancer prevention and research (Tab. 1). Enzymatically-catalyzed methylation of cytosine, observed mostly in so called CpG islands, is a frequent endogenous modification of genetic material. Such a DN A methylation is a key factor involved in regulation of gene expression, and methylation status of oncogenes and tumor supressor genes is an important biomarker of carcinogenesis. As such, analytical methods for assessment of DN A methylation are of great importance for molecular diagnostics of cancer. During the last decade significant progress has been made in methods available for quantitative, qualitative and structural analyses of biological molecules. Among intensively developed tools for bioanalyses are methods of mass spectrometry. Spectrometers that are based on two methods of ionization, namely electrospray ionization (ESI ) [30] and matrix-assisted laser desorption-ionization (MALDI ) [48], are particularly suitable for analyses of biological macromolecules: proteins and nucleic acids. Currently available mass spectrometers, together with microscale methods for sample preparation and separation, significantly increased sensitivity and accessible mass range of analyses. New generation of “user-friendly” instruments is developed to bring the techniques directly into the workplaces of biological and clinical investigators. This review demonstrates representative examples of mass spectrometry techniques used for qualitative analyses of nucleotide modifications and adducts present in genetic material of humans. In this field several methods base on spectrometers with electrospray ionization. Generated ions are separated according to their mass-to-charge ratio in an analyzer by electric fields; among different ion analyzers frequently used in this methods are single or triple quadrupole and ion traps (Fig. 1). Among other methods available for assessment of DN A adducts is so called Accelerator Mass Spectrometry (Fig. 2) [41]. The most frequently applied method for the assessment of DN A methylation is based on methylation-specific PCR reaction. Products of such PCR reactions are analyzed using MALDI mass spectrometry [54] (Fig. 3). In summary, new powerful methods of mass spectrometry that made available qualitative analyses of damage and modifications of human genetic material found their important place in modern biological and medical laboratories.

4

Chemiczna synteza oligorybonukleotydów

Milecki J.

Wiadomości Chemiczne

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2002

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[Z] 56, 3-4

255-277

EN

Basic issues and problems of chemical synthesis of oligoribonucleotides are presented. The paper describes three methods for construction of oligonucleotide chains: (1) a triester method which involves activation of nucleoside phosphodiesters with different azole sulfonates, and currently widely used methods employing PIII synthetic intermediates: (2) a phosphoramidite method which makes use of activation of nucleoside phosphoramidites by weakly acidic azoles or azole salts, (3) an H-phosphonate method, which uses nucleoside H-phosphonates activated by acid chlorides, both PIII intermediates are applied mainly in solid-support synthetic methodology. Problems of choosing appropriate protecting group for the synthesis are discussed. The article presents properties of basic types of protecting groups for lactam, exo-amino (base-labile protection), and hydroxyl groups (acid-labile for 5' protection, acid- or specific reagent-labile for 2' protection). The problem of 2'OH protection is described in detail. In this respect acid-labile groups and alkylsilyl groups are compared and their advantages and disadvantages are discussed. More detailed discussion is devoted to the phenomenon of the silyl group migration during the synthesis of monomeric units for oligonucleotide chain assembly. Basing on the NMR study of the isomerisation reaction it was possible to determine limits of safety of the reaction conditions.

5

Interaction Centers of Purine and Pyrimidine Nucleotides in Their Reactions with Cu(II), Ni(II), Co(II), Cd(II) and Hg(II) Ions

Gąsowska A., Bregier-Jarzębowska R., Łomozik L.

Polish Journal of Chemistry

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2002

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Vol. 76 / nr 6

773-783

EN

It has been established that in ATP complexes with Cu(II), Co(II) and Cd(II) ions, the metallation centres are the oxygen atoms of the phosphate group and the nitrogen atom N(7) from the purine ring. The spectral data suggest some involvement of N(1) atom in these interactions. In the ATP complexes with Ni(II) the main centres of coordination were found to be N(7) and N(1), while the contribution of the oxygen atoms from the phosphate group is of secondary importance. In the ATP complexes with Hg(II) ions, above pH 7, the metallation involves only the oxygen atoms from the phosphate group, while the N(1) and N(7) atoms are outside the inner sphere of coordination. In the complexes of CTP with the metal ions studied the interaction centres are the oxygen atoms from the phosphate group and N(3) from the pyrimidine ring. However, in the case of complexes with Ni(II), the main centre of interaction is N(3), while the involvement of the oxygen atoms from the phosphate group is of minor importance.

6

Zastosowanie porfirynowych faz stacjonarnych w HPLC

Biesaga M.

Analityka : nauka i praktyka

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2002

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nr 4

13--19

PL

Jednym z podstawowych problemów chemii analitycznej jest selektywność metody oznaczania danego związku, zwłaszcza gdy występuje on w niskim stężeniu w próbce o skomplikowanej matrycy.

7

Thin layer chromatography of nucleotides on aminopropyl bonded silica plates

Szumiło H., Flieger J.

Chemia Analityczna

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2000

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Vol. 45, No. 3

363-370

EN

The conditions of mono-di and triphosphate nucleotide separation on thin layers of silica gel with chemically bonded aminopropyl groups (HPTLC-NH2) were elaborated on. The separation was achieved by analysing the effect of pH, and concentration of various inorganic salts in water and water-methanol mobile phases.The results were analysed using the stoichiometric displacement model developed for ion-exchange chromatography. It was shown that the model may be useful for optimising elution conditions of polianions on amine plates.

PL

Opracowano warunki rozdzielania nukleotydów mono- di- i trifosforanowych na cienkich warstwach żelu krzemionkowego z chemicznie związanymi fazami aminopropylowymi (HPTLC-NHa). Analizując wpływ pH, stężenia i rodzaju soli nieorganicznych w wodnych i wodno-metanolowych fazach ruchomych uzyskano rozdział badanych związków. Do analizy uzyskanych wyników zastosowano model steąhiometrycznej wymiany opracowany dla chromatografii jonowymiennej. Wykazano, że model ten może być przydatny do optymalizowania warunków elucji polianionów na płytkach ze związaną fazą aminową.

8

Complexes of cadmium(II) and mercury(II) with polyamines, nucleosides and nucleotides

Łomozik L., Brieger-Jarzębowska R.

Polish Journal of Chemistry

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1999

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vol. 73 nr 6

927-940

EN

Computer analysis of potentiometric titration data was applied for determination of stability constants of Cd(II) and Hg(II) complexes in binary systems with polyamines (PA), nucleosides (Nuc) and nucleotides (NMP). For the systems of Hg(II) and PA an untypical increase in the complex stability with increasing ring size was observed and interpreted as the mercury preference to formation of linear complexes. Results of the potentiometric and 13CNMR studies for the complexes of both metal indicate the involvement of all donor nitrogen atoms of di- and triamines in the coordination, leading to formation of N2 and N3 type chromophores, respectively. Monodentate complexes of Hg(II) with Cyd are formed already at very low pH (complexes with Cd from pH of about 4). In the systems with AMP apart from nitrogen donor atoms, also the phosphate groups are involved in coordination. In the solid complexes of Cd(II) and Hg(II) with PA all donor atoms from the polyamines were found to be involved in the coordination and the presence of nitrate ions was established both in the inner and in the outer coordination spheres.

9

Cobalt(II), nickel(II) and copper(II) complexes with adenosine 5'-monophosphate and cytidine 5'-monophosphate in aqueous solutions and in solids

Gąsowska A., Łomozik L.

Polish Journal of Chemistry

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1999

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vol. 73 nr 3

465-474

EN

Determination of stability constants and calculation of distribution of complexes formed by Co(II), Ni(II) and Cu(II) with adenosine monophosphate (AMP) and cytidine monophosphate (CMP) were performed by using computer -aided analysis of potentiometric titration data. On the basis of the comparison of the protonation constants of free ligands and MHL-type complexes the proton localization in the coordination compounds was established. The coordination mode in complexes in solution as well as in solids was determined from the results of spectral as well as equilibrium studies. Formation of macrochelate complexes and the occurrence of coordination dichotomy of the N(1)N(7) type as well as N(1)N(7)/O (phosphate group) was evidenced. Contrary to the similar complexes with Cu(II) and Co(II), the phosphate group of the nucleotide becomes essentially involved in the interactions with Ni(II) ions only at high pH values. The modes of coordination in aqueous solution and solid complexes are compared.