Search results for "Ribonucleotide"
showing 10 items of 104 documents
RNase H1 and H2 are differentially regulated to eliminate RNA-DNA hybrids
2019
SUMMARYRNA-DNA hybrids are tightly regulated to ensure genome integrity. The RNase H enzymes, RNase H1 and H2, contribute to chromosomal stability through the removal of RNA-DNA hybrids. Loss of RNase H2 function is implicated in human diseases of the nervous system and cancer. To better understand RNA-DNA hybrid dynamics, we have focused on elucidating the regulation of the RNase H enzymes themselves. Using yeast as a model system, we demonstrate that RNase H1 and H2 are controlled in different manners. RNase H2 is regulated in a strict cell cycle dependent manner, both in terms of its R-loop removal, and ribonucleotide excision repair functions. RNase H1, however, can function independent…
Kinetic properties of a nucleoside phosphotransferase of chick embryo
1981
1. A nonspecific nucleoside phosphotransferase (nucleotide : 3'-deoxynucleotide 5'-phosphotransferase, EC 2.7.1.77), purified from chick embryos, catalyzes the transfer of phosphate ester from a nucleotide donor to a nucleoside acceptor. 2. The enzyme exhibits sigmoidal kinetics with respect to nucleoside monophosphate donors, but with respect to nucleoside di- or triphosphate donors and nucleoside acceptors hyperbolic kinetics were obtained. 3. The nucleoside phosphotransferase of chick embryo is unstable to heat and is protected from inactivation by a large number of nucleosides. 4. Nucleoside di- and triphosphates lower both the concentration of nucleoside monophosphates required for hal…
Interaction of polyribosomal components and polyribonucleotides with microtubule proteins
1982
To demonstrate the affinity of RNA-containing polyribosomal components (isolated from L5178y cells) to microtubules, microtubule protein was attached to an insoluble matrix. In contrast to ribosomes, poly(A) (+) mRNA and poly(A)-RNP were found to bind to the matrix. Using synthetic polyribonucleotides, no significant differences in the binding properties of single- and double stranded polymers of different base composition to microtubule protein were observed. However, binding is dependent on the size of the polymer; a minimal chain length of 12 nucleotide units is required.
tRNA stabilization by modified nucleotides.
2010
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation …
2013
Selective alkylation of RNA nucleotides is an important field of RNA biochemistry, e.g. in applications of fluorescent labeling or in structural probing experiments, yet detailed structure-function studies of labeling agents are rare. Here, bromomethylcoumarins as reactive compounds for fluorescent labeling of RNA are developed as an attractive scaffold on which electronic properties can be modulated by varying the substituents. Six different 4-bromomethyl-coumarins of various substitution patterns were tested for nucleotide specificity of RNA alkylation using tRNA from Escherichia coli as substrate. Using semi-quantitative LC-MS/MS analysis, reactions at mildly acidic and slightly alkaline…
Validation strategies for antibodies targeting modified ribonucleotides
2020
Chemical modifications are found on almost all RNAs and affect their coding and noncoding functions. The identification of m6A on mRNA and its important role in gene regulation stimulated the field to investigate whether additional modifications are present on mRNAs. Indeed, modifications including m1A, m5C, m7G, 2′-OMe, and Ψ were detected. However, since their abundances are low and tools used for their corroboration are often not well characterized, their physiological relevance remains largely elusive. Antibodies targeting modified nucleotides are often used but have limitations such as low affinity or specificity. Moreover, they are not always well characterized and due to the low abun…
Nucleoside phosphotransferase of chick embryo
1979
This paper describes a purification procedure and some properties of a nonspecific nucleoside phosphotransferase of chick embryo, an activity which catalyzes the transfer of chick embryo, an activity which catalyzes the transfer of the phosphate ester from a deoxyribonucleotide or a pyrimidine ribonucleotide to a deoxyribonucleoside acceptor. The enzyme is very unstable to heat, dilution and dialysis and it is almost entirely inactivated by DEAE-cellulose chromatography or gel filtration. A marked enhancement in its stability is caused by numerous nucleotides. In these experiments at least 920-fold purification was obtained by using dTTP (50 microM) as nucleotide protector. The enzyme, puri…
Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis.
2007
To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 ′. Similar energetic profiles featuring two minima corresponding to the anti and syn Gχ regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of ∼4 kcal/mol were obtained for the anti → syn transition. Str…
Synthesis and antiproliferative activity of 2'-O-allyl-1-beta-D-arabynofuranosyl-uracil, -cytosine and -adenine
1997
Abstract With the aim to design potential inhibitors of ribonucleotide reductase (RR), 2′-O-allyl-β-D-arabinofuranosyl-uracil ( 4 ), -cytosine ( 7 ) and -adenosine ( 10 ) were prepared and evaluated for their cytostatic activity against Molt4/C8, CEM and L1210 cell lines. Although our preliminary data do not allow to assess if RR is the intracellular target, the results point to differences in the (anti)metabolic behavior of these compounds. This study also offers a general synthesis of 2′-O-allyl-β-D-arabinofuranosyl nucleosides for potential applications in the preparation of 2′-O-allyl-β-D-oligoarabino nucleotides.