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At least 307 records · Page 17Linked to original sources
PubMed2000

Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm.

The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalyzing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus. Much less is known about the XRN-like proteins of multicellular eukaryotes; however, differences in their activities could explain differences in mRNA degradation between multicellular and unicellular eukaryotes. One such difference is the lack in plants and animals of mRNA decay intermediates like those generated in yeast when Xrn1p is blocked by poly(G) tracts that are inserted within mRNAs. We investigated the XRN-family in Arabidopsis thaliana and found it to have several novel features. First, the Arabidopsis genome contains three XRN-like genes (AtXRNs) that are structurally similar to Xrn2p/Rat1p, a characteristic unique to plants. Furthermore, our experimental results and sequence database searches indicate that Xrn1p orthologs may be absent from higher plants. Second, the lack of poly(G) mRNA decay intermediates in plants cannot be explained by the activity of the AtXRNs, because they are blocked by poly(G) tracts. Finally, complementation of yeast mutants and localization studies indicate that two of the AtXRNs likely function in the nucleus, whereas the third acts in the cytoplasm. Thus, the XRN-family in plants is more complex than in other eukaryotes, and, if an XRN-like enzyme plays a role in mRNA decay in plants, the likely participant is a cytoplasmic Xrn2p/Rat1p ortholog, rather than an Xrn1p ortholog.

Amino Acid Sequence↗
PubMed2003

Microcontact printing of novel co-polymers in combination with proteins for cell-biological applications.

Microcontact printing (microcP) is a cost effective and simple method to create chemically micropatterned surfaces for cell biological applications. We have combined the technique with the spontaneous molecular assembly of a polycationic PEG-grafted copolymer, poly-L-lysine-g-poly(ethylene glycol) (PLL-g-PEG). PLL-g-PEG with omega-functionalized PEG chains was print-transferred onto tissue culture polystyrene (TCPS) or glass substrates, resulting in patterns with a lateral resolution down to 1 microm. Subsequently, dipping in an aqueous solution of non-functionalized PLL-g-PEG was used to backfill the non-printed regions of the surface, rendering them highly protein and thus cell resistant. In a second approach, proteins were stamped and a PLL-g-PEG backfill was applied for passivation of the bare surface regions. Printing of peptide(RGD)-functionalized PLL-g-PEG or proteins combined with a subsequent PLL-g-PEG backfill can be applied to a wide variety of substrate materials with negatively charged surfaces such as TCPS, glass and many metal oxides. We have tested the printed surfaces with human foreskin fibroblasts for cell adhesion and long-term performance and with fish epidermal keratocytes for cell motility and short-time behaviour. Both cell types reacted selectively to the surface micropatterns. Fibroblasts adhered to the printed (adhesive) regions only, where they remained attached up to at least 1 week and were even able to proliferate. Keratocyte spreading and motility were also directed by the geometry of the underlying patterns. The results prove that microcP in conjunction with the use of PLL-g-PEG and its derivatives provides a simple and robust alternative to previously reported micropatterning methods for future cell biological and biotechnological applications.

Animals↗
PubMed2003

Polystyrene nanoparticles based on poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers.

The solubilization of styrene by poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers has been examined. From turbidity measurements the solubility limit of the monomer in the micelles was obtained and the distribution coefficients were evaluated. Dynamic light scattering revealed that below the solubility limit, solubilization leads to a slight increase in micelle size, while above the solubility limit, there is a dramatic increase in particle size and turbidity as oil-in-water emulsions are formed through coalescence of monomer-swollen micelles. Polymerizations carried out below the solubility limit using the graft copolymer micelles as templates resembled microemulsion polymerizations in nature and led to very fine sterically stabilized polystyrene latex particles. Through careful control of the monomer concentration and the polymerization temperature it was possible to obtain spherical nanosize latex particles with similar size to those of the micelle precursors (10 nm) up to 11% monomer by weight. Polymerizations above the solubility limit, on the other hand, showed similarities with emulsion polymerizations and resulted in larger particles with higher polydispersity.

Emulsions↗
PubMed1979

Covalent binding of polycyclic aromatic hydrocarbons to adenine correlates with tumorigenesis in mouse skin.

Mouse epidermal homogenates were utilized to convert various polycyclic aromatic hydrocarbons to metabolites capable of binding covalently with nucleic acids. Poly(G) showed the highest capacity to bind covalently with the hydrocarbons; however, there was no correlation between binding to poly(G) and mouse skin tumorigenicity. On the other hand, covalent binding to poly(A) correlated well with values obtained for binding to DNA and mouse skin tumorigenicity. The order of binding to poly(A) was; 7,12-dimethylbenza[a]anthracene greater than benzo[a]pyrene greater than dibenz[a,h]anthracene greater than dibenz[a,c]anthracene.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1976

Peptides isolated from Enterobacter nuclease as potential polyamine binding sites.

The Enterobacter nuclease, which cleaves RNA between the 3'-phosphate group of cytidylic acid and the 5'-hydroxyl group of adenylic acid, has been shown to be affected by the polyamines, spermidine, spermine and putrescine. These substances enhance the hydrolytic activity of the enzyme against both poly(C) and yeast RNA. Sperimidine and spermine also reverse the inhibition of the enzyme by the ordered polynucleotides, apparently by removing them from the surface of the enzyme. Treatment of poly(G)-bound peptides (obtained from tryptic digests of poly(G)-bound nuclease) with an excess of spermidine resulted in the isolation of spermidine-bound peptides. Purification of these peptides through ion-exchange chromatography resulted in the isolation of three spermidine-bound peptides which consisted of 17 residues (6 amino acids), 19 residues (10 amino acids), and 12 residues (9 amino acids). The binding ratio of spermidine to peptides varied from 1:1 to 3:1.

Amino Acids↗
PubMed1981

Amino acid conjugation of N-hydroxy-4-aminoazobenzene dyes: a possible activation process of carcinogenic 4-aminoazobenzene dyes to the ultimate mutagenic or carcinogenic metabolites.

The activation process of N-hydroxy-4-aminoazobenzene (N-OH-AAB) dyes, proximate mutagenic or carcinogenic metabolites of AAB dyes, to the ultimate mutagenic or carcinogenic metabolites was studied by the use of an amino acid conjugation (aminoacylation) system catalyzed by yeast seryl-tRNA synthetase and [3H]ATP. A potent mutagen, N-hydroxy-3-methoxy-AAB (N-OH-3-MeO-AAB), as well as a non-mutagen, N-OH-2-MeO-AAB, were equally susceptible to N-O-serine conjugation. A weak mutagen, N-OH-AAB, and a moderate mutagen, N-OH-2,5-diMeO-AAB, were also susceptible to the aminoacylation, but to a lesser extent than the 2- or 3-methoxyl homologs. In contrast, N-hydroxy-N-methyl-4-aminoazobenzene and a moderate mutagen, N-OH-4'-MeO-AAB, were not susceptible to the aminoacylation. The ability of these N-OH-AAB dyes to bind with nucleic acid after serine conjugation was proportional to the susceptibility of the dyes to serine conjugation. Serine conjugates of N-OH-AAB dyes reacted with poly G, but not with poly A, poly C or poly U, suggesting that the azo dyes selectively bind with guanine base of nucleic acids. The susceptibility of N-OH-AAB dyes to aminoacylation was compared with the carcinogenic, mutagenic and unscheduled DNA synthesis-inducing activities of these and the mother AAB dyes.

Animals↗
PubMed1980

A ribonucleic acid-specific antibody produced during autoimmune disease: evidence for nucleotide sequence specificity.

A hybridoma secreting RNA-binding autoantibody has been produced by fusion of spleen cells from autoimmune NZB/NZWF1 mice with drug-resistant IgG2b-producing myeloma cells from BALB/c mice. Studies on the specificity of the purified monoclonal autoantibody revealed: (a) absolute specificity for ribopolynucleotides as compared with deoxyribopolynucleotides; (b) specificity for single-stranded RNA as compared with double-stranded RNA; (c) high affinity for the random copolymer poly(G, C); and (d) preference for the random heteropolymer poly(G, C, U). These studies were complemented by stoichiometric measurements of the antibody-RNA complex and computer analysis of the abundance of various di-, tri- and tetranucleotide sequences in native RNA. Taken together, these data suggest that the antigenic determinant recognized by the monoclonal autoantibody is largely composed of a trinucleotide sequence of single-stranded RNA containing, G, C and U residues.

Animals↗
PubMed1969

Role of base-pairing in the control of an enzyme reaction.

In an attempt to ascertain whether specific base-pairing could have a regulating function in an enzyme system in which nucleotides serve as the substrate, we studied the effects of the addition of the various homopolymers of the ribonucleotide series on the action of adenylate kinase on ADP or CDP, and found that the results support this possibility. Poly U strongly inhibits the enzyme action on ADP, and poly G that on CDP, both to the extent of about 70 per cent. Lesser effects are shown when poly G is used with ADP and poly U with CDP. The other homopolymers tested, poly A and poly C, are ineffective.

Adenine Nucleotides↗
PubMed2001

Modulatory factors on temperature-synchronized degradation of dextran grafted with thermoresponsive polymers and their hydrogels.

Several types of dextran grafted with poly(N-isopropylacrylamide-co-N,N-dimethylacrylamide [dextran-g-poly(NIPAAm-co-DMAAm)] with different graft lengths and numbers were synthesized in a preciously controlled fashion, and their enzymatic degradation was examined by viscosity measurement and gel permeation chromatography as a function of temperature. Degradation of dextran-g-poly(NIPAAm-co-DMAAm)s decreased with increasing the graft length below their lower critical solution temperatures (LCSTs). Above the LCST, enzymatic degradation was independent of the graft length. A larger amount of the graft chain with increasing the graft length rather than the graft number was effective to modulate the temperature-synchronized degradation. Hydrogels were prepared by cross-linking the graft copolymers using 1,6-hexamethylenediamine. While all the hydrogels have water content of about 93-96% in a wide range of temperatures, their degradation behaviors show a significant dependence on a temperature change. Such a unique property is closely related to the structure of graft copolymers such as graft lengths. Consequently, introducing thermoresponsive grafts with longer length to dextran and its hydrogels is suggested to be an important factor for modulating enzymatic degradation of dextran in synchronization with temperature.

Biocompatible Materials↗
PubMed2001

Effects of 3' terminus modifications on mRNA functional decay during in vitro protein synthesis.

The pcnB gene, which encodes the principal poly(A) polymerase of Escherichia coli, promotes 3'-polyadenylation and chemical decay of mRNA. However, there is no evidence that pcnB-mediated mRNA destabilization decreases protein synthesis, suggesting that polyadenylation may enhance translational efficiency. Using in vitro translation by E. coli cell extracts and toeprinting analysis of transcripts encoded by the chloramphenicol acetyltransferase (CAT) and beta-galactosidase genes to investigate this notion, we found no effect of poly(A) tails on protein synthesis. However, we observed that 3'-polyguanylation delayed the chemical decay of CAT mRNA and, even more dramatically, increased the ability of CAT mRNA to produce enzymatically active full-length protein in 30 S E. coli cell fractions. This resulted from interference with the primary mechanism for inactivation of CAT transcript function in cell extracts, which occurred by 3'-exonucleolytic degradation rather than endonucleolytic fragmentation by RNase E. Using bacteriophage T7 RNA polymerase to install poly(G) tails on mRNAs transcribed from polymerase chain reaction-generated DNA templates, we observed sharply increased synthesis of active proteins in vitro in coupled transcription/translation reactions. The ability of poly(G) tails to functionally stabilize transcripts from polymerase chain reaction-generated templates allows proteins encoded by translational open reading frames on genomic DNA or cDNA to be synthesized directly and efficiently in vitro.

3' Untranslated Regions↗
PubMed2003

Annexin A2 is a novel RNA-binding protein.

Annexin A2 (ANXA2) is a Ca(2+)-binding protein that is up-regulated in virally transformed cell lines and in human tumors. Here, we show that ANXA2 binds directly to both ribonucleotide homopolymers and human c-myc RNA. ANXA2 was shown to bind specifically to poly(G) with high affinity (K(d) = 60 nM) and not to poly(A), poly(C), or poly(U). The binding of ANXA2 to poly(G) required Ca(2+) (A(50%) = 10 microM). The presence of RNA in the immunoprecipitates of ANXA2 isolated from HeLa cells established that ANXA2 formed a ribonucleoprotein complex in vivo. Sucrose gradient analysis showed that ANXA2 associates with ribonucleoprotein complexes and not with polyribosomes. Reverse transcriptase-PCR identified c-myc mRNA as a component of the ribonucleoprotein complex formed by ANXA2 in vivo, and binding studies confirmed a direct interaction between ANXA2 and c-myc mRNA. Transfection of LNCaP cells with the ANXA2 gene resulted in the up-regulation of c-Myc protein. These findings identify ANXA2 as a Ca(2+)-dependent RNA-binding protein that interacts with the mRNA of the nuclear oncogene, c-myc.

Annexin A2↗
PubMed1998

Deadenylation-dependent and -independent decay pathways for alpha1-tubulin mRNA in Chlamydomonas reinhardtii.

The alpha- and beta-tubulin mRNAs of Chlamydomonas reinhardtii exhibit different half-lives under different conditions: when expressed constitutively, they degrade with half-lives of about 1 h, whereas when induced by deflagellation, they degrade with half-lives of only 10 to 15 min. To investigate the decay pathway(s) used under these two conditions, an alpha1-tubulin gene construct which included an insert of 30 guanidylate residues within the 3' untranslated region was introduced into cells. This transgene was efficiently expressed in stably transformed cells, and the mRNA exhibited constitutive and postinduction half-lives like those of the alpha1-tubulin mRNA. Northern blot analysis revealed the occurrence of a 3' RNA fragment derived from the poly(G)-containing alpha1-tubulin transcripts. The 3' fragment was shown to accumulate as full-length mRNA disappeared in actinomycin D-treated cells, indicating a precursor-product relationship. Insertion of a second poly(G) tract upstream of the first resulted in accumulation of only a longer 3' fragment, suggesting that the decay intermediate is generated by 5'-to-3' exonucleolytic digestion. A translational requirement for generation of the 3' fragment was demonstrated by experiments in which cells were deflagellated in the presence of cycloheximide. Analysis of fragment poly(A) length revealed that the fragments were, at most, oligoadenylated in nondeflagellated cells but had a long poly(A) tail in deflagellated cells. These findings suggest that the oligoadenylated fragment is a decay intermediate in a deadenylation-dependent, constitutive degradation pathway and that the requirement for deadenylation is bypassed in deflagellated cells. This represents the first example in which a single transcript has been shown to be targeted to different decay pathways under different cellular conditions.

Animals↗
PubMed1986

[Immunoglobulins acquire the ability to interact with DNA after chromatography on QAE-Sephadex].

The composition of IgG isolated from normal human serum includes a significant amount of antibodies interacting with native DNA. This ability of antibodies is revealed only after anion-exchange chromatography, resulting in the division of IgG into two fractions, i.e., acid and alkaline immunoglobulins. The peculiarities of interaction of the both fractions with DNA and the specificity of this reaction were investigated. The IgG tested were shown to interact with native and denaturated DNA, dextran sulfate, poly-G and poly-I. The possibility of interaction of antibodies with the charged structures of the cell and their significance under normal and pathological conditions are discussed.

Antibodies, Antinuclear↗
PubMed2001

Features of the 3'-consensus sequence of rotavirus mRNAs critical to minus strand synthesis.

The last seven nucleotides of the 3'-end of rotavirus mRNAs, 5'-UGUGACC-3', are highly conserved and form a cis-acting signal that can promote the synthesis of (-) strand RNA to produce the viral dsRNA genome in vitro. Previous studies have shown that the sequence, location, and strandedness (single- versus double-stranded) of the 3'-consensus sequence of the mRNA affect the efficiency of (-) strand synthesis. In this study, we have used exhaustive mutagenesis of the SA11 gene 8 mRNA and an in vitro replication system to define the importance of each of the residues in the consensus sequence in (-) strand synthesis. The analysis showed that the CC of the consensus sequence was the most critical for (-) strand synthesis. Furthermore, the data revealed that other, but not all, residues of the consensus sequence contributed to efficient (-) strand synthesis in vitro. Mutant gene 8 RNAs supported an intermediate level of (-) strand synthesis when the 15 nt sequence upstream of the CC was replaced with long tracts of poly(A) or poly(U), but not with poly(G). Predictions of the secondary structure of the mutant RNAs suggested that the poly(G)-RNA could not replicate because its 3'-terminus was largely basepaired, instead of extending as a single-stranded tail as is the case for the 3'-termini of the poly(A)- and poly(U)-RNAs and wild-type gene 8 RNA. Subsequent experiments performed with complementary oligonucleotides indicated that efficient RNA replication occurs in vitro only when the last four residues of the 3'-consensus sequence, and most importantly the two terminal C's, existed in a single-stranded form. A single-stranded CC may be crucial for formation of an initiation complex for (-) strand synthesis consisting of viral RdRP, mRNA, and the dinucleotide pGpG.

Animals↗
PubMed1977

Nucleoside adducts from the in vitro reaction of benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide or benzo[a]pyrene 4,5-oxide with nucleic acids.

The covalent binding of benzo[a]pyrene 4,5-oxide and benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide isomer I and isomer II to nucleic acids in aqueous acetone solution has been investigated. Benzo[a]pyrene 4,5-oxide reacted preferentially with guanosine residues. On the other hand, benzo[a]pyrene-7,8-dihydrodiol 9,10-oxide isomer I and II reacted extensively with guanosine, adenosine, and cytidine residues. Time course studies showed that the reactivity of isomer I or isomer II with homopolyribonucleotides followed the order poly(G) greater than poly(A) greater than poly(C). Alkaline or enzymatic hydrolysis of the modified nucleic acids and subsequent chromatography on Sephadex LH-20 columns yielded benzo[a]pyrene-nucleotide adducts. These were enzymatically converted to the corresponding nucleosides which were resolved into several distinct components by high-pressure liquid chromatography. Evidence was obtained for the presence of multiple nucleoside adducts of guanosine, adenosine, cytidine, deoxyguanosine, deoxyadenosine, and deoxycytidine. The HPLC profiles of adducts formed with isomer I were different from the corresponding profiles of adducts formed with isomer II. Structural aspects of these nucleoside adducts are discussed.

Alcohols↗
PubMedDate not supplied

[Study of the relationship between secondary DNA strucure and base sequence by the technic of theoretical conformational analysis].

An investigation of double-stranded polynucleotide conformations using the algorithm for exclusion of redundant dihedral angles and flexible sugar unit has been performed. The fragment of DNA including three nucleotide pairs was taken into account for polynucleotides poly[d(A--T)].poly[d(T--A)], poly[d(G--C)].poly[d(C--G)], poly(dA).poly(dT) and poly(dG).poly(dC). The resulting structures being energetically optimal have helical parameters corresponding to X-ray experimental values for A- and B-forms. It was revealed that B-form is the most energetically favorable structure, therefore the earlier conception that water is of importance for B-form stabilisation may be revised. Relative stabilities of B- and A-forms depend upon base sequence because unequal contributions of the stacking and backbone energy in whole potential energy of the structrues with different sequences.

Base Sequence↗
PubMed1974

Escherichia coli initiation factor IF3 binding to AUG and AUG-containing single strands and hairpin loops, and nonspecific binding to polymers.

Nitrocellulose filter binding and equilibrium dialysis detected the binding of Escherichia coli initiation factor IF3 to AUG, An UGUm single strands and hairpin loops, poly(A,U,G), poly(U), and f2 RNA. No binding was detected for GUA, A8 U, or the hairpin loop A5 GC5 U5. AUG-specific binding, per nucleotide, is strong; nonspecific binding, per nucleotide, is weak.

Binding, Competitive↗
PubMed1976

Puromycin inhibition of eucaryotic ribosomes. Differences in sensitivity between polypeptide synthesis directed by endogenous mRNA and synthetic templates including poly(U).

In a protein synthesis sytem derived from porcine uteri we have made the following observations: 1. Synthesis directed by the endogenous mRNA of the system is more sensitive to inhibition by puromycin than poly(U) directed synthesis. 2. Synthesis directed by the synthetic templates poly(G,U) and poly(C,U) is more sensitive to inhibition by puromycin than poly(U) directed synthesis and frequently shows a sensitivity to puromycin similar to that directed by endogenous mRNA. 3. Protein synthesis was inhibited by three aminoacyloligonucleotides (C-A-Phe, C-A-Asp, and C-A-Pro) which are analogs of the 3' terminus of aminoacyl tRNAs. Of the three, C-A-Phe was the most active and C-A-Asp the least active but, unlike puromycin, inhibition by these compounds was the same for endogenous and poly(U) directed synthesis. These results are interpreted as supporting the proposal that the acceptor site of ribosomes contains an hydrophobic binding region which interacts with the side chain of aliphatic amino acids, and particularly with the aromatic side chain of phenylalanine.

Amino Acids↗