scholarly journals tRNA Ligase Catalyzes the GTP-Dependent Ligation of RNA with3′-Phosphate and 5′-Hydroxyl Termini

Biochemistry ◽  
2012 ◽  
Vol 51 (7) ◽  
pp. 1333-1335 ◽  
Author(s):  
Kevin K. Desai ◽  
Ronald T. Raines
Keyword(s):  
Hydroxyl Termini

Phosphorylation of DNA Molecules with Protruding 5'-Hydroxyl Termini

2006 ◽  
Vol 2006 (1) ◽  
pp. pdb.prot3864
Author(s):  
Joseph Sambrook ◽  
David W. Russell
Keyword(s):  
Dna Molecules ◽  
Hydroxyl Termini

scholarly journals Ribonuclease "XlaI," an activity from Xenopus laevis oocytes that excises intervening sequences from yeast transfer ribonucleic acid precursors.

1981 ◽  
Vol 1 (3) ◽  
pp. 269-280 ◽  
Author(s):  
A Otsuka ◽  
A de Paolis ◽  
G P Tocchini-Valentini
Keyword(s):  
Xenopus Laevis ◽  
Ribonucleic Acid ◽  
Rnase A ◽  
Xenopus Laevis Oocytes ◽  
Cleavage Sites ◽  
Reaction Products ◽  
Yeast Trna ◽  
Intervening Sequences ◽  
Nuclear Extracts ◽  
Hydroxyl Termini

A ribonuclease (RNase) activity, RNase "XlaI," responsible for the excision of intervening sequences from two yeast transfer ribonucleic acid (tRNA) precursors, pre-tRNA(Tyr) and pre-tRNA(3Leu), has been purified 54-fold from nuclear extracts of Xenopus laevis oocytes. The RNase preparation is essentially free of contaminating RNase. A quantitative assay for RNase XlaI was developed, and the reaction products were characterized. RNase XlaI cleavage sites in the yeast tRNA precursors were identical to those made by yeast extracts (including 3'-phosphate and 5'-hydroxyl termini). Cleavage of pre-tRNA(3Leu) by RNase XlaI and subsequent ligation of the half-tRNA molecules do not require removal of the 5' leader or 3' trailer sequences.

The 3′-hydroxyl termini in yeast ribosomal RNA

1970 ◽  
Vol 48 (10) ◽  
pp. 1113-1121 ◽  
Author(s):  
K. M. Olver ◽  
B. G. Lane
Keyword(s):  
Gradient Centrifugation ◽  
Group Analysis ◽  
Ribosomal Subunit ◽  
Sucrose Density Gradient ◽  
Sucrose Density Gradient Centrifugation ◽  
Selective Precipitation ◽  
Ribosomal Subunits ◽  
Hydroxyl Termini ◽  
End Group ◽  
Total Yeast

(1) A fraction of high molecular weight RNA was prepared by subjecting total yeast RNA to selective precipitation from aqueous 2.5 M sodium chloride solution at 0°. This "insoluble" RNA accounted for about 80% of the total yeast RNA.(2) The "insoluble" RNA and various of its subfractions obtained by preparative sucrose density-gradient centrifugation were subjected to electrophoretic and end-group analyses.(3) One subfraction, largely composed of 17 S RNA from the smaller ribosomal subunit, was found to contain adenosine as the principal 3′-hydroxyl terminal nucleoside residue. Based on the analysis of 3′-hydroxyl termini, RNA in this subfraction had a mean residue length of about 1600 nucleotides.(4) Another subfraction, largely composed of 26 S RNA from the larger ribosomal subunit, was found to contain uridine as the principal 3′-hydroxyl terminal nucleoside residue. Based on the analysis of 3′-hydroxyl termini, RNA in this subfraction had a mean residue length of about 2400 nucleotides.(5) Electrophoretic and end-group analyses of other subfractions have been reported and discussed in terms of the possible origin of the RNA in these fractions, and also in terms of the way in which the RNA of these fractions might tend to affect the end-group analysis of both the parent fraction and the principal subfractions, which contain RNA from the ribosomal subunits.

Wheat embryo ribonucleates. X. Metabolism of 3′-hydroxyl termini in the conserved mRNA and tRNA of imbibing wheat embryos

1978 ◽  
Vol 56 (3) ◽  
pp. 197-202 ◽  
Author(s):  
T. D. Kennedy ◽  
B. G. Lane
Keyword(s):  
Ribosomal Rna ◽  
Messenger Rna ◽  
Insoluble Fraction ◽  
Wheat Embryo ◽  
Selective Labelling ◽  
Wheat Embryos ◽  
Chain Lengths ◽  
Hydroxyl Termini ◽  
Terminal Poly ◽  
Mass Component

There are conserved complements of ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) in dry wheat embryos. Although early labelling of RNA is largely directed toward the synthesis of complete molecules of nascent rRNA and mRNA, there is also selective labelling at 3′-hydroxyl termini in conserved polynucleotides when dry wheat embryos are subjected to short-term (0.5 h) imbibition in a medium that contains tritium-labelled adenosine, guanosine, cytidine, and uridine. Conserved tRNA is the principal mass component in NaCl-soluble RNA (sRNA) and most of the 'rapid labelling' of sRNA (rl-sRNA) is a result of labelling at 3′-hydroxyl termini in conserved tRNA. By contrast, although conserved rRNA is the principal mass component in NaCl-insoluble RNA (iRNA), most of the labelled 3′-hydroxyl termini in 'rapidly labelled' iRNA (rl-iRNA) do not appear to derive from rRNA. Although about 10% of the labelled 3′-hydroxyl termini in rl-iRNA originates in conserved poly(A)-rich mRNA, the available evidence leads to the conclusion that most of the labelled 3′-hydroxyl termini in rl-iRNA originates in an unusual NaCl-insoluble fraction of conserved tRNA. During the course of extended imbibition, between 0.5 and 5 h, there are characteristic changes in the chain lengths and labelling patterns for 3′-hydroxyl terminal poly(A) sequences in mRNA. Analytical and physiological implications of these data are subjects of discussion.

scholarly journals Tracking the processing of damaged DNA double-strand break ends by ligation-mediated PCR: increased persistence of 3′-phosphoglycolate termini in SCAN1 cells

2013 ◽  
Vol 42 (5) ◽  
pp. 3125-3137 ◽  
Author(s):  
Konstantin Akopiants ◽  
Susovan Mohapatra ◽  
Vijay Menon ◽  
Tong Zhou ◽  
Kristoffer Valerie ◽  
...  
Keyword(s):  
Strand Break ◽  
Double Strand Break ◽  
Dna Double Strand Break ◽  
Alu Repeat ◽  
Polymerase Chain ◽  
Cellular Dna ◽  
Hydroxyl Termini ◽  
Taqman Polymerase Chain Reaction ◽  
Damaged Dna

Abstract To track the processing of damaged DNA double-strand break (DSB) ends in vivo, a method was devised for quantitative measurement of 3′-phosphoglycolate (PG) termini on DSBs induced by the non-protein chromophore of neocarzinostatin (NCS-C) in the human Alu repeat. Following exposure of cells to NCS-C, DNA was isolated, and labile lesions were chemically stabilized. All 3′-phosphate and 3′-hydroxyl ends were enzymatically capped with dideoxy termini, whereas 3′-PG ends were rendered ligatable, linked to an anchor, and quantified by real-time Taqman polymerase chain reaction. Using this assay and variations thereof, 3′-PG and 3′-phosphate termini on 1-base 3′ overhangs of NCS-C-induced DSBs were readily detected in DNA from the treated lymphoblastoid cells, and both were largely eliminated from cellular DNA within 1 h. However, the 3′-PG termini were processed more slowly than 3′-phosphate termini, and were more persistent in tyrosyl-DNA phosphodiesterase 1-mutant SCAN1 than in normal cells, suggesting a significant role for tyrosyl-DNA phosphodiesterase 1 in removing 3′-PG blocking groups for DSB repair. DSBs with 3′-hydroxyl termini, which are not directly induced by NCS-C, were formed rapidly in cells, and largely eliminated by further processing within 1 h, both in Alu repeats and in heterochromatic α-satellite DNA. Moreover, absence of DNA-PK in M059J cells appeared to accelerate resolution of 3′-PG ends.

scholarly journals Nonreplicative RNA Recombination in Poliovirus

1999 ◽  
Vol 73 (11) ◽  
pp. 8958-8965 ◽  
Author(s):  
Anatoly P. Gmyl ◽  
Evgeny V. Belousov ◽  
Svetlana V. Maslova ◽  
Elena V. Khitrina ◽  
Alexander B. Chetverin ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Hot Spots ◽  
Significant Proportion ◽  
Rna Recombination ◽  
Genomic Rna ◽  
Viral Rnas ◽  
Rna Fragments ◽  
Cyclic Phosphate ◽  
Template Switch ◽  
Hydroxyl Termini

ABSTRACT Current models of recombination between viral RNAs are based on replicative template-switch mechanisms. The existence of nonreplicative RNA recombination in poliovirus is demonstrated in the present study by the rescue of viable viruses after cotransfections with different pairs of genomic RNA fragments with suppressed translatable and replicating capacities. Approximately 100 distinct recombinant genomes have been identified. The majority of crossovers occurred between nonhomologous segments of the partners and might have resulted from transesterification reactions, not necessarily involving an enzymatic activity. Some of the crossover loci are clustered. The origin of some of these “hot spots” could be explained by invoking structures similar to known ribozymes. A significant proportion of recombinant RNAs contained the entire 5′ partner, if its 3′ end was oxidized or phosphorylated prior to being mixed with the 3′ partner. All of these observations are consistent with a mechanism that involves intermediary formation of the 2′,3′-cyclic phosphate and 5′-hydroxyl termini. It is proposed that nonreplicative RNA recombination may contribute to evolutionarily significant RNA rearrangements.

scholarly journals The Enzymatic Phosphorylation of Nucleic Acids and Its Application to End-Group Analysis

1966 ◽  
Vol 49 (6) ◽  
pp. 81-97 ◽  
Author(s):  
Charles C. Richardson ◽  
Bernard Weiss
Keyword(s):  
Molecular Weight ◽  
Group Analysis ◽  
Single Strand ◽  
Selective Labeling ◽  
Phosphodiester Bond ◽  
Polynucleotide Kinase ◽  
End Groups ◽  
Hydroxyl Termini ◽  
End Group

Polynucleotide kinase catalyzes the transfer of a phosphate group from ATP to the 5'-hydroxyl termini of polynucleotides. Selective labeling of the 5'-hydroxyl termini of DNA with polynucleotide kinase has been used to study the number and the identity of the 5'-terminal residues of bacteriophage DNA's, and to examine the nature of the phosphodiester bond cleavages produced by endonucleases and by sonic irradiation. The intact strands of T7 DNA bear 5'-phosphoryl end-groups; only deoxyadenylate and deoxythymidylate are present as 5'-terminal residues. The intact strands of native λ-DNA bear 5'-hydroxyl end-groups. M13 DNA, a circular molecule, cannot be phosphorylated. End-group labeling of DNA provides a method for determination of molecular weight; calibration against other DNA preparations is not required. The molecular weight of a single strand of T7 DNA, determined by end-group labeling, is 13.1 x 106; the molecular weight of a single strand of λ-DNA is 16.0 x 106. These values are in agreement with molecular weight estimates by sedimentation analysis and electron microscopy. Sonic irradiation of DNA has been shown to favor the production of polynucleotides terminated by 5'-phosphomonoester groups. All four deoxyribonucleotides are present as 5'-terminal residues of sonicated DNA.

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