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Human SUV3 helicase regulates growth rate of the HeLa cells and can localize in the nucleoli. Acta Biochim Pol 2017; 64:177-181. [PMID: 28291845 DOI: 10.18388/abp.2016_1419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/10/2022]
Abstract
The human SUV3 helicase (SUV3, hSUV3, SUPV3L1) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome with exonuclease PNP (polynucleotide phosphorylase). Association of this complex with the polyA polymerase can modulate mitochondrial polyA tails. Silencing of the SUV3 gene was shown to inhibit the cell cycle and to induce apoptosis in human cell lines. However, since small amounts of the SUV3 helicase were found in the cell nuclei, it was not clear whether the observed phenotypes of SUV3 depletion were of mitochondrial or nuclear origin. In order to answer this question we have designed gene constructs able to inhibit the SUV3 activity exclusively in the cell nuclei. The results indicate that the observed growth rate impairment upon SUV3 depletion is due to its nuclear function(s). Unexpectedly, overexpression of the nuclear-targeted wild-type copies of the SUV3 gene resulted in a higher growth rate. In addition, we demonstrate that the SUV3 helicase can be found in the HeLa cell nucleoli, but it is not detectable in the DNA-repair foci. Our results indicate that the nucleolar-associated human SUV3 protein is an important factor in regulation of the cell cycle.
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A highly specific microRNA-mediated mechanism silences LTR retrotransposons of strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:70-82. [PMID: 26611654 DOI: 10.1111/tpj.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/06/2015] [Accepted: 11/20/2015] [Indexed: 06/05/2023]
Abstract
Small RNAs are involved in a plethora of functions in plant genomes. In general, transcriptional gene silencing is mediated by 24-nucleotide siRNAs and is required for maintaining transposable elements in a silenced state. However, microRNAs are not commonly associated with transposon silencing. In this study, we performed small RNA transcriptome and degradome analyses of the Rosaceae model plant Fragaria vesca (the woodland strawberry) at the genome-wide level, and identified miRNA families and their targets. We report a highly specific mechanism of LTR retrotransposon silencing mediated by an abundant, ubiquitously expressed miRNA (fve-miR1511) generated from a single locus. This miRNA specifically targets LTR retroelements, silencing them post-transcriptionally by perfectly pairing to the highly conserved primer binding site for methionyl initiator tRNA that is essential for reverse transcription. We investigated the possible origins of this miRNA, and present evidence that the pre-miR1511 hairpin structure probably derived from a locus coding for tRNA(iM) (et) through a single microinversion event. Our study shows that this miRNA targets retrotransposons specifically and constitutively, and contributes to features such as genome stability, size and architecture in a far more direct way than previously thought.
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High-throughput sequencing and degradome analysis reveal neutral evolution of Cercis gigantea microRNAs and their targets. PLANTA 2016; 243:83-95. [PMID: 26342708 PMCID: PMC4698290 DOI: 10.1007/s00425-015-2389-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/20/2015] [Indexed: 05/24/2023]
Abstract
High-throughput sequencing and degradome analysis for Cercis gigantea identified 194 known miRNAs and 23 novel miRNAs with 61 targets. The comparison results of highly conserved miRNAs and non-conserved miRNAs implied that C. gigantea miRNAs were subjected to the neutral evolution. MicroRNAs play a key role in post-transcriptionally regulating gene expression during plant growth, development and other various biological processes. Although numerous miRNAs have been identified and documented, to date, there are no reports on Cercis gigantea (C. gigantea) miRNAs. In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among these, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. The comparison results revealed that highly conserved miRNAs have higher expression levels, more family members and more targets than non-conserved miRNAs, indicating that C. gigantea miRNAs were subjected to the neutral evolution. Meanwhile, these conserved miRNAs were also found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes, which will help further understanding regulatory mechanisms of C. gigantea miRNAs.
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Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:17-24. [PMID: 23415324 DOI: 10.1016/j.plantsci.2012.12.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/20/2012] [Accepted: 12/23/2012] [Indexed: 05/24/2023]
Abstract
Wheat is the most highly cultivated plant species for its grain production throughout the world. Because small RNA-dependent gene regulation is critical for successful completion of plant life cycle including its productivity, identification of not only miRNAs but also confirming their targets in wheat is important. To identify small RNAs including novel miRNAs as well as miRNA targets in wheat, we constructed small RNA and degradome libraries from wheat seedlings. Small RNA analysis resulted in identification of most conserved miRNAs including novel miRNAs that can be grouped into 32 miRNA families. The sequence analysis also led to the characterization of two abundantly expressed rRNA-derived small RNAs. To identify miRNA targets, degradome library was sequenced and the bioinformatic analysis confirmed 53 genes as targets for miRNAs and Tas3-siRNAs. Degradome analysis also confirmed a conserved fine-tuning mechanism of Tas3-siRNA abundance by siRNA-mediated silencing of TAS3 transcripts in diverse plant species. These findings added additional information to the small RNA knowledge-base in wheat.
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POLYNUCLEOTIDE PHOSPHORYLASE IN NEISSERIA MENINGITIDIS. ACTA PATHOLOGICA MICROBIOLOGICA SCANDINAVICA 2009; 59:63-72. [PMID: 14058782 DOI: 10.1111/j.1699-0463.1963.tb01772.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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AN EXAMINATION OF THE MECHANISM OF ACTION OF POLYNUCLEOTIDE PHOSPHORYLASE BY THE USE OF ACRIDINE ORANGE*. Ann N Y Acad Sci 2006; 81:645-59. [PMID: 13798247 DOI: 10.1111/j.1749-6632.1959.tb49346.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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THE EFFECT OF END GROUPS AND THE INITIAL SITE OF ATTACK ON POLYNUCLEOTIDES BY POLYNUCLEOTIDE PHOSPHORYLASE AND CERTAIN PHOSPHODIESTERASES. Ann N Y Acad Sci 2006; 81:660-74. [PMID: 14401822 DOI: 10.1111/j.1749-6632.1959.tb49347.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Inhibition and activation of polynucleotide phosphorylase through the formation of complexes between acridine orange and polynucleotides. Nature 2000; 182:242-4. [PMID: 13577797 DOI: 10.1038/182242a0] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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The action of polynucleotide phosphorylase on 5-halogenouridine-5' pyrophosphates. ACTA ACUST UNITED AC 1998; 55:529-40. [PMID: 14473445 DOI: 10.1016/0006-3002(62)90986-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Adenine nucleotide breakdown and its relationship to polynucleotide phosphorylase in the crown-gall tumor inducing organism Agrobacterium tumefaciens. ACTA ACUST UNITED AC 1998; 39:773-85. [PMID: 13780231 DOI: 10.1139/o61-080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell-free extracts of the crown-gall tumor inducing organism Agrobacterium tumefaciens (strain B6) have been shown to convert ATP to ADP relatively slowly. An adenylate kinase of only moderate activity has been found.Crude extracts of this organism contain an extremely active polynucleotide phosphorylase which rapidly catalyzes the synthesis of polyadenylate from ADP, releasing Piin stoichiometric proportions. Extracts are also shown to exhibit some phosphodiesterase activity towards the polyadenylate so formed.Even though the enzymatic conversions of adenosine and of IMP to hypoxanthine are shown to occur readily it has not been possible to demonstrate any metabolic link between AMP and either adenosine or IMP. Extracts of A. tumefaciens have the unusual property of being unable to metabolize further AMP or other similar mononucleotides (with the exception of IMP).It is shown also that polynucleotide phosphorylase is active not only in extracts of crown-gall tumor inducing organisms but also in those of at least one related non-tumorogenic species of Agrobacterium.
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The synthesis of N1- and N6- methyladenosine 5'-pyrophosphates. Possible substrates for polynucleotide phosphorylase. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 68:185-92. [PMID: 13950388 DOI: 10.1016/0006-3002(63)90134-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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SYNTHESIS IN VIVO OF POLYNUCLEOTIDE PHOSPHORYLASE IN ESCHERICHIA COLI. I. EFFECT OF AMINO ACIDS ON POLYNUCLEOTIDE PHOSPHORYLASE ACTIVITY IN A CHLORAMPHENICOL-INHIBITED SYSTEM. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 76:558-71. [PMID: 14099615 DOI: 10.1016/0006-3002(63)90082-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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[IN VIVO SYNTHESIS OF POLYNUCLEOTIDE PHOSPHORYLASE IN ESCHERICHIA COLI. II. DE NOVO SYNTHESIS OF POLYNUCLEOTIDE PHOSPHORYLASE IN THE PRESENCE OF CHLORAMPHENICOL]. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 76:572-88. [PMID: 14099616 DOI: 10.1016/0006-3002(63)90083-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
The rho-dependent transcription terminator tR1 of bacteriophage lambda stops RNA synthesis downstream of the major rightward promoter, PR, shortly after the cro gene. Terminated transcripts produced in a purified in vitro transcription system display a heterodisperse set of 3' termini, occurring in clusters located at +290-300, 308-312, 340-345, 385-390, and 440-450 nucleotides from the transcription start site [Morgan, W.D., Bear, D.G., & von Hippel, P.H. (1983) J. Biol. Chem. 258, 9553-9564]. However, transcripts from the same promoter in vivo have been reported to end primarily at +310-312 [Court, D., Brady, C., Rosenberg, M., Wulff, D. L., Behr, M., Mahoney, M., & Izumi, S. (1980) J. Mol. Biol. 138, 231-254]. In order to understand the nature of this discrepancy, we have carried out a comparative analysis of lambda PR transcription products produced in translationally active S30 cell extracts, in a purified in vitro system and in vivo. RNAs from the cell extracts coupled to translation show primarily three PR-derived transcripts beginning at one predominant 5' end and terminating at +263, 308, and 318. Sites +263 and +308 appear to be RNA processing sites. S1 nuclease mapping studies of RNAs produced in vivo show one 5' end and two 3' termini ending at +263 and 311; the +263 site is the predominant 3' end. When transcripts produced in a purified in vitro transcription system are incubated in the S30 cell extract under various conditions, the RNAs are degraded to two primary products with lengths of 263 and 308-311 nt.(ABSTRACT TRUNCATED AT 250 WORDS)
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[Enzymatic incorporation into oligonucleotides of modified nucleosides]. BIOORGANICHESKAIA KHIMIIA 1987; 13:1037-44. [PMID: 3675647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Behaviour of modified nucleosides, tRNA components, and their analogues has been studied in the internucleotide bond formation catalysed by ribonucleases of various substrate specificity, polynucleotide phosphorylases, and T4 RNA ligase and the results are summarised in this paper. Pseudouridine, dihydrouridine, ribothymidine, 5-methylcytidine, inosine, and 6-methyladenosine can participate in the reaction of internucleotide bond formation the presence of most ribonucleases used, viz. Pb2, Pcl2, Pb1, Pch1, C2, T1, pancreatic RNase. 3-Methylcytidine and 4-acetylcytidine form internucleotide bond (as phosphate acceptors) usually by means of guanyl-specific ribonucleases, whereas 1-methylandenosine is incorporated with ribonuclease Pel2. 7-Methylguanosine and 1-methylguynosine 2',3'-cyclophosphates can be used as phosphate donors in the presence of ribonuclease Pb2; in the similar enzymatic reaction 6-isopentenyladenosine is an uneffective acceptor.
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Enzymatic synthesis of uniformly 32P-labeled polyribonucleotides and high-specific-activity ribonucleoside 5'-[alpha-32P]diphosphates. Anal Biochem 1985; 144:291-5. [PMID: 3157330 DOI: 10.1016/0003-2697(85)90119-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Uniformly 32P-labeled polyribonucleotides of high specific activity can be rapidly and easily synthesized from commercially available ribonucleoside 5'-[alpha-32P]triphosphates by using two enzymes in sequence. Myosin ATPase completely and irreversibly converted any triphosphates to diphosphates in 10 min. The product diphosphates, without purification, can be polymerized by polynucleotide phosphorylase (PNPase) in 1 h with an average yield of 60%. By choosing the desired molar ratio of radioactive and nonradioactive tri- or diphosphates, polymers of a wide range of specific activity can be obtained. Since myosin ATPase and PNPase both have little base specificity, the method can be used to synthesize a radiolabeled polymer of any desired base composition.
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Poly(2-methylthio-7-deazainosinic acid)--hydrophobic stabilization of polynucleotide secondary structure by the 2-methylthio group. Nucleic Acids Res 1983; 11:6107-20. [PMID: 6889137 PMCID: PMC326338 DOI: 10.1093/nar/11.17.6107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Poly(2-methylthio-7-deazainosinic acid) [poly(ms2c7I)] was enzymatically synthesized by polymerization of 2-methylthio-7-deazainosine 5'-diphosphate with polynucleotide phosphorylase from Micrococcus luteus in high yield. The homopolymer shows much higher thermal stability than its parent polynucleotides poly(7-deazainosinic acid) [poly(c7I)] and poly(I). Its sigmoidal melting curve and pronounced hypochromicity imply a rigid, ordered structure. Poly(ms2c7I), like poly(2-methylthio-inosinic acid) [poly(ms2I)], does not form a complex with poly(C) because of the bulky 2-methylthio substituent. On the other hand, two poly(ms2c7I) strands form very rigid triple strands with poly(A). Different from poly(I) and poly(c7I) the homopolymer poly(ms2c7I) is very stable against cleavage by nuclease S1 and ribonuclease T2 as expected from its rigid secondary structure.
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Methacrylate polymerization by AzoRNA: potential usefulness for chromosomal localization of genes. Biopolymers 1981; 20:2635-48. [PMID: 6173078 DOI: 10.1002/bip.1981.360201210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Biophysical applications of NMR to phosphoryl transfer enzymes and metal nuclei of metalloproteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOENGINEERING 1980; 9:363-92. [PMID: 6104944 DOI: 10.1146/annurev.bb.09.060180.002051] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Abstract
One evening in the late nineteen forties my wife and I were at a party given in honor of Otto Loewi and Sir Henry Dale, corecipients of the 1936 Nobel Prize in Medicine for their discovery of the chemical transmission of the nerve impulse. We were all asked to sign the guest book and state our hobby and I did this as Sir Henry looked over my shoulder. As I put down my hobby as Biochemistry he roared with laughter. At that time I was Professor of Pharmacology and Chairman of the Department at the New York University School of Medicine and Sir Henry said, “now that he is a pharmacologist, he has biochemistry as a hobby.” I tell this story to justify the title of this essay, because in my life biochemistry has been my only and real hobby.
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Abstract
Polynucleotides containing adenosine and 8-azidoadenosine or inosine and 8-azidoinosine residues have been prepared from mixtures of nucleoside diphosphates using polynucleotide phosphorylase from Escherichia coli. These copolymers can form complexes with polyuridylic or polycytidylic acids respectively. Single stranded poly(adenylic, 8-azidoadenylic acid) [poly(A,z8A)] has been used as a photoaffinity reagent to explore the subunit topography of RNA polymerase from E. coli.
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Abstract
The structure of polio replicative form (RF) has been investigated by 3' end labeling and the use of polynucleotide phosphorylase to now allow a complete composite of the RF structure. The evidence presented indicates that the 3' terminal sequence of the minus strand is an exact complement to the 5' end of polio RNA. This suggests that the 5' terminal U of polio RNA is genetically coded. Other data is presented to show that in addition to the genetically coded poly(A) tract of the plus strand in RF, a single-stranded poly(A) tail protrudes beyond the double-stranded RNA.
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A method for the synthesis of oligonucleotide by single addition of 2'-O-(o-nitrobenzyl)nucleoside 5'-diphosphates using polynucleotide phosphorylase. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 565:192-8. [PMID: 389286 DOI: 10.1016/0005-2787(79)90095-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two hexanucleotides A-U-G-U-G-A and C-A-A-U-U-G were synthesized from the chemically synthesized trimers C-A-A and A-U-G by addition of 2'-O-(o-nitrobenzyl)nucleoside diphosphates using polynucleotide phosphorylase isolated from either Escherichia coli or Micrococcus luteus. In each reaction the preference of the enzyme was tested. The o-nitrobenzyl group was removed after addition of the mononucleotide and the deblocked product was isolated by chromatography on DEAE-Sephadex in high yields.
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Poly(2-fluoroadenylic acid). The role of basicity in the stabilization of complementary helices. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 563:508-17. [PMID: 37911 DOI: 10.1016/0005-2787(79)90069-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The polymerization of 2-fluoroadenosine 5'-diphosphate by polynucleotide phosphorylase to give high molecular weight poly(2-fluoroadenylic acid), poly(fl2A), is described. Both the single-stranded and double-stranded (acid) forms of poly(fl2A) exhibit strikingly similar ultraviolet and circular dichroism spectra to those of poly(A), and the enzymatic polymerization rates and thermal hyperchromicities of the two polymers are also very similar. However, the pKa of poly(fl2A) for protonation at N-1 is 2.9 compared to 5.9 for poly(A) under similar conditions. Poly(fl2A) forms a triple-stranded helix with poly(U) which has ultraviolet and cd spectra very reminiscent of poly(A) . 2 poly(U), but no conditions could be found which permitted the formation of a double helix. In the Escherichia coli ribosome system poly(fl2A) codes for the synthesis of polylysine, as does poly(A), although the rate and extent of incorporation were less in the former case. The role of basicity of adenine N-1 in these interactions is discussed.
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Polynucleotides. LVII. Synthesis and properties of poly (2'-chloro-2'-deoxyinosinic acid). Nucleic Acids Res 1979; 6:2627-36. [PMID: 461198 PMCID: PMC327876 DOI: 10.1093/nar/6.7.2627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Poly (2'-chloro-2'-deoxyinosinic acid) [poly(Icl)] was synthesized from Icl 5'-DP by polymerization with polynucleotide phosphorylase. UV absorption properties of poly(Icl) are very similar to those of poly(I). Poly(Icl) adopted a multi-stranded ordered form in the presence of 0.95M Na ion. The Tm value of this form was 36 degrees, which resembles that of poly(I) quadruple-stranded form at high salt. CD spectra also suggested presence of these two forms. Upon mixing with poly(C), poly-(Icl) forms a double-stranded 1 : 1 complex, which had very similar Tm-log[Na+] relationship to that of poly(I) . poly(C). Thus it was concluded that the chlorine substitution at 2'-position of the polynucleotide had the similar effect to OH on physical properties of polynucleotides.
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Abstract
The synthesis of poly(mo5U) requires a high concentration (2.7 mg/ml) of polynucleotide phosphorylase as well as a long reaction time (48 h). The resulting polynucleotide has a chain length of approximately 100 nucleotides. It shows no indication of a stable secondary structure. When poly(mo5U) is mixed with poly(A), a triple-stranded complex poly(A) . 2poly(mo5U) is formed. This complex has a melting temperature of 68.5 +/- 0.5 degrees C at 150 mMNa+ and exhibits a hysteresis loop between melting and reformation of the complex having a delta Tm of 11.5 degrees C. Poly-5-methoxyuridylic acid stimulates the binding of Phe-tRNA to 70-S ribosomes but is inactive in directing poly(Phe) synthesis.
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Polynucleotides. XLIV. Synthesis and properties of poly (2-azaadenylic acid) and poly(2-azainosinic acid). BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:441-51. [PMID: 361091 DOI: 10.1016/0005-2787(78)90241-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemically synthesized 2-azaadenosine 5'-diphosphate (n2ADP) and 2-azainosine 5'-diphosphate (n2IDP) were polymerized to yield poly(2-azaadenylic acid), poly(n2A), and poly(2-azainosinic acid), poly(n2I), using Escherichia coli polynucleotide phosphorylase. In neutral solution, poly(n2A) and poly(n2I) had hypochromicities of 32 and 5.5%, respectively. Poly(n2A) formed an ordered structure, which had a melting temperature (Rm) of 20 degrees C at 0.15 M salt concentration. Upon mixing with poly(U), poly(n2A) formed a 1 : 2 complex with Tm of 41 degrees C at 0.15 M salt concentration. Poly(n2A) and poly(n2I) formed three-stranded complexes with poly(I), and poly(A), respectively. Poly(n2A) . 2poly(I), poly(A) . 2poly(n2I), and poly(n2A) . 2poly(n2I) complexes had Tm values of 23, 48, and 31 degrees C at 0.15 M salt concentration, respectively. Poly(n2I) formed a double-stranded complex with poly(C), but its Tm was very low.
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Polynucleotides. LII. Synthesis and properties of poly(2'-deoxy-2'-fluoroadenylic acid). Nucleic Acids Res 1978; 5:1877-87. [PMID: 673838 PMCID: PMC342131 DOI: 10.1093/nar/5.6.1877] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
2'-Deoxy-2'-fluoroadenosine was chemically transformed to its 5'-diphosphate and polymerized with polynucleotide phosphorylase to give poly(2'-deoxy-2'-fluoroadenylic acid) [poly(Af)]. Polymerization proceeded smoothly as in the case of poly(A) and the yield of the polymerization was 55%. The UV absorption spectra of poly(Af) closely resembled those of poly(A) and the hypochromicity was 32% at pH 7.0. The CD profile at 25 degrees and neutrality showed similar pattern to that of other poly(2'-deoxy-2'-halogenoadenylic acids) with somewhat larger [theta] values both in the positive and negative maxima. Acid titration of poly(Af) showed a transition point at pH 5.2 and the Tm of the acid form was 37 degrees which was significantly lower than that of poly(A), but similar to that of poly(2'-azido-2'-deoxyadenylic acid). Poly(Af) formed 1:1 and 1:2 complexes with poly-(U) having Tm of 49 degrees and 62 degrees at 0.04M and 0.15M Na(+) concentration, respectively. Poly(Af) also formed a 1:2 complex with poly(I) and its Tm was 36 degrees at 0.05M Na(+) concentration. These data showed that poly(Af) has rather similar properties to those of poly(A), but not to poly(dA).
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Immunochemical measurement of conformational heterogeneity of poly(inosinic acid). EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:339-46. [PMID: 342235 DOI: 10.1111/j.1432-1033.1978.tb12028.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Several pure poly(I) preparations differed in: (a) their complement fixation reactivity with anti-poly(I) antiserum; (b) their ability to bind to a solid-phase anti-poly(I) antibody-Sepharose column; (c) their ability to inactivate serum complement; and (d) their reactivity with purified antibodies to double-stranded RNA. In particular, poly(I) samples that could induce interferon production differed from non-inducer poly(I)s; the inducers reacted weakly with anti-poly(I) antiserum and were the only ones that reacted with antibodies to double-stranded RNA. One inducer poly(I) did not inactivate complement, and differed from non-inducer poly(I) in quantitative aspects of poly(I) . poly(C) formation with varying amounts of poly(C). An additional type of poly(I) preparation reacted poorly with anti-poly(I) antiserum, did not react with anti-double-stranded-RNA antibodies and failed to induce interferon production. The varying forms of poly(I) were not interconvertible by boiling and rapid chilling. These results indicate that several different stable structural forms of poly(I) may result from a standardized synthetic procedure.
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Polynucleotides. L. Synthesis and properties of poly (2'-chloro-2'-deoxyadenylic acid) and poly (2'-bromo-2'-deoxyadenylic acid). Nucleic Acids Res 1977; 4:4249-60. [PMID: 341084 PMCID: PMC343238 DOI: 10.1093/nar/4.12.4249] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Poly (2'-chloro-2'-deoxyadenylic acid) and poly (2'-bromo-2'-deoxyadenylic acid) were synthesized from the corresponding diphosphates with the aid of polynucleotide phosphorylase from E. coli. UV, CD, acid titration and mixing with poly (U) were investigated. Comparing these properties with those of poly (A) and poly (2'-azido-2'-deoxyadenylic acid), it was found that 2''substituents exert significant effects on the thermal stability of these polynucleotides, though the overall conformational structure was not greatly changed.
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Polyribonucleotides containing thiopurines. Synthesis and properties of poly(1-methyl-6-thioguanylic acid). BIOCHIMICA ET BIOPHYSICA ACTA 1977; 479:16-23. [PMID: 20955 DOI: 10.1016/0005-2787(77)90121-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The synthesis of 1-methyl-6-thioguanosine 5'-diphosphate and its conversion to poly(1-methyl-6-thioguanylic acid) by means of polynucleotide phosphorylase are described. The polymer exhibited cooperative behavior (Tm = 294 K in the absence of added NaCl) characteristic of a highly stacked single-stranded helical array. In a high salt environment (0.5 M NaCl) the melting was much less cooperative and gave a higher Tm (313 K); this is suggestive of interstrand aggregation involving hydrogen bonding. The polynucleotide exhibited a remarkably high pKa (6.2) compared to that of the mononucleotide (2.6), and formed a very stable acid structure (Tm = 356 K in 50% ethylene glycol). Comparisons with poly(1-methyl-6-thioinosinic acid) and poly(6-thioguanylic acid) establish that both the 2-amino group and the 1-methyl group are required for the formation of the stable acid structure.
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A simplified method for selective removal of 3'-polyadenylic acid segments from ribonucleic acid [proceedings]. Biochem Soc Trans 1977; 5:956-7. [PMID: 334600 DOI: 10.1042/bst0050956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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41
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Synthesis and thermal melting behavior of oligomer-polymer complexes containing defined lengths of mismatched dA-dG and dG-dG nucleotides. Biochemistry 1977; 16:2367-74. [PMID: 301042 DOI: 10.1021/bi00630a009] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Model DNA polymers containing heteroduplex regions of defined sequence and size were synthesized using polynucleotide phosphorylase and calf thymus terminal transferase. Heteroduplexes were of the form (dG)n-d(C12AmC-x), where m - 1-6, and (dG)n-d(C10GmC-x), where m = 1 and 3-5. Thermal melting studies of the model DNAs indicated that the heteroduplex regions did not disrupt the cooperative interaction between the flanking regions of dG-dC base pairs. thus, it is possible that the heteroduplex nucleotides are accommodated in a stacked helical structure.
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A continuous high molecular weight base-paired structure is not an absolute requirement for a potential polynucleotide inducer of interferon. FEBS Lett 1977; 76:159-65. [PMID: 324799 DOI: 10.1016/0014-5793(77)80143-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Structural studies on intact and deadenylylated rabbit globin mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:233-52. [PMID: 1019346 DOI: 10.1016/s0079-6603(08)60922-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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45
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Polyribonucleotides containing thiopurines: synthesis and properties of poly (6-thioguanylic acid). Biochemistry 1976; 15:4386-9. [PMID: 974065 DOI: 10.1021/bi00665a006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The synthesis of poly(2-amino-6-chloropurinylic acid) [poly(n2cl6Pu)] by the polynucleotide phosphorylase catalyzed polymerization of 2-amino-6-chloro-9-(beta-D-ribofuranosyl)purine 5'-diphosphate and its chemical conversion to poly(6-thioguanylic acid) [poly(s6G)] is described. Poly(s6G) was found to form a relatively unstable complex with poly(C), the properties of which were incompatible with those previously reported for the same complex prepared by another method [Darlix, J.L., Fromageot, P., and Reich, E. (1973), Biochemistry 12, 914]. It was found that poly(s6G) could be thermally converted to a copolymer of which with poly(C) was strikingly similar to that reported earlier for poly(s6G)-poly(C).
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46
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Binding of complementary oligonucleotides to amino-acylated tRNAPhe from yeast. Biochem Biophys Res Commun 1976; 71:1025-33. [PMID: 788711 DOI: 10.1016/0006-291x(76)90757-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Preparation and properties of an analogue of poly(A) and poly(G): poly(isoguanylic acid). EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 65:183-92. [PMID: 776626 DOI: 10.1111/j.1432-1033.1976.tb10404.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isoguanosine-5'-pyrosphosphate, in the presence of an oligonucleotide primer, was polymerized by Escherichia coli polynucleotide phosphorylase under conditions analogous to those required for polymerization of 5'-GMP. The resulting poly(isoguanylic acid), poly(isoG), was a multistranded helix with a stability considerably higher than that of poly(G), and fully resistant to various nucleolytic enzymes. The polymer exhibited a two-step temperature transition profile in moderately alkaline propylene glycol. Alkaline titration in aqueous medium, by ultraviolet and circular dichroism spectroscopy, showed two clearly defined transitions, the second of which was fully cooperative. The accompanying changes in sedimentation constants were consistent with a structure for poly(isoG) of a fourstranded helix, like neutral poly(G). In acid medium, spectral and potentiometric titrations demonstrated the existence of more than one transition in the pH range 6-12, with accompanying protonation of the isoguanosine residues. In neutral medium the polymer formed no complexes with other potentially complementary homopolymers. In acid medium, on the other hand, the protonated form of poly(isoG) did form a triple-stranded complex with poly(I), viz. 2poly(I) . poly(isoG)+. Possible structures are formulated for the neural and protonated forms of poly(isoG) which account for the two-step thermal transition in alkaline propylene glycol and on alkaline titration in aqueous medium. The nature of the protonated form, and its complex with poly(I) is also discussed.
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The effect of thioketo substitution on uracil-2-aminopurine and uracil-2, 6-diaminopurine interactions in polynucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 432:192-8. [PMID: 773435 DOI: 10.1016/0005-2787(76)90161-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The existence of the complexes poly[r(s4U)] . poly[r(n2h6A] and poly-[r(s4U)] . poly[r(n2A)] was demonstrated by means of spectrophotometric titration and sedimentation veolicty analysis. According to the absorption-temperature profiles thioketo substitution of poly[r(U)] . poly[r(n2h6A)] led to stabilisation of the helical structure, thus implying that the 4-thioketo group does not participate in s4U . n2h6A base pairing. In the case of poly[r(s4U)] . poly[r(n2A)] drastic destabilistaion of the helical structure by thioketo substitution was observed. This indicates that the thioketo substituents participate in s4U .n2A base pairing.
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Combined enzymatic and chemical approaches to the synthesis of unique polyribonucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 425:278-86. [PMID: 177053 DOI: 10.1016/0005-2787(76)90254-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The enzymatic polymerization by polynucleotide phosphorylase of 6-chloro-9-(beta-D-ribofuranosyl)purine 5'-diphosphate to poly(6-chloropurinylic acid) and its conversion to poly(6-thioninosinic acid) is described. The sulfur isostere of poly(I) was found not to form a complex with poly(C), but to form a self-association complex with a Tm around 295 degrees K. The sedimentation velocities, pKa and Tm values of the polymer have been examined under various conditions. A two (or more) stranded helical array is suggested as the most probable structure. Thermal loss of the thione chromophore was noted for poly- (S6I), S6IMP and S6I; the degradation product from S6I was shown to be inosine.
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[Effect on coacervate systems of enzymatic synthesis of polyadenylic acid]. DOKLADY AKADEMII NAUK SSSR 1976; 226:972-4. [PMID: 1253689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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