Database : MEDLINE
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[PMID]: 29295980
[Au] Autor:Barragán-Iglesias P; Lou TF; Bhat VD; Megat S; Burton MD; Price TJ; Campbell ZT
[Ad] Address:School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, 75080, USA.
[Ti] Title:Inhibition of Poly(A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice.
[So] Source:Nat Commun;9(1):10, 2018 01 02.
[Is] ISSN:2041-1723
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:Nociceptors rely on cap-dependent translation to rapidly induce protein synthesis in response to pro-inflammatory signals. Comparatively little is known regarding the role of the regulatory factors bound to the 3' end of mRNA in nociceptor sensitization. Poly(A)-binding protein (PABP) stimulates translation initiation by bridging the Poly(A) tail to the eukaryotic initiation factor 4F complex associated with the mRNA cap. Here, we use unbiased assessment of PABP binding specificity to generate a chemically modified RNA-based competitive inhibitor of PABP. The resulting RNA mimic, which we designated as the Poly(A) SPOT-ON, is more stable than unmodified RNA and binds PABP with high affinity and selectivity in vitro. We show that injection of the Poly(A) SPOT-ON at the site of an injury can attenuate behavioral response to pain. Collectively, these results suggest that PABP is integral for nociceptive plasticity. The general strategy described here provides a broad new source of mechanism-based inhibitors for RNA-binding proteins and is applicable for in vivo studies.
[Mh] MeSH terms primary: Pain/metabolism
Poly A/metabolism
Poly(A)-Binding Proteins/metabolism
RNA/metabolism
[Mh] MeSH terms secundary: Animals
Cell Line, Tumor
Cells, Cultured
Ganglia, Spinal/cytology
Humans
Mice
Neurons/drug effects
Neurons/metabolism
Nociceptive Pain/metabolism
Nociceptive Pain/prevention & control
Pain/prevention & control
Pain Measurement
Poly A/chemistry
Poly A/pharmacology
Poly(A)-Binding Proteins/chemistry
Protein Binding
RNA/chemistry
RNA/pharmacology
[Pt] Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Name of substance:0 (Poly(A)-Binding Proteins); 24937-83-5 (Poly A); 63231-63-0 (RNA)
[Em] Entry month:1803
[Cu] Class update date: 180305
[Lr] Last revision date:180305
[Js] Journal subset:IM
[Da] Date of entry for processing:180104
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02449-5

  2 / 17225 MEDLINE  
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[PMID]: 29197495
[Au] Autor:Ramos-Alemán F; González-Jasso E; Pless RC
[Ad] Address:Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Instituto Politécnico Nacional, Cerro Blanco 141, Colonia Colinas del Cimatario, Querétaro, QRO 76090, Mexico.
[Ti] Title:Use of alternative alkali chlorides in RT and PCR of polynucleotides containing G quadruplex structures.
[So] Source:Anal Biochem;543:43-50, 2018 Feb 15.
[Is] ISSN:1096-0309
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Several alkali chlorides were compared for their use in reverse transcription (RT) and PCR of different types of nucleic acid templates. On a test region of biological DNA incapable of forming G quadruplex (G4) structures, Taq DNA polymerase showed similar PCR performance with 50 mM KCl, CsCl, LiCl, and NaCl. In contrast, on a synthetic model polydeoxyribonucleotide prone to G4 formation, good PCR amplification was obtained with 50 mM CsCl, but little or none with LiCl or KCl. Similarly, in RT of a G4-prone model polyribonucleotide, MMLV reverse transcriptase produced a good yield with 50 mM CsCl, mediocre yields with LiCl or without added alkali chloride, and a poor yield with 50 mM KCl. The full RT-PCR assay starting from the G4-prone polyribonucleotide, showed good results with CsCl in both stages, poor results with LiCl, and no product formation with KCl. The model polynucleotides showed fast G quadruplex formation under PCR or RT conditions with 50 mM KCl, but not with CsCl or LiCl. The results argue for the use of CsCl instead of KCl for RT and PCR of G4-prone sequences. No advantage was observed when using the 7-deaza type nucleotide analog c dGTP in PCR amplification of the G4-prone polydeoxyribonucleotide.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1712
[Cu] Class update date: 180224
[Lr] Last revision date:180224
[St] Status:In-Data-Review

  3 / 17225 MEDLINE  
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[PMID]: 29364650
[Au] Autor:Cao C; Long YT
[Ad] Address:Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology , Shanghai 200237, P. R. China.
[Ti] Title:Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.
[So] Source:Acc Chem Res;51(2):331-341, 2018 Feb 20.
[Is] ISSN:1520-4898
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1801
[Cu] Class update date: 180220
[Lr] Last revision date:180220
[St] Status:In-Data-Review
[do] DOI:10.1021/acs.accounts.7b00143

  4 / 17225 MEDLINE  
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[PMID]: 29247733
[Au] Autor:Stojkovic MR; Gonzalez-Garcia J; Supljika F; Galiana-Rosello C; Guijarro L; Gazze SA; Francis LW; Piantanida I; Garcia-Espana E
[Ad] Address:Division of Organic Chemistry & Biochemistry, Ruder Boskovic Institute, P. O. Box 180, 10002 Zagreb, Croatia.
[Ti] Title:Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives.
[So] Source:Int J Biol Macromol;109:143-151, 2018 Apr 01.
[Is] ISSN:1879-0003
[Cp] Country of publication:Netherlands
[La] Language:eng
[Ab] Abstract:Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1712
[Cu] Class update date: 180210
[Lr] Last revision date:180210
[St] Status:In-Process

  5 / 17225 MEDLINE  
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[PMID]: 29377197
[Au] Autor:McCue AC; Moreau WM; Shell TA
[Ad] Address:Department of Chemistry, Saint Anselm College, 100 Saint Anselm Drive, Manchester, New Hampshire, 03102, United States.
[Ti] Title:Visible Light-Induced Radical Mediated DNA Damage.
[So] Source:Photochem Photobiol;, 2018 Jan 27.
[Is] ISSN:1751-1097
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Light-responsive compounds have been used to manipulate biological systems with spatial and temporal control of the event of interest. Illumination of alkylcobalamins with green light (500 - 570 nm) produces carbon-centered radicals, which have been demonstrated to effectively cause DNA damage. Molecules that cause DNA and RNA strand scission are useful for studying polynucleotide structure and the binding of small molecules and proteins to polynucleotides. Most molecules that cause DNA damage in a light-dependent manner require high energy, short wavelength ultraviolet light, which is readily absorbed by nucleotide bases causing damage to the polynucleotides. Therefore, using alkylcobalamins is advantageous for causing strand scission of polynucleotides, because they are activated by light wavelengths that are not absorbed by nucleotide bases. Green light illumination of methylcobalamin effectively causes DNA strand scission based on gel mobility assays. This cleavage is due to the generation of carbon-centered radicals based on the results of a radical trapping study. In addition, synthesis of an alkylcobalamin with a DNA binding moiety, spermine, improves DNA cleavage efficacy by an order of magnitude in comparison to methylcobalamin. This article is protected by copyright. All rights reserved.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1801
[Cu] Class update date: 180206
[Lr] Last revision date:180206
[St] Status:Publisher
[do] DOI:10.1111/php.12890

  6 / 17225 MEDLINE  
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[PMID]: 29292352
[Au] Autor:Gallistel CR
[Ad] Address:Rutgers Center for Cognitive Science, 152 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA galliste@ruccs.rutgers.edu.
[Ti] Title:Finding numbers in the brain.
[So] Source:Philos Trans R Soc Lond B Biol Sci;373(1740), 2017 02 19.
[Is] ISSN:1471-2970
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:After listing functional constraints on what numbers in the brain must do, I sketch the two's complement fixed-point representation of numbers because it has stood the test of time and because it illustrates the non-obvious ways in which an effective coding scheme may operate. I briefly consider its neurobiological implementation. It is easier to imagine its implementation at the cell-intrinsic molecular level, with thermodynamically stable, volumetrically minimal polynucleotides encoding the remembered numbers, than at the circuit level, with plastic synapses encoding them.This article is part of a discussion meeting issue 'The origins of numerical abilities'.
[Pt] Publication type:JOURNAL ARTICLE; REVIEW
[Em] Entry month:1801
[Cu] Class update date: 180206
[Lr] Last revision date:180206
[St] Status:In-Process

  7 / 17225 MEDLINE  
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[PMID]: 29244187
[Au] Autor:Salinas-Giegé T; Cavaiuolo M; Cognat V; Ubrig E; Remacle C; Duchêne AM; Vallon O; Maréchal-Drouard L
[Ad] Address:Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France.
[Ti] Title:Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii.
[So] Source:Nucleic Acids Res;45(22):12963-12973, 2017 Dec 15.
[Is] ISSN:1362-4962
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:The unicellular photosynthetic organism, Chlamydomonas reinhardtii, represents a powerful model to study mitochondrial gene expression. Here, we show that the 5'- and 3'-extremities of the eight Chlamydomonas mitochondrial mRNAs present two unusual characteristics. First, all mRNAs start primarily at the AUG initiation codon of the coding sequence which is often marked by a cluster of small RNAs. Second, unusual tails are added post-transcriptionally at the 3'-extremity of all mRNAs. The nucleotide composition of the tails is distinct from that described in any other systems and can be partitioned between A/U-rich tails, predominantly composed of Adenosine and Uridine, and C-rich tails composed mostly of Cytidine. Based on 3' RACE experiments, 22% of mRNAs present C-rich tails, some of them composed of up to 20 consecutive Cs. Polycytidylation is specific to mitochondria and occurs primarily on mRNAs. This unprecedented post-transcriptional modification seems to be a specific feature of the Chlorophyceae class of green algae and points out the existence of novel strategies in mitochondrial gene expression.
[Mh] MeSH terms primary: Chlamydomonas reinhardtii/genetics
Mitochondria/genetics
RNA, Messenger/genetics
Transcription, Genetic
[Mh] MeSH terms secundary: Base Sequence
Chlamydomonas reinhardtii/metabolism
Chlorophyta/classification
Chlorophyta/genetics
Genome, Mitochondrial/genetics
Mitochondria/metabolism
Phylogeny
Poly C/metabolism
RNA, Messenger/metabolism
Sequence Homology, Nucleic Acid
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (RNA, Messenger); 0 (mitochondrial messenger RNA); 30811-80-4 (Poly C)
[Em] Entry month:1801
[Cu] Class update date: 180115
[Lr] Last revision date:180115
[Js] Journal subset:IM
[Da] Date of entry for processing:171216
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx903

  8 / 17225 MEDLINE  
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[PMID]: 28456523
[Au] Autor:Chikne V; Gupta SK; Doniger T; K SR; Cohen-Chalamish S; Waldman Ben-Asher H; Kolet L; Yahia NH; Unger R; Ullu E; Kolev NG; Tschudi C; Michaeli S
[Ad] Address:The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel.
[Ti] Title:The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei.
[So] Source:J Mol Biol;429(21):3301-3318, 2017 Oct 27.
[Is] ISSN:1089-8638
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:The parasite Trypanosoma brucei is the causative agent of African sleeping sickness and is known for its unique RNA processing mechanisms that are common to all the kinetoplastidea including Leishmania and Trypanosoma cruzi. Trypanosomes possess two canonical RNA poly (A) polymerases (PAPs) termed PAP1 and PAP2. PAP1 is encoded by one of the only two genes harboring cis-spliced introns in this organism, and its function is currently unknown. In trypanosomes, all mRNAs, and non-coding RNAs such as small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs), undergo trans-splicing and polyadenylation. Here, we show that the function of PAP1, which is located in the nucleus, is to polyadenylate non-coding RNAs, which undergo trans-splicing and polyadenylation. Major substrates of PAP1 are the snoRNAs and lncRNAs. Under the silencing of either PAP1 or PAP2, the level of snoRNAs is reduced. The dual polyadenylation of snoRNA intermediates is carried out by both PAP2 and PAP1 and requires the factors essential for the polyadenylation of mRNAs. The dual polyadenylation of the precursor snoRNAs by PAPs may function to recruit the machinery essential for snoRNA processing.
[Mh] MeSH terms primary: Poly A/genetics
Polyadenylation/genetics
Polynucleotide Adenylyltransferase/genetics
RNA, Messenger/genetics
RNA, Small Nucleolar/biosynthesis
RNA, Untranslated/genetics
Trypanosoma brucei brucei/enzymology
[Mh] MeSH terms secundary: Amino Acid Sequence
Pancreatitis-Associated Proteins
RNA Splicing
Sequence Alignment
Trypanosoma brucei brucei/genetics
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (Pancreatitis-Associated Proteins); 0 (REG3A protein, human); 0 (RNA, Messenger); 0 (RNA, Small Nucleolar); 0 (RNA, Untranslated); 24937-83-5 (Poly A); EC 2.7.7.19 (Polynucleotide Adenylyltransferase)
[Em] Entry month:1710
[Cu] Class update date: 180116
[Lr] Last revision date:180116
[Js] Journal subset:IM
[Da] Date of entry for processing:170501
[St] Status:MEDLINE

  9 / 17225 MEDLINE  
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[PMID]: 29245352
[Au] Autor:Mun JU; Cho HR; Choi YS; Kim YU
[Ad] Address:aDepartment of Orthopaedic Surgery, Changwon Gyeongsang National University Hospital, Republic of KoreabMyongji Hospital, College of Medicine, Seonam University, Goyang, KoreacDepartment of Anesthesiology and Pain Medicine, Catholic Kwandong University of Korea College of Medicine, International St. Mary's Hospital, Incheon, Republic of Korea.
[Ti] Title:Effect of multiple intra-articular injections of polynucleotides on treatment of intractable knee osteoarthritis: A case report.
[So] Source:Medicine (Baltimore);96(49):e9127, 2017 Dec.
[Is] ISSN:1536-5964
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:RATIONALE: Knee osteoarthritis (KOA) is a chronic joint degenerative disease. Intra-articular injection (IAI) of hyaluronic acid (HA) is widely used to treat KOA. However, some HA injections have no effect at all. Polynucleotides (PN) are recently noted as a valid substitute for HA. PATIENT CONCERNS: A 61-year-old female was admitted to the pain center with symptoms of pain over the knee and warmth feeling with stiffness in the left knee. The patient reported chronic severe pain in the left knee area despite 6 times IAI of HA. She had past medical history of breast cancer and thyroid cancer. DIAGNOSES: She was diagnosed as having KOA. INTERVENTIONS: Ultrasound-guided IAI of PN was carried out 3 times in 3 weeks. OUTCOMES: She was followed-up for more than 5 months with good improvement in intractable knee pain without any adverse event. LESSONS: IAI of PN is an efficient therapeutic option for KOA treatment if HA injection is unsuccessful.
[Mh] MeSH terms primary: Osteoarthritis, Knee/therapy
Polynucleotides/administration & dosage
[Mh] MeSH terms secundary: Female
Humans
Injections, Intra-Articular
Middle Aged
Polynucleotides/therapeutic use
Range of Motion, Articular
Ultrasonography, Interventional
[Pt] Publication type:CASE REPORTS; JOURNAL ARTICLE
[Nm] Name of substance:0 (Polynucleotides)
[Em] Entry month:1801
[Cu] Class update date: 180105
[Lr] Last revision date:180105
[Js] Journal subset:AIM; IM
[Da] Date of entry for processing:171217
[St] Status:MEDLINE
[do] DOI:10.1097/MD.0000000000009127

  10 / 17225 MEDLINE  
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[PMID]: 28741753
[Au] Autor:Vujcic V; Radic Brkanac S; Radojcic Redovnikovic I; Ivankovic S; Stojkovic R; Zilic I; Radic Stojkovic M
[Ad] Address:University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6/III, HR-10 000, Zagreb, Croatia.
[Ti] Title:Phytochemical and Bioactive Potential of in vivo and in vitro Grown Plants of Centaurea ragusina L. - Detection of DNA/RNA Active Compounds in Plant Extracts via Thermal Denaturation and Circular Dichroism.
[So] Source:Phytochem Anal;28(6):584-592, 2017 Nov.
[Is] ISSN:1099-1565
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:INTRODUCTION: The phytochemical composition and biological activity of non-volatile components of Centaurea ragusina L. has not been studied previously. OBJECTIVES: Our aim was to evaluate the phytochemical and bioactive potential (including interactions with polynucleotides) of C. ragusina L. depending on the origin of plant material (in vivo - leaves from natural habitats, ex vitro - leaves from plants acclimated from culture media, in vitro - leaves and calli from plants grown in culture media) and polarity of solvents used in extract preparation (80 and 96% ethanol and water combinations or single solvents). METHODOLOGY: The polyphenol composition was determined by spectrophotometric and HPLC analysis. Biological activity of extracts was evaluated by following methods: 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods for antioxidative activity, 2,3,5-triphenyl tetrazolium chloride (TTC) microdilution method for antibacterial activity, crystal-violet test for cytotoxic activity and thermal denaturation (TD) and circular dichroism (CD) for DNA/RNA interactions. RESULTS: Conditions for the most efficient polyphenol extraction were determined: the 80% ethanol/water solvent system was the most suitable for callus and leaf ex vitro samples and 80 or 96% ethanol for leaf in vivo samples. Significantly higher levels of chlorogenic acid and naringenin were detected in callus tissue than in vivo plant. Ethanolic extracts exhibited the significant antibacterial activity against Staphylococcus aureus ATCC 25923. DNA/RNA active compounds in plant extracts were detected by TD and CD methods. CONCLUSIONS: Callus tissue and ex vitro leaves represent a valuable source of polyphenols as in vivo leaves. TD and CD can be applied for detection of DNA/RNA active compounds in extracts from natural resources. Copyright © 2017 John Wiley & Sons, Ltd.
[Mh] MeSH terms primary: Centaurea/chemistry
DNA/chemistry
Phytochemicals/chemistry
Plant Extracts/chemistry
Polyphenols/chemistry
RNA/chemistry
[Mh] MeSH terms secundary: Chromatography, High Pressure Liquid
Circular Dichroism
Phytochemicals/metabolism
Spectrophotometry
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (Phytochemicals); 0 (Plant Extracts); 0 (Polyphenols); 63231-63-0 (RNA); 9007-49-2 (DNA)
[Em] Entry month:1801
[Cu] Class update date: 180105
[Lr] Last revision date:180105
[Js] Journal subset:IM
[Da] Date of entry for processing:170726
[St] Status:MEDLINE
[do] DOI:10.1002/pca.2708


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