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Guo X, Wang X, Huang D, Zhang J, Xu D, Yang W, Hu Q, Fang Z, Huang T. Method study on determination of total purine content in fish meat by diazotization reaction combined with SERS. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Morla-Folch J, Alvarez-Puebla RA, Guerrini L. Direct Quantification of DNA Base Composition by Surface-Enhanced Raman Scattering Spectroscopy. J Phys Chem Lett 2016; 7:3037-3041. [PMID: 27441814 DOI: 10.1021/acs.jpclett.6b01424] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Design of ultrasensitive DNA sensors based on the unique physical properties of plasmonic nanostructures has become one of the most exciting areas in nanomedicine. However, despite the vast number of proposed applications, the determination of the base composition in nucleic acids, a fundamental parameter in genomic analyses and taxonomic classification, is still restricted to time-consuming and poorly sensitive conventional methods. Herein, we demonstrate the possibility of determining the base composition in single- and double-stranded DNA by using a simple, low-cost, high-throughput, and label-free surface-enhanced Raman scattering (SERS) method in combination with cationic nanoparticles.
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Affiliation(s)
- Judit Morla-Folch
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
- Centro Tecnológico de la Química de Catalunya and Universitat Rovira I Virgili , Carrer de Marcel•lí Domingo s/n, 43007 Tarragona, Spain
| | - Ramon A Alvarez-Puebla
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
- Centro Tecnológico de la Química de Catalunya and Universitat Rovira I Virgili , Carrer de Marcel•lí Domingo s/n, 43007 Tarragona, Spain
- ICREA , Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Luca Guerrini
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
- Centro Tecnológico de la Química de Catalunya and Universitat Rovira I Virgili , Carrer de Marcel•lí Domingo s/n, 43007 Tarragona, Spain
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Stentoft C, Vestergaard M, Løvendahl P, Kristensen NB, Moorby JM, Jensen SK. Simultaneous quantification of purine and pyrimidine bases, nucleosides and their degradation products in bovine blood plasma by high performance liquid chromatography tandem mass spectrometry. J Chromatogr A 2014; 1356:197-210. [PMID: 25017393 DOI: 10.1016/j.chroma.2014.06.065] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 05/09/2014] [Accepted: 06/11/2014] [Indexed: 11/17/2022]
Abstract
Improved nitrogen utilization in cattle is important in order to secure a sustainable cattle production. As purines and pyrimidines (PP) constitute an appreciable part of rumen nitrogen, an improved understanding of the absorption and intermediary metabolism of PP is essential. The present work describes the development and validation of a sensitive and specific method for simultaneous determination of 20 purines (adenine, guanine, guanosine, inosine, 2'-deoxyguanosine, 2'-deoxyinosine, xanthine, hypoxanthine), pyrimidines (cytosine, thymine, uracil, cytidine, uridine, thymidine, 2'-deoxyuridine), and their degradation products (uric acid, allantoin, β-alanine, β-ureidopropionic acid, β-aminoisobutyric acid) in blood plasma of dairy cows. The high performance liquid chromatography-based technique coupled to electrospray ionization tandem mass spectrometry (LC-MS/MS) was combined with individual matrix-matched calibration standards and stable isotopically labelled reference compounds. The quantitative analysis was preceded by a novel pre-treatment procedure consisting of ethanol precipitation, filtration, evaporation and reconstitution. Parameters for separation and detection during the LC-MS/MS analysis were investigated. It was confirmed that using a log-calibration model rather than a linear calibration model resulted in lower CV% and a lack of fit test demonstrated a satisfying linear regression. The method covers concentration ranges for each metabolite according to that in actual samples, e.g. guanine: 0.10-5.0 μmol/L, and allantoin: 120-500 μmol/L. The CV% for the chosen quantification ranges were below 25%. The method has good repeatability (CV%≤25%) and intermediate precision (CV%≤25%) and excellent recoveries (91-107%). All metabolites demonstrated good long-term stability and good stability within-runs (CV%≤10%). Different degrees of absolute matrix effects were observed in plasma, urine and milk. The determination of relative matrix effects revealed that the method was suitable for almost all examined PP metabolites in plasma drawn from an artery and the portal hepatic, hepatic and gastrosplenic veins and, with a few exceptions, also for other species such as chicken, pig, mink, human and rat.
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Affiliation(s)
- Charlotte Stentoft
- Department of Animal Science, Aarhus University, Blichers Allé 20, DK 8830 Tjele, Denmark.
| | - Mogens Vestergaard
- Department of Animal Science, Aarhus University, Blichers Allé 20, DK 8830 Tjele, Denmark.
| | - Peter Løvendahl
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, DK 8830 Tjele, Denmark.
| | | | - Jon M Moorby
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE Wales, UK.
| | - Søren Krogh Jensen
- Department of Animal Science, Aarhus University, Blichers Allé 20, DK 8830 Tjele, Denmark.
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Zitka O, Skutkova H, Adam V, Trnkova L, Babula P, Hubalek J, Provaznik I, Kizek R. A New Approach how to Define the Coefficient of Electroactivity of Adenine and Its Twelve Derivatives Using Flow Injection Analysis with Amperometric Detection. ELECTROANAL 2011. [DOI: 10.1002/elan.201100064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Reiter GF, Senesi R, Mayers J. Changes in the zero-point energy of the protons as the source of the binding energy of water to A-phase DNA. PHYSICAL REVIEW LETTERS 2010; 105:148101. [PMID: 21230870 DOI: 10.1103/physrevlett.105.148101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Indexed: 05/30/2023]
Abstract
The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6 water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Å.
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Affiliation(s)
- G F Reiter
- Physics Department, University of Houston, Houston, Texas 77204, USA
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Liang L, Dou P, Dong M, Ke X, Bian N, Liu Z. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing. Anal Chim Acta 2009; 650:106-10. [PMID: 19720180 DOI: 10.1016/j.aca.2009.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 12/16/2008] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
Abstract
Nuclease P1 is an important enzyme that hydrolyzes RNA or single-stranded DNA into nucleotides, and complete digestion is an essential basis for assays based on this enzyme. To digest a doubled-stranded DNA, the enzyme is usually combined with heat denaturing, which breaks doubled-stranded DNA into single strands. This paper presents an un-expected phenomenon that nuclease P1, in combination with heat denaturing, fails to completely digest a DNA sample extracted from salmon sperm. Under the experimental conditions used, at which nuclease P1 can completely digest calf thymus DNA, the digestion yield of salmon sperm DNA was only 89.5%. Spectrometric measurement indicated that a total protein of 4.7% is present in the DNA sample. To explain the reason for this phenomenon, the dynamic kinetic capillary isoelectric focusing (DK-CIEF) approach proposed previously, which allows for the discrimination of different types of protein-DNA interactions and the measurement of the individual dissociation rate constants, was modified and applied to examine possible protein-DNA interactions involved. It was found that a non-specific DNA-protein binding occurs in the sample, the dissociation rate constant for which was measured to be 7.05+/-0.83x10(-3) s(-1). The formation of DNA-protein complex was suggested to be the main reason for the incomplete digestion of the DNA sample. The modified DK-CIEF approach can be applied as general DNA samples, with the advantages of fast speed and low sample consumption.
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Affiliation(s)
- Liang Liang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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Hua NP, Hamza-Chaffai A, Vreeland RH, Isoda H, Naganuma T. Virgibacillus salarius sp. nov., a halophilic bacterium isolated from a Saharan salt lake. Int J Syst Evol Microbiol 2008; 58:2409-14. [PMID: 18842865 DOI: 10.1099/ijs.0.65693-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, endospore-forming, rod-shaped and moderately halophilic bacterium was isolated from a salt-crust sample collected from Gharsa salt lake (Chott el Gharsa), Tunisia. The newly isolated bacterium, designated SA-Vb1(T), was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Strain SA-Vb1(T) was closely related to the type strains of Virgibacillus marismortui and Virgibacillus olivae, with 16S rRNA gene sequence similarities of 99.7 and 99.4 %, respectively. However, strain SA-Vb1(T) was distinguished from these two type strains on the basis of phenotypic characteristics and DNA-DNA relatedness (29.4 and 5.1 %, respectively). The genetic relationship between strain SA-Vb1(T) and Virgibacillus pantothenticus IAM 11061(T) (the type strain of the type species) and other type strains of the genus was 96-98 % based on 16S rRNA gene sequence similarity and 18.3-22.3 % based on DNA-DNA hybridization. Biochemical analysis resulted in determination of major fatty acids iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0) (33.3, 29.2 and 9.8 %, respectively); phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine were the main polar lipids and MK-7 was the predominant menaquinone ( approximately 100 %). The distinct characteristics demonstrated by strain SA-Vb1(T) represent properties of a novel species of the genus Virgibacillus, for which the name Virgibacillus salarius sp. nov. is proposed. The type strain is SA-Vb1(T) (=JCM 12946(T) =DSM 18441(T)).
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Affiliation(s)
- Ngoc-Phuc Hua
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-hiroshima 739-8528, Japan
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Separation of purine and pyrimidine bases by ion chromatography with direct conductivity detection. J Chromatogr A 2008; 1193:104-8. [DOI: 10.1016/j.chroma.2008.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 04/01/2008] [Accepted: 04/08/2008] [Indexed: 11/21/2022]
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Hua NP, Kanekiyo A, Fujikura K, Yasuda H, Naganuma T. Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep. Int J Syst Evol Microbiol 2007; 57:1243-1249. [PMID: 17551037 DOI: 10.1099/ijs.0.64817-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1
ω7c alcohol and C18 : 1
ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.
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MESH Headings
- Bacillaceae/classification
- Bacillaceae/cytology
- Bacillaceae/isolation & purification
- Bacillaceae/physiology
- Bacterial Typing Techniques
- Base Composition
- Cold Temperature
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Hydrostatic Pressure
- Japan
- Locomotion
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Quinones/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spores, Bacterial
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Affiliation(s)
- Ngoc-Phuc Hua
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
| | - Atsuko Kanekiyo
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka 237-0061, Japan
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
| | - Hisato Yasuda
- Center for Advanced Marine Core Research, Kochi University, Monobe, Nankoku 783-8502, Japan
| | - Takeshi Naganuma
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
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