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García JF, Reguera D, Valls A, Aviñó A, Dominguez A, Eritja R, Gargallo R. Detection of pyrimidine-rich DNA sequences based on the formation of parallel and antiparallel triplex DNA and fluorescent silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122752. [PMID: 37084680 DOI: 10.1016/j.saa.2023.122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.
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Affiliation(s)
- Juan Fernando García
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - David Reguera
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Andrea Valls
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Arnau Dominguez
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain.
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Flexible Implementation of the Trilinearity Constraint in Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) of Chromatographic and Other Type of Data. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072338. [PMID: 35408738 PMCID: PMC9000239 DOI: 10.3390/molecules27072338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 04/02/2022] [Indexed: 11/16/2022]
Abstract
Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) can analyze three-way data under the assumption of a trilinear model using the trilinearity constraint. However, the rigid application of this constraint can produce unrealistic solutions in practice due to the inadequacy of the analyzed data to the characteristics and requirements of the trilinear model. Different methods for the relaxation of the trilinear model data requirements have been proposed, like in the PARAFAC2 and in the direct non-trilinear decomposition (DNTD) methods. In this work, the trilinearity constraint of MCR-ALS is adapted to different data scenarios where the profiles of all or some of the components of the system are shifted (not equally synchronized) or even change their shape among different slices in one of their data modes. This adaptation is especially useful in gas and liquid chromatography (GC and LC) and in Flow Injection Analysis (FIA) with multivariate spectroscopic detection. In a first data example, a synthetic LC-DAD dataset is built to investigate the possibilities of the proposed method to handle systematic changes (shifts) in the retention times of the elution profiles and the results are compared with those obtained using alternative methods like ATLD, PARAFAC, PARAFAC2 and DNTD. In a second data example, multiple wine samples were simultaneously analyzed by GC-MS where elution profiles presented large deviations (shifts) in their peak retention times, although they still preserve the same peak shape. Different modelling scenarios are tested and the results are also compared. Finally, in the third example, sample mixtures of acid compounds were analyzed by FIA under a pH gradient and monitored by UV spectroscopy and also examined by different chemometric methods using a different number of components. In this case, however, the departure of the trilinear model comes from the acid base speciation of the system depending on the pH more than from the shifting of the FIA diffusion profiles.
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3
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de la Hoz A, Navarro A, Aviñó A, Eritja R, Gargallo R. Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences. RSC Adv 2021; 11:9029-9042. [PMID: 35423401 PMCID: PMC8695332 DOI: 10.1039/d1ra00194a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/15/2021] [Indexed: 12/22/2022] Open
Abstract
Silver nanoclusters (AgNCs) prepared by the reduction of silver ions in the presence of DNA oligonucleotides have attracted great interest as potential diagnostic tools for their tunable and high fluorescent properties. In this work, three DNA sequences that consist of a 12-nucleotide long probe sequence at the 5′-end linked to the complementary sequence to three miRNAs are studied. First, the interaction of these sequences with Ag(i) was characterized by means of circular dichroism spectroscopy. By applying multivariate methods to the analysis of spectroscopic data, two complexes with different Ag(i) : DNA ratios were resolved. Secondly, the impact of several experimental variables, such as temperature, borohydride concentration and reaction time, on the formation of AgNCs templated by these three sequences was studied. Finally, the fluorescence properties of the duplexes formed by DNA probes with complementary DNA or miRNA sequences were studied. The results presented here highlight the role of the secondary structure adopted by the DNA probe on the fluorescence properties of DNA-stabilized AgNCs which, in turn, affect the development of methods for miRNA detection. Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.![]()
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Affiliation(s)
- Alejandra de la Hoz
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Alba Navarro
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
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4
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de Juan A, Tauler R. Multivariate Curve Resolution: 50 years addressing the mixture analysis problem – A review. Anal Chim Acta 2021; 1145:59-78. [DOI: 10.1016/j.aca.2020.10.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/25/2020] [Indexed: 12/20/2022]
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5
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Abstract
Multivariate analysis (MA) is becoming a fundamental tool for processing in an efficient way the large amount of data collected in X-ray diffraction experiments. Multi-wedge data collections can increase the data quality in case of tiny protein crystals; in situ or operando setups allow investigating changes on powder samples occurring during repeated fast measurements; pump and probe experiments at X-ray free-electron laser (XFEL) sources supply structural characterization of fast photo-excitation processes. In all these cases, MA can facilitate the extraction of relevant information hidden in data, disclosing the possibility of automatic data processing even in absence of a priori structural knowledge. MA methods recently used in the field of X-ray diffraction are here reviewed and described, giving hints about theoretical background and possible applications. The use of MA in the framework of the modulated enhanced diffraction technique is described in detail.
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6
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Bruno F, Francischello R, Bellomo G, Gigli L, Flori A, Menichetti L, Tenori L, Luchinat C, Ravera E. Multivariate Curve Resolution for 2D Solid-State NMR spectra. Anal Chem 2020; 92:4451-4458. [PMID: 32069028 PMCID: PMC7997113 DOI: 10.1021/acs.analchem.9b05420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a processing method, based on the multivariate curve resolution approach (MCR), to denoise 2D solid-state NMR spectra, yielding a substantial S/N ratio increase while preserving the lineshapes and relative signal intensities. These spectral features are particularly important in the quantification of silicon species, where sensitivity is limited by the low natural abundance of the 29Si nuclei and by the dilution of the intrinsic protons of silica, but can be of interest also when dealing with other intermediate-to-low receptivity nuclei. This method also offers the possibility of coprocessing multiple 2D spectra that have the signals at the same frequencies but with different intensities (e.g.: as a result of a variation in the mixing time). The processing can be carried out on the time-domain data, thus preserving the possibility of applying further processing to the data. As a demonstration, we have applied Cadzow denoising on the MCR-processed FIDs, achieving a further increase in the S/N ratio and more effective denoising also on the transients at longer indirect evolution times. We have applied the combined denoising on a set of experimental data from a lysozyme-silica composite.
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Affiliation(s)
- Francesco Bruno
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Roberto Francischello
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Bellomo
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Alessandra Flori
- Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Luca Menichetti
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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7
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Benabou S, Mazzini S, Aviñó A, Eritja R, Gargallo R. A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor. Sci Rep 2019; 9:15807. [PMID: 31676783 PMCID: PMC6825181 DOI: 10.1038/s41598-019-52311-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023] Open
Abstract
Some lung and ovarian tumors are connected to the loss of expression of SMARCA4 gene. In its promoter region, a 44-nucleotides long guanine sequence prone to form G-quadruplex structures has been studied by means of spectroscopic techniques (circular dichroism, molecular absorption and nuclear magnetic resonance), size exclusion chromatography and multivariate analysis. The results have shown that the central 21-nucleotides long sequence comprising four guanine tracts of disparate length is able to fold into a pH-dependent ensemble of G-quadruplex structures. Based on acid-base titrations and melting experiments of wild and mutated sequences, the formation of a C·C+ base pair between cytosine bases present at the two lateral loops is shown to promote a reduction in conformational heterogeneity, as well as an increase in thermal stability. The formation of this base pair is characterized by a pKa value of 7.1 ± 0.2 at 20 °C and 150 mM KCl. This value, higher than those usually found in i-motif structures, is related to the additional stability provided by guanine tetrads in the G-quadruplex. To our knowledge, this is the first thermodynamic description of this base pair in loops of antiparallel G-quadruplex structures.
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Affiliation(s)
- Sanae Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain.
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8
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de Juan A, Tauler R. Data Fusion by Multivariate Curve Resolution. DATA HANDLING IN SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1016/b978-0-444-63984-4.00008-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Benito S, Ferrer A, Benabou S, Aviñó A, Eritja R, Gargallo R. Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:185-195. [PMID: 29448171 DOI: 10.1016/j.saa.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/16/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105M-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.
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Affiliation(s)
- S Benito
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Ferrer
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - S Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain.
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10
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Pandey S, Agarwala P, Jayaraj GG, Gargallo R, Maiti S. The RNA Stem-Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell. Biochemistry 2015; 54:7067-78. [PMID: 26554903 DOI: 10.1021/acs.biochem.5b00574] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K(+) and Mg(2+) ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quadruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.
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Affiliation(s)
- Satyaprakash Pandey
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Prachi Agarwala
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Gopal G Jayaraj
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Raimundo Gargallo
- Solution Equilibria and Chemometrics Group, Department of Analytical Chemistry, University of Barcelona , Diagonal 645, E-08028 Barcelona, Spain
| | - Souvik Maiti
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.,Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
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11
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Xia Z, Liu Y, Cai W, Shao X. Band target entropy minimization for retrieving the information of individual components from overlapping chromatographic data. J Chromatogr A 2015; 1411:110-5. [DOI: 10.1016/j.chroma.2015.07.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
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12
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13
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Wu X, Cai W, Shao X. Resolving overlapping GC–MS signals with a multistep screening chemometric approach for the fast determination of pesticides. J Sep Sci 2014; 37:828-34. [DOI: 10.1002/jssc.201301268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/26/2013] [Accepted: 01/13/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Xi Wu
- State Key Laboratory of Medicinal Chemical BiologyCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)Research Center for Analytical SciencesCollege of Chemistry, Nankai University Tianjin P.R. China
| | - Wensheng Cai
- State Key Laboratory of Medicinal Chemical BiologyCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)Research Center for Analytical SciencesCollege of Chemistry, Nankai University Tianjin P.R. China
| | - Xueguang Shao
- State Key Laboratory of Medicinal Chemical BiologyCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)Research Center for Analytical SciencesCollege of Chemistry, Nankai University Tianjin P.R. China
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14
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Chemometric Resolution for Rapid Determination of Prometryn in Leek Samples Using GC–MS. Chromatographia 2013. [DOI: 10.1007/s10337-013-2487-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Liu Z, Cai W, Shao X. High-throughput approach for analysis of multicomponent gas chromatographic–mass spectrometric signals. J Chromatogr A 2009; 1216:1469-75. [DOI: 10.1016/j.chroma.2008.12.098] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Revised: 12/24/2008] [Accepted: 12/31/2008] [Indexed: 11/28/2022]
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16
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Benavente F, Andón B, Giménez E, Olivieri AC, Barbosa J, Sanz-Nebot V. A multiway approach for classification and characterization of rabbit liver apothioneins by CE-ESI-MS. Electrophoresis 2008; 29:4355-67. [DOI: 10.1002/elps.200800212] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Richards SE, Wang Y, Lawler D, Kochhar S, Holmes E, Lindon JC, Nicholson JK. Self-modeling curve resolution recovery of temporal metabolite signal modulation in NMR spectroscopic data sets: application to a life-long caloric restriction study in dogs. Anal Chem 2008; 80:4876-85. [PMID: 18510345 DOI: 10.1021/ac702584g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A novel model-free statistical approach (self modeling curve resolution, SMCR) has been applied to recover biochemical information from complex overlapping signals in (1)H NMR spectra of blood serum in a long-term study of caloric restriction (CR) in the dog (n = 24 control fed (CF) and n = 24 CR animals). A new statistical spectroscopic construct, the spectrotype, is proposed which is a spectroscopic subset description or component of a metabolic phenotype. Characterization of the (1)H NMR profiles according to their evolutionary contribution of each spectrotype gives clues to the kinetics of the macro-biochemical response profiles and the identity of the underlying biochemical constituents, governing the evolutionary global response to an intervention. This information can be used to monitor and predict the end point of the biological process and to identify the mechanisms responsible for those changes. Here a SMCR strategy together with a pattern recognition method, principal component analysis (PCA) was used to resolve sets of spectrotypes, without a priori information. From the (1)H NMR evolutionary response profiles, two spectrotypes were identified and resolved; spectrotype 1 dominated by lipids featuring contributions from phosphatidylcholine, lipoprotein lipid fatty acyl groups from triglycerides, phospholipids, and cholesteryl esters plus total cholesterol (i.e., both esterified and unesterified); spectrotype 2 comprising glucose signals and a poorly resolved envelope of albumin and N-acetylated glycoprotein resonances. The relative contributions of these spectrotypes in each sample were calculated. For both caloric restricted (CR) and control fed (CF) dogs between ages 1 and 9 years, the contribution of spectrotype 2 > spectrotype 1, whereas for dogs aged between 9 and 12 years spectrotype 1 > spectrotype 2. Therefore, SMCR analysis pinpointed ages where nutrition and aging metabolic changes became significant within serum samples as well as providing the individual longitudinal contribution profiles associated with each spectrotype, which could potentially be used as part of a strategy to monitor and predict longevity and morbidity in populations. Hence SMCR is a useful addition to the chemometric "toolbox" for metabolic analysis and should have diverse applications within other biomedical conditions characterized by subtle time-dependent changes.
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Affiliation(s)
- Selena E Richards
- Department of Biomolecular Medicine, SORA Division, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington London, SW7 2AZ, UK.
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18
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de Juan A, Tauler R. Multivariate Curve Resolution (MCR) from 2000: Progress in Concepts and Applications. Crit Rev Anal Chem 2006. [DOI: 10.1080/10408340600970005] [Citation(s) in RCA: 396] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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