1
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Naoumi N, Michaelidou K, Papadakis G, Simaiaki AE, Fernández R, Calero M, Arnau A, Tsortos A, Agelaki S, Gizeli E. Acoustic Array Biochip Combined with Allele-Specific PCR for Multiple Cancer Mutation Analysis in Tissue and Liquid Biopsy. ACS Sens 2022; 7:495-503. [PMID: 35073481 DOI: 10.1021/acssensors.1c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regular screening of point mutations is of importance to cancer management and treatment selection. Although techniques like next-generation sequencing and digital polymerase chain reaction (PCR) are available, these are lacking in speed, simplicity, and cost-effectiveness. The development of alternative methods that can detect the extremely low concentrations of the target mutation in a fast and cost-effective way presents an analytical and technological challenge. Here, an approach is presented where for the first time an allele-specific PCR (AS-PCR) is combined with a newly developed high fundamental frequency quartz crystal microbalance array as biosensor for the amplification and detection, respectively, of cancer point mutations. Increased sensitivity, compared to fluorescence detection of the AS-PCR amplicons, is achieved through energy dissipation measurement of acoustically "lossy" liposomes binding to surface-anchored dsDNA targets. The method, applied to the screening of BRAF V600E and KRAS G12D mutations in spiked-in samples, was shown to be able to detect 1 mutant copy of genomic DNA in an excess of 104 wild-type molecules, that is, with a mutant allele frequency (MAF) of 0.01%. Moreover, validation of tissue and plasma samples obtained from melanoma, colorectal, and lung cancer patients showed excellent agreement with Sanger sequencing and ddPCR; remarkably, the efficiency of this AS-PCR/acoustic methodology to detect mutations in real samples was demonstrated to be below 1% MAF. The combined high sensitivity and technology-readiness level of the methodology, together with the ability for multiple sample analysis (24 array biochip), cost-effectiveness, and compatibility with routine workflow, make this approach a promising tool for implementation in clinical oncology labs for tissue and liquid biopsy.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Agapi E. Simaiaki
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Román Fernández
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Maria Calero
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Antonio Arnau
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, Crete 71500, Greece
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
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2
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Samarentsis AG, Pantazis AK, Tsortos A, Friedt JM, Gizeli E. Hybrid Sensor Device for Simultaneous Surface Plasmon Resonance and Surface Acoustic Wave Measurements. Sensors (Basel) 2020; 20:s20216177. [PMID: 33138312 PMCID: PMC7662402 DOI: 10.3390/s20216177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/19/2022]
Abstract
Surface plasmon resonance (SPR) and Love wave (LW) surface acoustic wave (SAW) sensors have been established as reliable biosensing technologies for label-free, real-time monitoring of biomolecular interactions. This work reports the development of a combined SPR/LW-SAW platform to facilitate simultaneous optical and acoustic measurements for the investigation of biomolecules binding on a single surface. The system’s output provides recordings of two acoustic parameters, phase and amplitude of a Love wave, synchronized with SPR readings. We present the design and manufacturing of a novel experimental set-up employing, in addition to the SPR/LW-SAW device, a 3D-printed plastic holder combined with a PDMS microfluidic cell so that the platform can be used in a flow-through mode. The system was evaluated in a systematic study of the optical and acoustic responses for different surface perturbations, i.e., rigid mass loading (Au deposition), pure viscous loading (glycerol and sucrose solutions) and protein adsorption (BSA). Our results provide the theoretical and experimental basis for future application of the combined system to other biochemical and biophysical studies.
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Affiliation(s)
- Anastasios G. Samarentsis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
| | - Alexandros K. Pantazis
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
- Institute of Electronic Structure & Laser, FO.R.T.H, Vassilika Vouton, 71409 Heraklion, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
| | - Jean-Michel Friedt
- SENSeOR SAS, Time and Frequency Department, FEMTO-ST Institute, 15B Avenue des Montboucons, 25030 Besançon, France;
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece; (A.G.S.); (A.T.)
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece;
- Correspondence: ; Tel.: +30-2810-394373
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3
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Milioni D, Mateos-Gil P, Papadakis G, Tsortos A, Sarlidou O, Gizeli E. Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection. Anal Chem 2020; 92:8186-8193. [PMID: 32449355 DOI: 10.1021/acs.analchem.0c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.
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Affiliation(s)
- Dimitra Milioni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Olga Sarlidou
- Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece.,Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
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4
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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5
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Papadakis G, Palladino P, Chronaki D, Tsortos A, Gizeli E. Sample-to-answer acoustic detection of DNA in complex samples. Chem Commun (Camb) 2017; 53:8058-8061. [DOI: 10.1039/c6cc10175e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The present study demonstrates the sensitive and label-free acoustic detection of dsDNA amplicons produced from whole Salmonella Thyphimurium cells without employing any DNA extraction and/or purification step, in the presence of the lysed bacterial cells and in a hybridization-free assay.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | | | - Dimitra Chronaki
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH
- Heraklion
- Greece
- Dept. of Biology
- Univ. of Crete
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6
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Chronaki D, Stratiotis DI, Tsortos A, Anastasiadou E, Gizeli E. Screening between normal and cancer human thyroid cells through comparative adhesion studies using the Quartz Crystal Microbalance. Sensing and Bio-Sensing Research 2016. [DOI: 10.1016/j.sbsr.2016.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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7
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Mansfield ML, Tsortos A, Douglas JF. Persistent draining crossover in DNA and other semi-flexible polymers: Evidence from hydrodynamic models and extensive measurements on DNA solutions. J Chem Phys 2016; 143:124903. [PMID: 26429037 DOI: 10.1063/1.4930918] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the scaling theory of polymer solutions has had many successes, this type of argument is deficient when applied to hydrodynamic solution properties. Since the foundation of polymer science, it has been appreciated that measurements of polymer size from diffusivity, sedimentation, and solution viscosity reflect a convolution of effects relating to polymer geometry and the strength of the hydrodynamic interactions within the polymer coil, i.e., "draining." Specifically, when polymers are expanded either by self-excluded volume interactions or inherent chain stiffness, the hydrodynamic interactions within the coil become weaker. This means there is no general relationship between static and hydrodynamic size measurements, e.g., the radius of gyration and the hydrodynamic radius. We study this problem by examining the hydrodynamic properties of duplex DNA in solution over a wide range of molecular masses both by hydrodynamic modeling using a numerical path-integration method and by comparing with extensive experimental observations. We also considered how excluded volume interactions influence the solution properties of DNA and confirm that excluded volume interactions are rather weak in duplex DNA in solution so that the simple worm-like chain model without excluded volume gives a good leading-order description of DNA for molar masses up to 10(7) or 10(8) g/mol or contour lengths between 5 μm and 50 μm. Since draining must also depend on the detailed chain monomer structure, future work aiming to characterize polymers in solution through hydrodynamic measurements will have to more carefully consider the relation between chain molecular structure and hydrodynamic solution properties. In particular, scaling theory is inadequate for quantitative polymer characterization.
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Affiliation(s)
- Marc L Mansfield
- Bingham Research Center, Utah State University, Vernal, Utah 84078, USA
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (FORTH), Vassilika Vouton, 70013 Heraklion, Greece
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institutes of Standards and Technology, Gaithersburg, Maryland 20899, USA
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8
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - George Papadakis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
- Department
of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion, Greece
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9
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Mateos-Gil P, Tsortos A, Vélez M, Gizeli E. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA. Chem Commun (Camb) 2016; 52:6541-4. [DOI: 10.1039/c6cc02127a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of structural changes in an intrinsically disordered protein attached on a QCM-D, with a sensitivity of 1.8 nm or better.
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Affiliation(s)
- Pablo Mateos-Gil
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | | | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica (ICP-CSIC)
- 28049 Madrid
- Spain
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Heraklion
- Greece
- Department of Biology
- University of Crete
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10
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Tsiavos T, Ioannidis NE, Tsortos A, Gizeli E, Kotzabasis K. Spermine is a potent modulator of proton transport through LHCII. J Plant Physiol 2015; 177:44-50. [PMID: 25659334 DOI: 10.1016/j.jplph.2015.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/18/2015] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
The effect of spermine on proton transport across large unilamellar liposomes containing incorporated complexes of the PSII antenna has been studied with the application of a pH-sensitive dye entrapped inside the vesicles. Both monomeric LHCbs and trimeric LHCII increased the permeability of proteoliposomes to protons when in a partly aggregated state within the lipid membrane. We have previously shown that a spermine-induced conformational change in LHCII results in its aggregation and ultimately in the enhancement of excitation energy as heat (qE). In this paper, spermine-induced aggregation of LHCII was found to facilitate proton transport across the proteoliposomes, indicating that a second protective mechanism (other than qE) might exist and might be regulated in vivo by polyamines when photosynthesis is saturated in excess light.
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Affiliation(s)
- Theodoros Tsiavos
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Nikolaos E Ioannidis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, FORTH, GR-70013 Heraklion, Crete, Greece
| | - Electra Gizeli
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece; Institute of Molecular Biology and Biotechnology, FORTH, GR-70013 Heraklion, Crete, Greece
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece.
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11
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Tsortos A, Grammoustianou A, Lymbouridou R, Papadakis G, Gizeli E. The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor. Chem Commun (Camb) 2015; 51:11504-7. [DOI: 10.1039/c5cc03436a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.
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12
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Papadakis G, Tsortos A, Kordas A, Tiniakou I, Morou E, Vontas J, Kardassis D, Gizeli E. Acoustic detection of DNA conformation in genetic assays combined with PCR. Sci Rep 2014; 3:2033. [PMID: 23778520 PMCID: PMC3686166 DOI: 10.1038/srep02033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 06/03/2013] [Indexed: 11/09/2022] Open
Abstract
Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.
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Affiliation(s)
- G Papadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Vassilika Vouton, 70013 Heraklion, Greece.
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13
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Mitsakakis K, Tsortos A, Gizeli E. Quantitative determination of protein molecular weight with an acoustic sensor; significance of specific versus non-specific binding. Analyst 2014; 139:3918-25. [DOI: 10.1039/c4an00616j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multi-analyte acoustic biosensor determines the molecular weight of proteinsviathe phase change of the acoustic signal.
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Affiliation(s)
- Konstantinos Mitsakakis
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Materials Science & Technology
- University of Crete
| | - Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology
- Foundation for Research & Technology Hellas
- GR-70013 Heraklion, Greece
- Department of Biology
- University of Crete
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14
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
| | - Florian Bender
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of
Electrical and
Computer Engineering, Marquette University, 1515 West Wisconsin Avenue, Milwaukee, Wisconsin 53233, United
States
| | - Elena E. Ferapontova
- Danish National Research
Foundation:
Center for DNA Nanotechnology, and Department of Chemistry and iNANO, Aarhus University, Ny Munkegade 1521, DK-8000 Aarhus
C, Denmark
| | - Electra Gizeli
- Institute of Molecular Biology
and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion,
Greece
- Department of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion,
Greece
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15
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Tsortos A, Papadakis G, Gizeli E. The intrinsic viscosity of linear DNA. Biopolymers 2011; 95:824-32. [PMID: 21638275 DOI: 10.1002/bip.21684] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 04/07/2011] [Accepted: 05/20/2011] [Indexed: 11/05/2022]
Abstract
We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research & Technology - Hellas (FO.R.T.H), Vassilika Vouton, 70013 Heraklion, Greece.
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16
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Papadakis G, Tsortos A, Gizeli E. Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction. Nano Lett 2010; 10:5093-5097. [PMID: 21038866 DOI: 10.1021/nl103491v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100 N. Plastira, Vassilika Vouton, 70013 Heraklion, Greece
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Saitakis M, Tsortos A, Gizeli E. Probing the interaction of a membrane receptor with a surface-attached ligand using whole cells on acoustic biosensors. Biosens Bioelectron 2010; 25:1688-93. [DOI: 10.1016/j.bios.2009.12.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/20/2009] [Accepted: 12/07/2009] [Indexed: 01/17/2023]
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18
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Tsortos A, Papadakis G, Gizeli E. Shear acoustic wave biosensor for detecting DNA intrinsic viscosity and conformation: A study with QCM-D. Biosens Bioelectron 2008; 24:842-7. [DOI: 10.1016/j.bios.2008.07.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/18/2008] [Accepted: 07/04/2008] [Indexed: 10/21/2022]
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Abstract
Acoustic devices were employed to characterize variations in the mechanical properties (density and viscoelasticity) of liposomes composed of 1-oleoyl-2-palmitoyl- sn-glycero-3-phosphocholine (POPC) and cholesterol. Liposome properties were modified in three ways. In some experiments, the POPC/cholesterol ratio was varied prior to deposition on the device surface. Alternatively, the ratio was changed in situ via either insertion of cholesterol or removal of cholesterol with beta-cyclodextrin. This was done for liposomes adsorbed directly on the device surface and for liposomes attached via a biotin-terminated poly(ethylene glycol) linker. The acoustic measurements make use of two simultaneous time-resolved signals: one signal is related to the velocity of the acoustic wave, while the second is related to dissipation of acoustic energy. Together, they provide information not only about the mass (or density) of the probed medium but also about its viscoelastic properties. The cholesterol-induced increase in the surface density of the lipid bilayer was indeed observed in the acoustic data, but the resulting change in signal was larger than expected from the change in surface density. In addition, increasing the bilayer resistance to stretching was found to lead to a greater dissipation of the acoustic energy. The acoustic response is assessed in terms of the possible distortions of the liposomes and the known effects of cholesterol on the mechanical properties of the lipid bilayer that encloses the aqueous core of the liposome. To aid the interpretation of the acoustic response, it is discussed how the above changes in the lipid bilayer will affect the effective viscoelastic properties of the entire liposome/solvent film on the scale of the acoustic wavelength. It was found that the acoustic device is very sensitive to the mechanical properties of lipid vesicles; the response of the acoustic device is explained, and the basic underlying mechanisms of interaction are identified.
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Affiliation(s)
- Kathryn A Melzak
- Institute of Molecular Biology and Biotechnology, FORTH, Vassilika Vouton, Heraklion/Crete, Greece
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20
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Tsortos A, Papadakis G, Mitsakakis K, Melzak KA, Gizeli E. Quantitative determination of size and shape of surface-bound DNA using an acoustic wave sensor. Biophys J 2008; 94:2706-15. [PMID: 18178642 PMCID: PMC2267124 DOI: 10.1529/biophysj.107.119271] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 11/12/2007] [Indexed: 11/18/2022] Open
Abstract
DNA bending plays a significant role in many biological processes, such as gene regulation, DNA replication, and chromosomal packing. Understanding how such processes take place and how they can, in turn, be regulated by artificial agents for individual oriented therapies is of importance to both biology and medicine. In this work, we describe the application of an acoustic wave device for characterizing the conformation of DNA molecules tethered to the device surface via a biotin-neutravidin interaction. The acoustic energy dissipation per unit mass observed upon DNA binding is directly related to DNA intrinsic viscosity, providing quantitative information on the size and shape of the tethered molecules. The validity of the above approach was verified by showing that the predesigned geometries of model double-stranded and triple-helix DNA molecules could be quantitatively distinguished: the resolution of the acoustic measurements is sufficient to allow discrimination between same size DNA carrying a bent at different positions along the chain. Furthermore, the significance of this analysis to the study of biologically relevant systems is shown during the evaluation of DNA conformational change upon protein (histone) binding.
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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research & Technology Hellas, Vassilika Vouton, 71110 Heraklion, Greece
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21
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Pyrpassopoulos S, Vlassi M, Tsortos A, Papanikolau Y, Petratos K, Vorgias CE, Nounesis G. Equilibrium heat-induced denaturation of chitinase 40 from Streptomyces thermoviolaceus. Proteins 2006; 64:513-23. [PMID: 16685709 DOI: 10.1002/prot.21003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
High-precision differential scanning calorimetry (DSC) and circular dichroism (CD) have been employed to study the thermal unfolding of chitinase 40 (Chi40) from Streptomyces thermoviolaceus. Chi40 belongs to family 18 of glycosyl hydrolase superfamily bearing a catalytic domain with a "TIM barrel"-like fold, which exhibits deviations from the (beta/alpha)8 fold. The thermal unfolding is reversible at pH = 8.0 and 9.0. The denatured state is characterized by extensive structural changes with respect to the native. The process is characterized by slow relaxation kinetics. Even slower refolding rates are recorded upon cooling. It is shown that the denaturation calorimetric data obtained at slow heating rate (0.17 K/min) are in excellent agreement with equilibrium data obtained by extrapolation of the experimental results to zero scanning rate. Analysis of the DSC results reveals that the experimental data can be successfully fitted using either a non-two-state sequential model involving one equilibrium intermediate, or an independent transitions model involving the unfolding of two Chi40 energetic domains to intermediate states. The stability of the native state with respect to the final denatured state is estimated, deltaG = 24.0 kcal/mol at 25 degrees C. The thermal results are in agreement with previous findings from chemical denaturation studies of a wide variety of (beta/alpha)8 barrel proteins, that their unfolding is a non-two-state process, always involving at least one unfolding intermediate.
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Maswadeh H, Demetzos C, Daliani I, Kyrikou I, Mavromoustakos T, Tsortos A, Nounesis G. A molecular basis explanation of the dynamic and thermal effects of vinblastine sulfate upon dipalmitoylphosphatidylcholine bilayer membranes. Biochim Biophys Acta 2002; 1567:49-55. [PMID: 12488037 DOI: 10.1016/s0005-2736(02)00564-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Differential scanning calorimetry has been employed to study the thermal effects of vinblastine sulfate upon aqueous, single and multiple bilayer dispersions of 1,2-dipalmitoyl-3-sn-phosphatidylcholine (DPPC). The calorimetric results summarized to an increase in the gel to liquid-crystalline phase transition enthalpy and the abolishment of the L(beta)' (gel phase) to P(beta)' (ripple phase) pretransition for the uni- and multilamellar dispersions, as well as an increase in the transition temperature T(m) and the transition cooperativity for single bilayer DPPC/vinblastine mixed vesicles, are consistent with an induced, partially interdigitated, gel phase. Computational analysis has been successfully applied to clarify the intermolecular effects and verify the feasibility of the proposed interdigitation for the vinblastine sulfate molecules and also for the ursodeoxycholic acid (UDCAH) and bromocylated taxanes, which have been shown to induce an interdigitated gel phase in DPPC bilayers.
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Affiliation(s)
- H Maswadeh
- Department of Pharmacognosy and Pharmaceutical Technology, School of Pharmacy, University of Athens, Panepistimioupolis Zographou, Athens 15571, Greece
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23
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Tsortos A, Yannakopoulou K, Eliadou K, Mavridis IM, Nounesis G. Partial Thermal Dethreading of [3]pseudorotaxanes of α-Cyclodextrin with Linear Aliphatic α,ω-Amino Acids in Aqueous Solution. J Phys Chem B 2001. [DOI: 10.1021/jp004015v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Achilleas Tsortos
- I/RRP and Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, 15310 Aghia Paraskevi, Athens, Greece
| | - Konstantina Yannakopoulou
- I/RRP and Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, 15310 Aghia Paraskevi, Athens, Greece
| | - Kyriaki Eliadou
- I/RRP and Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, 15310 Aghia Paraskevi, Athens, Greece
| | - Irene M. Mavridis
- I/RRP and Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, 15310 Aghia Paraskevi, Athens, Greece
| | - George Nounesis
- I/RRP and Institute of Physical Chemistry, National Center for Scientific Research “Demokritos”, 15310 Aghia Paraskevi, Athens, Greece
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Nock B, Maina T, Tsortos A, Pelecanou M, Raptopoulou CP, Papadopoulos M, Pietzsch HJ, Stassinopoulou CI, Terzis A, Spies H, Nounesis G, Chiotellis E. Glutathione Interaction with SNS/S Mixed-Ligand Complexes of Oxorhenium(V): Kinetic Aspects and Characterization of the Products. Inorg Chem 2000. [DOI: 10.1021/ic000350m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berthold Nock
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Theodosia Maina
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Achilleas Tsortos
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Maria Pelecanou
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Catherine P. Raptopoulou
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Minas Papadopoulos
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Hans-Jürgen Pietzsch
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Chariklia I. Stassinopoulou
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Aris Terzis
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Hartmut Spies
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Georgios Nounesis
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
| | - Efstratios Chiotellis
- Institute of RadioisotopesRadiodiagnostic Products, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Biology, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, Institute of Materials Science, National Centre for Scientific Research “Demokritos”, 15310 Ag. Paraskevi, Athens, Greece, and Institut für Bioanorganische und Radiopharmazeutische Chemie, Forschungszentrum Rossendorf, Postfach 510119, D-0314 Dresden,
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Abstract
The adsorption of two polyelectrolytes, poly-L-Glutamate and poly-L-Aspartate, on hydroxyapatite (HAP) crystals was studied both experimentally and theoretically. Langmuir adsorption isotherms were obtained for both these molecules, with binding constants K = 6 x 10(6) and 3 x 10(6) M-1, respectively, at 37.0 degreesC, pH 7.4, and 0.15 M ionic strength. A theoretical analysis of the data, based on a model proposed by Hesselink, suggested a "train-loop" type of adsorption with non-electrostatic energy terms 3.51 and 4.76 (kT) for poly-L-Glu and poly-L-Asp, respectively. Copyright 1999 Academic Press.
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Affiliation(s)
- A Tsortos
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 14260
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26
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Nancollas GH, Tsortos A, Zieba A. The nucleation and growth of calcium phosphate crystals at protein and phosphatidylserine liposome surfaces. Scanning Microsc 1998; 10:499-507; discussion 508. [PMID: 9813627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The kinetics of calcium phosphate crystal growth at the surfaces of proteins and phospholipids has been investigated using free drift and constant composition methods in supersaturated calcium phosphate solutions (relative supersaturations: with respect to hydroxyapatite, HAP, sigma HAP = 15.0, and with respect to octacalcium phosphate, OCP, sigma OCP = 1.9). Fibrinogen and collagen molecules adsorbed at hydrophobic surfaces as well as uncross-linked collagen fibrils induce ion binding and subsequent nucleation of calcium phosphate. The formation of OCP on phosphatidylserine vesicles introduced to highly supersaturated calcium phosphate solutions probably involves the interaction of the calcium ions with the ionized carboxylic groups of the phospholipid.
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Affiliation(s)
- G H Nancollas
- Department of Chemistry, State University of New York at Buffalo, Amherst, USA
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27
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Tsortos A, Ohki S, Zieba A, Baier RE, Nancollas GH. The Dual Role of Fibrinogen as Inhibitor and Nucleator of Calcium Phosphate Phases: The Importance of Structure. J Colloid Interface Sci 1996; 177:257-262. [PMID: 10479440 DOI: 10.1006/jcis.1996.0029] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Constant composition and free drift methods have been used to investigate the abilities of human serum albumin (HSA) and fibrinogen to influence calcium phosphate precipitation. Both molecules inhibit hydroxyapatite (HAP) crystal growth when present in the solution phase. Fibrinogen, when immobilized at hydrophobicized germanium or silica surfaces, is able to nucleate calcium phosphate phases; at clean germanium or silica surfaces, it appears to be inactive. The apparent configuration of fibrinogen molecules at germanium or silica surfaces on which octadecyltrichlorosilane (OTS) was deposited probably exposes more negative sites for participation in nucleation.
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Affiliation(s)
- A Tsortos
- Chemistry Department, State University of New York at Buffalo, Buffalo, New York, 14260
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