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Wettstein C, Kyne C, Doolan AM, Möhwald H, Crowley PB, Lisdat F. Study of cytochrome c-DNA interaction--evaluation of binding sites on the redox protein. NANOSCALE 2014; 6:13779-13786. [PMID: 25286363 DOI: 10.1039/c4nr05301j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Artificial assemblies consisting of the cationic cytochrome c (cyt c) and double-stranded DNA are interesting for the field of biohybrid systems because of the high electro-activity of the incorporated redox protein. However, little is known about the interactions between these two biomolecules. Here, the complex of reduced cyt c and a 41 base pair oligonucleotide was characterized in solution as a function of pH and ionic strength. Persistent cyt c-DNA agglomerates were observed by UV-vis and DLS (dynamic light scattering) at pH 5.0 and low ionic strength. The strength of the interaction was attenuated by raising the pH or the ionic strength. At pH 7.0 agglomerates were not formed, allowing interaction analysis by NMR spectroscopy. Using TROSY (transverse relaxation-optimized spectroscopy)-HSQC (heteronuclear single quantum coherence) experiments it was possible to identify the DNA binding site on the cyt c surface. Numerous residues surrounding the exposed heme edge of cyt c were involved in transient binding to DNA under these conditions. This result was supported by SEC (size exclusion chromatography) experiments at pH 7.0 showing that the interaction is sufficient for co-elution of cyt c and DNA.
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Affiliation(s)
- Christoph Wettstein
- Technical University of Applied Sciences Wildau, Institute of Applied Life Sciences, Biosystems Technology, Hochschulring 1, 15745 Wildau, Germany.
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Pavón N, Buelna-Chontal M, Hernández-Esquivel L, Hernández S, Chávez E, Condé R, Lanz-Mendoza H. Mitochondrial inactivation by Anopheles albimanus cecropin 3: molecular mechanisms. Peptides 2014; 53:202-9. [PMID: 23880546 DOI: 10.1016/j.peptides.2013.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 01/14/2023]
Abstract
Cecropin 3 (Ccrp3) is an antimicrobial peptide from Anopheles albimanus, which is expressed during Plasmodium berghei infection. Here, we report that synthetic Ccrp3, aside from antibacterial activity, also shows cardio regulatory functions. In rats, Ccrp3 significantly diminishes blood pressure as well as the heartbeat frequency at nanomolar concentration. Ccrp3 affect the rat cardiac muscle mitochondria, inducing uncoupling of oxidative phosphorylation, oxygen consumption and transport of Ca(2). Ccrp3 treatment of the mitochondria causes mitochondrial damage promoting oxidative stress, causing overproduction of reactive oxygen species (ROS) and inhibition of superoxide dismutase. At nM concentration, Ccrp3 inhibits superoxide dismutase activity through direct interaction, diminishing by its enzymatic activity. Ccrp3 induces the release of the pro-apoptotic marker Bax from the mitochondria. Altogether, these results suggest that Ccrp3 pro-oxidative activity on cardiac muscle mitochondria could be responsible for triggering the heartbeat frequency and blood pressure lowering observed the Ccrp3 injected rats.
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Affiliation(s)
- Natalia Pavón
- Departamento de Farmacología. Dirección de investigación, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, CP 14080 Tlalpan, DF, Mexico
| | - Mabel Buelna-Chontal
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, CP 14080 Tlalpan, DF, Mexico
| | - Luz Hernández-Esquivel
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No.1, Col. Sección XVI, CP 14080 Tlalpan, DF, Mexico
| | - Sauri Hernández
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, CP 14080 Tlalpan, DF, Mexico
| | - Edmundo Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No.1, Col. Sección XVI, CP 14080 Tlalpan, DF, Mexico
| | - Renaud Condé
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, CP 62501 Cuernavaca, Morelos, Mexico
| | - Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, CP 62501 Cuernavaca, Morelos, Mexico.
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Properties of an LNA-modified ricin RNA aptamer. Biochem Biophys Res Commun 2012; 419:60-5. [PMID: 22326915 DOI: 10.1016/j.bbrc.2012.01.127] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 11/21/2022]
Abstract
'Locked nucleic acids' (LNAs) are sugar modified nucleic acids containing the 2'-O-4'C-methylene-β-D-ribofuranoses. The substitution of RNAs with LNAs leads to an enhanced thermostability. Aptamers are nucleic acids, which are selected for specific target binding from a large library pool by the 'SELEX' method. Introduction of modified nucleic acids into aptamers can improve their stability. The stem region of a ricin A chain RNA aptamer was substituted by locked nucleic acids. Different constructs of the LNA-substituted aptamers were examined for their thermostability, binding activity, folding and RNase sensitivity as compared to the natural RNA counterpart. The LNA-modified aptamers were active in target binding, while the loop regions and the adjacent stem nucleotides remained unsubstituted. The thermostability and RNase resistance of LNA substituted aptamers were enhanced as compared to the native RNA aptamer. This study supports the approach to substitute the aptamer stem region by LNAs and to leave the loop region unmodified, which is responsible for ligand binding. Thus, LNAs possess an encouraging potential for the development of new stabilized nucleic acids and will promote future diagnostic and therapeutic applications.
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Schlachter C, Lisdat F, Frohme M, Erdmann VA, Konthur Z, Lehrach H, Glökler J. Pushing the detection limits: the evanescent field in surface plasmon resonance and analyte-induced folding observation of long human telomeric repeats. Biosens Bioelectron 2011; 31:571-4. [PMID: 22152989 DOI: 10.1016/j.bios.2011.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/02/2011] [Accepted: 11/03/2011] [Indexed: 12/17/2022]
Abstract
Conventional analysis of molecular interactions by surface plasmon resonance is achieved by the observation of optical density changes due to analyte binding to the ligand on the surface. Low molecular weight interaction partners are normally not detected. However, if a macromolecule such as DNA can extend beyond the evanescent field and analyte interaction results in a large-scale contraction, then the refractive index changes due to the increasing amount of macromolecules close to the surface. In our proof-of-principle experiment we could observe the direct folding of long, human telomeric repeats induced by the small analyte potassium using surface plasmon resonance spectroscopy. This work demonstrates the feasibility of new evanescent field-based biosensors that can specifically observe small molecule interactions.
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Affiliation(s)
- Constanze Schlachter
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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Witte C, Lisdat F. Direct Detection of DNA and DNA-Ligand Interaction by Impedance Spectroscopy. ELECTROANAL 2010. [DOI: 10.1002/elan.201000410] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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McCarthy JEG, Marsden S, von der Haar T. Biophysical studies of the translation initiation pathway with immobilized mRNA analogs. Methods Enzymol 2008; 430:247-64. [PMID: 17913641 DOI: 10.1016/s0076-6879(07)30010-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
A growing number of biophysical techniques use immobilized reactants for the quantitative study of macromolecular reactions. Examples of such approaches include surface plasmon resonance, atomic force microscopy, total reflection fluorescence microscopy, and others. Some of these methods have already been adapted for work with immobilized RNAs, thus making them available for the study of many reactions relevant to translation. Published examples include the study of kinetic parameters of protein/RNA interactions and the effect of helicases on RNA secondary structure. The common denominator of all of these techniques is the necessity to immobilize RNA molecules in a functional state on solid supports. In this chapter, we describe a number of approaches by which such immobilization can be achieved, followed by two specific examples for applications that use immobilized RNAs.
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Affiliation(s)
- John E G McCarthy
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
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Tombelli S, Minunni M, Luzi E, Mascini M. Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 2005; 67:135-41. [PMID: 16027048 DOI: 10.1016/j.bioelechem.2004.04.011] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 03/04/2004] [Accepted: 04/01/2004] [Indexed: 11/29/2022]
Abstract
Two biosensors have been constructed using an RNA aptamer as biorecognition element. The aptamer, specific for HIV-1 Tat protein, has been immobilised on the gold surface of piezoelectric quartz crystals or surface plasmon resonance (SPR) chips to develop a quartz crystal microbalance (QCM)-based and an SPR-based biosensor, respectively. Both the biosensors were modified with the same immobilisation chemistry based on the binding of a biotinylated aptamer on a layer of streptavidin. The binding between the immobilised aptamer and its specific protein has been evaluated with the two biosensors in terms of sensitivity, reproducibility and selectivity. A protein very similar to Tat, Rev protein, has been used as negative control. The two biosensors both were very reproducible in the immobilisation and the binding steps. The selectivity was high in both cases.
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Affiliation(s)
- S Tombelli
- Università degli Studi di Firenze, Dipartimento di Chimica Polo Scientifico di Sesto Fiorentino Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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Minunni M, Tombelli S, Gullotto A, Luzi E, Mascini M. Development of biosensors with aptamers as bio-recognition element: the case of HIV-1 Tat protein. Biosens Bioelectron 2004; 20:1149-56. [PMID: 15556361 DOI: 10.1016/j.bios.2004.03.037] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 03/02/2004] [Accepted: 03/04/2004] [Indexed: 10/26/2022]
Abstract
The in vitro selection of combinatorial libraries of RNA/DNA, has allowed the identification of specific nucleic acids (aptamers) which bind to a wide range of target molecules with high affinity and specificity. In this work, an RNA aptamer, specific for the protein trans-activator of transcription (Tat) of HIV-1, has been used as bio-recognition element to develop a biosensor (aptasensor). The biosensor was optimised using piezoelectric quartz-crystals as transducers and the aptamer was immobilised on the gold electrode of the crystal. The immobilisation procedure was based on the interaction between the biotinylated aptamer and streptavidin previously deposited on the electrode. The main analytical characteristics of the biosensor, such as sensitivity, selectivity and reproducibility, have been studied in details. An optimised regeneration procedure allowed the multiple use of the aptamer-coated crystal. The aptasensor has been compared with the corresponding immunosensor, based on the specific monoclonal anti-Tat antibody. The antibody was immobilised on a layer of carboxylated dextran previously deposited on the gold electrode. The results demonstrated that the use of a biosensor with a specific aptamer as bio-recognition element could be an interesting approach in the detection of proteins, which has been here examined considering a model system.
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Affiliation(s)
- M Minunni
- Università degli Studi di Firenze, Dipartimento di Chimica, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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