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Solomun T, Cordsmeier L, Hallier DC, Seitz H, Hahn MB. Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study. J Phys Chem B 2023; 127:8131-8138. [PMID: 37704207 PMCID: PMC10544328 DOI: 10.1021/acs.jpcb.3c03669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Indexed: 09/15/2023]
Abstract
Gene-V protein (G5P/GVP) is a single-stranded (ss)DNA-binding protein (SBP) of bacteriophage f1 that is required for DNA synthesis and repair. In solution, it exists as a dimer that binds two antiparallel ssDNA strands with high affinity in a cooperative manner, forming a left-handed helical protein-DNA filament. Here, we report on fluorescence studies of the interaction of G5P with different DNA oligonucleotides having a hairpin structure (molecular beacon, MB) with a seven base-pair stem (dT24-stem7, dT18-stem7), as well as with DNA oligonucleotides (dT38, dT24) without a defined secondary structure. All oligonucleotides were end-labeled with a Cy3-fluorophore and a BHQ2-quencher. In the case of DNA oligonucleotides without a secondary structure, an almost complete quenching of their strong fluorescence (with about 5% residual intensity) was observed upon the binding of G5P. This implies an exact alignment of the ends of the DNA strand(s) in the saturated complex. The interaction of the DNA hairpins with G5P led to the unzipping of the base-paired stem, as revealed by fluorescence measurements, fluorescence microfluidic mixing experiments, and electrophoretic mobility shift assay data. Importantly, the disruption of ssDNA's secondary structure agrees with the behavior of other single-stranded DNA-binding proteins (SBPs). In addition, substantial protein-induced fluorescence enhancement (PIFE) of the Cy3-fluorescence was observed.
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Affiliation(s)
- Tihomir Solomun
- Bundesanstalt
für Materialforschung und -prüfung (BAM), Berlin 12205, Germany
| | - Leo Cordsmeier
- Bundesanstalt
für Materialforschung und -prüfung (BAM), Berlin 12205, Germany
- Institut
für Chemie, Freie Universität
Berlin, Berlin 14195, Germany
| | - Dorothea C. Hallier
- Bundesanstalt
für Materialforschung und -prüfung (BAM), Berlin 12205, Germany
- Institut
für Biochemie und Biologie, Universität
Potsdam, Potsdam 14476, Germany
- Fraunhofer
Institut für Zelltherapie und Immunologie Institutsteil Bioanalytik
und Bioprozesse IZI-BB, Potsdam 14476, Germany
| | - Harald Seitz
- Institut
für Biochemie und Biologie, Universität
Potsdam, Potsdam 14476, Germany
- Fraunhofer
Institut für Zelltherapie und Immunologie Institutsteil Bioanalytik
und Bioprozesse IZI-BB, Potsdam 14476, Germany
| | - Marc Benjamin Hahn
- Bundesanstalt
für Materialforschung und -prüfung (BAM), Berlin 12205, Germany
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2
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Yurenko YP, Novotný J, Mitoraj MP, Sklenář V, Michalak A, Marek R. Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems. J Chem Theory Comput 2014; 10:5353-65. [DOI: 10.1021/ct5007554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yevgen P. Yurenko
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
| | - Jan Novotný
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mariusz P. Mitoraj
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Vladimir Sklenář
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
| | - Artur Michalak
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Radek Marek
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
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3
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Yurenko YP, Novotný J, Sklenář V, Marek R. Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach. Phys Chem Chem Phys 2014; 16:2072-84. [DOI: 10.1039/c3cp53875c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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4
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Gold nanoparticle-based colorimetric detection of staphylococcal enterotoxin B using ssDNA aptamers. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-1995-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Prakash A, Natarajan A, Marky LA, Ouellette MM, Borgstahl GEO. Identification of the DNA-Binding Domains of Human Replication Protein A That Recognize G-Quadruplex DNA. J Nucleic Acids 2011; 2011:896947. [PMID: 21772997 PMCID: PMC3136212 DOI: 10.4061/2011/896947] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/11/2011] [Indexed: 12/26/2022] Open
Abstract
Replication protein A (RPA), a key player in DNA metabolism, has 6 single-stranded DNA-(ssDNA-) binding domains (DBDs) A-F. SELEX experiments with the DBDs-C, -D, and -E retrieve a 20-nt G-quadruplex forming sequence. Binding studies show that RPA-DE binds preferentially to the G-quadruplex DNA, a unique preference not observed with other RPA constructs. Circular dichroism experiments show that RPA-CDE-core can unfold the G-quadruplex while RPA-DE stabilizes it. Binding studies show that RPA-C binds pyrimidine- and purine-rich sequences similarly. This difference between RPA-C and RPA-DE binding was also indicated by the inability of RPA-CDE-core to unfold an oligonucleotide containing a TC-region 5′ to the G-quadruplex. Molecular modeling studies of
RPA-DE and telomere-binding proteins Pot1 and Stn1 reveal structural similarities between the proteins and illuminate potential DNA-binding sites for RPA-DE and Stn1. These data indicate that DBDs of RPA have different ssDNA recognition properties.
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Affiliation(s)
- Aishwarya Prakash
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
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6
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Taylor A, Taylor J, Watson GW, Boyd RJ. Electronic Energy Changes Associated with Guanine Quadruplex Formation: An Investigation at the Atomic Level. J Phys Chem B 2010; 114:9833-9. [DOI: 10.1021/jp912013k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexis Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Justine Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Graeme W. Watson
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
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7
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Selection and characterization of DNA aptamers for egg white lysozyme. Molecules 2010; 15:1127-40. [PMID: 20335968 PMCID: PMC6257241 DOI: 10.3390/molecules15031127] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/10/2010] [Accepted: 03/01/2010] [Indexed: 11/25/2022] Open
Abstract
We have selected aptamers binding to lysozyme from a DNA library using capillary electrophoresis-systematic evolution of ligands by exponential enrichment. During the selection process the dissociation constant of the ssDNA pool decreased from the micromolar to the low nanomolar range within five rounds of selection. The final aptamer had a dissociation constant of 2.8 ± 0.3 nM, 6.1 ± 0.5 nM, and 52.9 ± 9.1 nM as determined by fluorescence anisotropy, surface plasmon resonance and affinity capillary electrophoresis respectively. The aptamers were successfully challenged for specificity against other egg white proteins. The high affinity aptamers open up possibilities for the development of aptamer based food and medical diagnostics.
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8
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Fan JH, Bochkareva E, Bochkarev A, Gray DM. Circular dichroism spectra and electrophoretic mobility shift assays show that human replication protein A binds and melts intramolecular G-quadruplex structures. Biochemistry 2009; 48:1099-111. [PMID: 19187036 DOI: 10.1021/bi801538h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Noncanonical DNA structures such as G-quadruplexes might obstruct the binding of hRPA, compromising the accuracy of replication, and be a source of genomic instability. In this study, circular dichroism (CD) and electrophoretic mobility shift assay (EMSA) experiments were used to show that hRPA can bind and melt nontelomeric, intramolecular DNA G-quadruplexes under physiologically germane conditions. EMSA results show that hRPA binds to a 58-mer that includes an embedded quadruplex with an affinity equal to or greater than to nonquadruplex forming 58-mers. Moreover, hRPA binds to a 26-mer purine-rich quadruplex-forming sequence with an affinity indistinguishable from that for binding to the complementary pyrimidine-rich sequence. Under the same conditions, hRPA does not have significant affinity for binding to the duplex formed from the two sequences. Thus, DNA secondary structures can significantly modulate the binding affinity of hRPA over and above its known preference for pyrimidine-rich single-stranded sequences, so that at least some intramolecular G-quadruplex structures may not inhibit hRPA binding during DNA replication. CD spectral changes in combination with EMSA titrations suggest that one hRPA heterotrimer is sufficient to form a stable complex with an unfolded 26-mer G-quadruplex prior to the binding of a second hRPA molecule.
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Affiliation(s)
- Jun-Huei Fan
- Department of Molecular and Cell Biology, Mail Stop FO31, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, USA
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9
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Tombelli S, Bini A, Minunni M, Mascini M. Piezoelectric biosensors for aptamer-protein interaction. Methods Mol Biol 2009; 504:23-36. [PMID: 19159088 DOI: 10.1007/978-1-60327-569-9_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aptamers can be considered as a valid alternative to antibodies or other biomimetic receptors for the development of biosensors and other analytical methods. The production of aptamers is commonly performed by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) process, which, starting from large libraries of oligonucleotides, allows the isolation of large amounts of functional nucleic acids by an iterative process of in vitro selection and subsequent amplification through polymerase chain reaction. Aptamers are suitable for applications based on molecular recognition as analytical, diagnostic, and therapeutic tools. The use of aptamers as biorecognition element in piezoelectric biosensors will be here reported with particular application to the detection of thrombin.
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Affiliation(s)
- Sara Tombelli
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy
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10
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Ding JL, Gan ST, Ho B. Single-stranded DNA oligoaptamers: molecular recognition and LPS antagonism are length- and secondary structure-dependent. J Innate Immun 2008; 1:46-58. [PMID: 20375565 DOI: 10.1159/000145542] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 05/13/2008] [Indexed: 11/19/2022] Open
Abstract
In Gram-negative bacterial infection, lipopolysaccharide (LPS) readily overwhelms the host innate immune system, which could result in inflammation and sepsis in severe cases. Therefore, developing anti-LPS molecules would confer an efficient antibacterial strategy. We used SELEX (Systemic Evolution of Ligands by EXponential enrichment) to isolate single-stranded DNA (ssDNA) aptamers. By immobilizing and exposing different orientations of the LPS molecule on hydrophobic and hydrophilic surfaces, two populations of aptamers were captured from a library of 10(14-15) ssDNA oligonucleotides. Progressive SELEX enriched the aptamers towards thymidine residues. The more hydrophobic aptamers with T-rich loops showed strong molecular recognition for the lipid A moiety of LPS, binding at affinity of up to K(D) of 10(-9)M, and eliciting 95% neutralization of endotoxicity. The longer ssDNAs exhibited greater avidity for LPS and conferred more efficacious antagonism against LPS. The nucleotide composition imposes subtle influence on the aptamer folding and affinity for LPS.
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Affiliation(s)
- J L Ding
- Department of Biological Sciences, National University of Singapore, Singapore.
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11
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Gray DM, Wen JD, Gray CW, Repges R, Repges C, Raabe G, Fleischhauer J. Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality 2008; 20:431-40. [PMID: 17853398 DOI: 10.1002/chir.20455] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Circular dichroism (CD) spectroscopy is widely used to characterize the structures of DNA G-quadruplexes. CD bands at 200-300 nm have been empirically related to G-quadruplexes having parallel or antiparallel sugar-phosphate backbones. We propose that a more fundamental interpretation of the origin of the CD bands is in the stacking interactions of neighboring G-quartets, which can have the same or opposing polarities of hydrogen bond acceptors and donors. From an empirical summation of CD spectra of the d(G)5 G-quadruplex and of the thrombin binding aptamer that have neighboring G-quartets with the same and opposite polarities, respectively, the spectra of aptamers selected by the Ff gene 5 protein (g5p) appear to arise from a combination of the two types of polarities of neighboring G-quartets. The aptamer CD spectra resemble the spectrum of d(G3T4G3), in which two adjacent quartets have the same and two have opposite polarities. Quantum-chemical spectral calculations were performed using a matrix method, based on guanine chromophores oriented as in d(G3T4G3). The calculations show that the two types of G-quartet stacks have CD spectra with features resembling experimental spectra of the corresponding types of G-quadruplexes.
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Affiliation(s)
- Donald M Gray
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA.
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12
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Tombelli S, Minunni M, Mascini M. Aptamers-based assays for diagnostics, environmental and food analysis. ACTA ACUST UNITED AC 2007; 24:191-200. [PMID: 17434340 DOI: 10.1016/j.bioeng.2007.03.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/12/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Aptamers are single stranded DNA or RNA ligands which can be selected for different targets starting from a huge library of molecules containing randomly created sequences. Aptamers have been selected to bind very different targets, from proteins to small organic dyes. In addition to the very important aspect of having an unlimited source of identical affinity recognition molecules available due to the selection process, aptamers can offer advantages over antibodies that make them very promising for analytical applications. The use of aptamers as therapeutic tools is nowadays well established. On the contrary, the analytical application of aptamers in diagnostic devices or in systems for environmental and food analysis, is still under investigation and the scientific community still need further research to demonstrate the advancements brought by this new kind of ligands. This review will focus on these latter applications with particular attention to the detection of food pathogens, terrorism threat agents, thrombin and cytokines.
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Affiliation(s)
- Sara Tombelli
- Dipartimento di Chimica, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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13
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Phan AT, Kuryavyi V, Patel DJ. DNA architecture: from G to Z. Curr Opin Struct Biol 2006; 16:288-98. [PMID: 16714104 PMCID: PMC4689308 DOI: 10.1016/j.sbi.2006.05.011] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 04/10/2006] [Accepted: 05/10/2006] [Indexed: 12/27/2022]
Abstract
G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture. Results on novel structural elements, folding and unfolding kinetics, and interactions with small molecules and proteins have been reported recently for these forms. These results will enhance our understanding of the biology of these structures and provide a platform for drug design.
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Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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14
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Marin VL, Armitage BA. Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadruplex-forming RNA. Biochemistry 2006; 45:1745-54. [PMID: 16460021 PMCID: PMC2518313 DOI: 10.1021/bi051831q] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide nucleic acid (PNA) oligomers targeted to guanine quadruplex-forming RNAs can be designed in two different ways. First, complementary cytosine-rich PNAs can hybridize by the formation of Watson-Crick base pairs, resulting in hybrid PNA-RNA duplexes. Second, guanine-rich homologous PNAs can hybridize by the formation of G tetrads, resulting in hybrid PNA-RNA quadruplexes. UV thermal denaturation, circular dichroism, and fluorescence spectroscopy experiments were used to compare these two recognition modes and revealed 1:1 duplex formation for the complementary PNA and 2:1 (PNA2-RNA) quadruplex formation for the homologous PNA. Both hybrids were very stable, and hybridization was observed at low nanomolar concentrations. Hybrid quadruplex formation was equally efficient regardless of the PNA strand polarity, indicating a lack of interaction between the loop nucleobases on the PNA and RNA strands. The implications of this finding on sequence specificity as well as methods to improve affinity are also discussed.
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Affiliation(s)
| | - Bruce A. Armitage
- * To whom correspondence should be addressed. Phone: (412) 268-4196. Fax: (412) 268-1061. E-mail:
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15
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Tombelli S, Minunni M, Mascini M. Analytical applications of aptamers. Biosens Bioelectron 2004; 20:2424-34. [PMID: 15854817 DOI: 10.1016/j.bios.2004.11.006] [Citation(s) in RCA: 671] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/25/2004] [Accepted: 11/11/2004] [Indexed: 11/19/2022]
Abstract
So far, several bio-analytical methods have used nucleic acid probes to detect specific sequences in RNA or DNA targets through hybridisation. More recently, specific nucleic acids, aptamers, selected from random sequence pools, have been shown to bind non-nucleic acid targets, such as small molecules or proteins. The development of in vitro selection and amplification techniques has allowed the identification of specific aptamers, which bind to the target molecules with high affinity. Many small organic molecules with molecular weights from 100 to 10,000 Da have been shown to be good targets for selection. Moreover, aptamers can be selected against difficult target haptens, such as toxins or prions. The selected aptamers can bind to their targets with high affinity and even discriminate between closely related targets. Aptamers can thus be considered as a valid alternative to antibodies or other bio-mimetic receptors, for the development of biosensors and other analytical methods. The production of aptamers is commonly performed by the SELEX (systematic evolution of ligands by exponential enrichment) process, which, starting from large libraries of oligonucleotides, allows the isolation of large amounts of functional nucleic acids by an iterative process of in vitro selection and subsequent amplification through polymerase chain reaction. Aptamers are suitable for applications based on molecular recognition as analytical, diagnostic and therapeutic tools. In this review, the main analytical methods, which have been developed using aptamers, will be discussed together with an overview on the aptamer selection process.
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Affiliation(s)
- S Tombelli
- Università degli Studi di Firenze, Dipartimento di Chimica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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Wen JD, Gray DM. Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX. Nucleic Acids Res 2004; 32:e182. [PMID: 15601993 PMCID: PMC545477 DOI: 10.1093/nar/gnh179] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-stranded DNA or RNA libraries used in SELEX experiments usually include primer-annealing sequences for PCR amplification. In genomic SELEX, these fixed sequences may form base pairs with the central genomic fragments and interfere with the binding of target molecules to the genomic sequences. In this study, a method has been developed to circumvent these artificial effects. Primer-annealing sequences are removed from the genomic library before selection with the target protein and are then regenerated to allow amplification of the selected genomic fragments. A key step in the regeneration of primer-annealing sequences is to employ thermal cycles of hybridization-extension, using the sequences from unselected pools as templates. The genomic library was derived from the bacteriophage fd, and the gene 5 protein (g5p) from the phage was used as a target protein. After four rounds of primer-free genomic SELEX, most cloned sequences overlapped at a segment within gene 6 of the viral genome. This sequence segment was pyrimidine-rich and contained no stable secondary structures. Compared with a neighboring genomic fragment, a representative sequence from the family of selected sequences had about 23-fold higher g5p-binding affinity. Results from primer-free genomic SELEX were compared with the results from two other genomic SELEX protocols.
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Affiliation(s)
- Jin-Der Wen
- Department of Molecular and Cell Biology, Mail Stop FO 3.1, The University of Texas at Dallas, PO Box 830688, Richardson, TX 75083-0688, USA
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17
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Freede P, Brantl S. Transcriptional Repressor CopR: use of SELEX to study the copR operator indicates that evolution was directed at maximal binding affinity. J Bacteriol 2004; 186:6254-64. [PMID: 15342596 PMCID: PMC515161 DOI: 10.1128/jb.186.18.6254-6264.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CopR is one of the two copy number control elements of the streptococcal plasmid pIP501. It represses transcription of the repR mRNA encoding the essential replication initiator protein about 10- to 20-fold by binding to its operator region upstream of the repR promoter pII. CopR binds at two consecutive sites in the major groove of the DNA that share the consensus motif 5'-CGTG. Previously, the minimal operator was narrowed down to 17 bp, and equilibrium dissociation constants for DNA binding and dimerization were determined to be 0.4 nM and 1.4 microM, respectively. In this work, we used a SELEX procedure to study copR operator sequences of different lengths in combination with electrophoretic mobility shift assays of mutated copR operators as well as copy number determinations to assess the sequence requirements for CopR binding. The results suggest that in vivo evolution was directed at maximal binding affinity. Three simultaneous nucleotide exchanges outside the bases directly contacted by CopR only slightly affected CopR binding in vitro or copy numbers in vivo. Furthermore, the optimal spacer sequence was found to comprise 7 bp, to be AT rich, and to need an A/T and a T at the 3' positions, whereas broad variations in the sequences flanking the minimal 17-bp operator were well tolerated.
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Affiliation(s)
- Peggy Freede
- Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Hans-Knoll-Str. 2, Jena D-07745, Germany
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18
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Mou TC, Shen MC, Terwilliger TC, Gray DM. Binding and reversible denaturation of double-stranded DNA by Ff gene 5 protein. Biopolymers 2004; 70:637-48. [PMID: 14648774 DOI: 10.1002/bip.10500] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The gene 5 protein (g5p) from Ff filamentous virus is a model single-stranded DNA (ssDNA) binding protein that has an oligonucleotide/oligosaccharide binding (OB)-fold structure and binding properties in common with other ssDNA-binding proteins. In the present work, we use circular dichroism (CD) spectroscopy to analyze the effects of amino acid substitutions on the binding of g5p to double-stranded DNA (dsDNA) compared to its binding to ssDNA. CD titrations of poly[d(A). d(T)] with mutants of each of the five tyrosines of the g5p showed that the 229-nm CD band of Tyr34, a tyrosine at the interface of adjacent protein dimers, is reversed in sign upon binding to the dsDNA, poly[d(A). d(T)]. This effect is like that previously found for g5p binding to ssDNAs, suggesting there are similarities in the protein-protein interactions when g5p binds to dsDNA and ssDNA. However, there are differences, and the possible perturbation of a second tyrosine, Tyr41, in the complex with dsDNA. Three mutant proteins (Y26F, Y34F, and Y41H) reduced the melting temperature of poly[d(A). d(T)] by 67 degrees C, but the wild-type g5p only reduced it by 2 degrees C. This enhanced ability of the mutants to denature dsDNA suggests that their binding affinities to dsDNA are reduced more than are their binding affinities to ssDNA. Finally, we present evidence that when poly[d(A). d(T)] is melted in the presence of the wild-type, Y26F, or Y34F proteins, the poly[d(A)] and poly[d(T)] strands are separately sequestered such that renaturation of the duplex is facilitated in 2 mM Na(+).
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Affiliation(s)
- Tung-Chung Mou
- Department of Molecular and Cell Biology, Mail Stop FO31, University of Texas at Dallas, P.O. Box 830688, Richardson, TX 75083-0688, USA
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19
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Labrou NE. Design and selection of ligands for affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2003; 790:67-78. [PMID: 12767321 DOI: 10.1016/s1570-0232(03)00098-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Affinity chromatography is potentially the most selective method for protein purification. The technique has the purification power to eliminate steps, increase yields and thereby improve process economics. However, it suffers from problems regarding ligand stability and cost. Some of the most recent advances in this area have explored the power of rational and combinatorial approaches for designing highly selective and stable synthetic affinity ligands. Rational molecular design techniques, which are based on the ability to combine knowledge of protein structures with defined chemical synthesis and advanced computational tools, have made rational ligand design feasible and faster. Combinatorial approaches based on peptide and nucleic acid libraries have permitted the rapid synthesis of new synthetic affinity ligands of potential use in affinity chromatography. The versatility of these approaches suggests that, in the near future, they will become the dominant methods for designing and selection of novel affinity ligands with scale-up potential.
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Affiliation(s)
- N E Labrou
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855, Athens, Greece.
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You KM, Lee SH, Im A, Lee SB. Aptamers as functional nucleic acids:In vitro selection and biotechnological applications. BIOTECHNOL BIOPROC E 2003. [DOI: 10.1007/bf02940259] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Many important analytical methods are based on molecular recognition. Aptamers are oligonucleotides that exhibit molecular recognition; they are capable of specifically binding a target molecule, and have exhibited affinity for several classes of molecules. The use of aptamers as tools in analytical chemistry is on the rise due to the development of the "systematic evolution of ligands by exponential enrichment" (SELEX) procedure. This technique allows high-affinity aptamers to be isolated and amplified when starting from a large pool of oligonucleotide sequences. These molecules have been used in flow cytometry, biosensors, affinity probe electrophoresis, capillary electrochromatography, and affinity chromatography. In this paper, we will discuss applications of aptamers which have led to the development of aptamers as chromatographic stationary phases and applications of these stationary phases; and look towards future work which may benefit from the use of aptamers as stationary phases.
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Affiliation(s)
- Stacey L Clark
- Department of Chemistry, Oregon State University, Corvallis, OR 97331-4003, USA
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