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A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019; 24:molecules24162877. [PMID: 31398834 PMCID: PMC6718989 DOI: 10.3390/molecules24162877] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer-analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer's affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer's affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin-TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein-aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M-1s-1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer-ion and aptamer-protein interactions.
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Swiatkowska A, Kosman J, Juskowiak B. FRET study of G-quadruplex forming fluorescent oligonucleotide probes at the lipid monolayer interface. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:614-621. [PMID: 25698056 DOI: 10.1016/j.saa.2015.01.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
Spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes at the cationic dioctadecyldimethylammonium bromide (DODAB) monolayer interface are reported. Two oligonucleotides, a 19-mer bearing thrombin binding aptamer sequence and a 21-mer with human telomeric sequence, were end-labeled with fluorescent groups (FAM and TAMRA) to give FRET probes F19T and F21T, respectively. The probes exhibited abilities to fold into a quadruplex structure and to bind metal cations (Na(+) and K(+)). Fluorescence spectra of G-quadruplex FRET probes at the monolayer interface are reported for the first time. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter. The effect of the presence of DODAB monolayer, metal cations and the surface pressure of monolayer on spectral behavior of FRET probes were examined. Adsorption of probe at the cationic monolayer interface resulted in the FRET signal enhancement even in the absence of metal cations. Variation in the monolayer surface pressure exerted rather modest effect on the spectral properties of probes. The fluorescence energy transfer efficiency of monolayer adsorbed probes increased significantly in the presence of sodium or potassium ion in subphase, which indicated that the probes retained their cation binding properties when adsorbed at the monolayer interface.
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Affiliation(s)
- Angelika Swiatkowska
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland
| | - Joanna Kosman
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland
| | - Bernard Juskowiak
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland.
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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Yuminova AV, Smirnova IG, Arutyunyan AM, Kopylov AM, Golovin AV, Pavlova GV. The structure of G-quadruplex thrombine-binding DNA aptamer RA36. ACTA ACUST UNITED AC 2015. [DOI: 10.3103/s0027131415010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Effect of Cholesterol Anchoring Group on the Properties of G-Quadruplex-Based FRET Probes for Potassium Ion. CHEMOSENSORS 2014. [DOI: 10.3390/chemosensors2040267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jayaraj GG, Pandey S, Scaria V, Maiti S. Potential G-quadruplexes in the human long non-coding transcriptome. RNA Biol 2014; 9:81-6. [DOI: 10.4161/rna.9.1.18047] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Arnaut V, Langecker M, Simmel FC. Nanopore force spectroscopy of aptamer-ligand complexes. Biophys J 2014; 105:1199-207. [PMID: 24010663 DOI: 10.1016/j.bpj.2013.07.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 01/07/2023] Open
Abstract
The stability of aptamer-ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans-cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer-target interactions in this case, the stability of the ligand-free aptamer-containing G-quadruplexes-is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified.
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Affiliation(s)
- Vera Arnaut
- Lehrstuhl für Bioelektronik, Physik Department, Technische Universität München, Garching, Germany
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Liu B, Li D. Structural transformation induced by locked nucleic acid or 2'-O-methyl nucleic acid site-specific modifications on thrombin binding aptamer. Chem Cent J 2014; 8:19. [PMID: 24642032 PMCID: PMC4000052 DOI: 10.1186/1752-153x-8-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/13/2014] [Indexed: 11/25/2022] Open
Abstract
Background Locked nucleic acid (LNA) and 2'–O-methyl nucleic acid (OMeNA) are two of the most extensively studied nucleotide derivatives in the last decades. However, how they affect DNA quadruplex structures remains largely unknown. To explore their possible biological affinities for quadruplexes, we investigated how LNA- or OMeNA-substitutions affect G-quadruplex structure formation using a thrombin binding aptamer (TBA), the most studied extracorporal G-quadruplex-forming DNA sequence, which is frequently modified to increase its analytical performance. Results The experimental results showed that when two or more nucleotides were substituted with LNA or OMeNA, the anti-parallel TBA structure was transformed into an unstructured random conformation in a 50 mM K+ environment; OMeNA appeared to have greater power to induce this transformation. However, the native TBA was unstructured in a 50 mM Ca2+ environment, whereas four or more LNA- or OMeNA- substitutions could convert this unstructured TBA into a parallel quadruplex structure. PAGE mobility measurements suggested that these TBAs might be a dimeric form. Conclusion LNA or 2'-OMeNA site-specific modifications induced G-quadruplex structural transformation of TBA, which enriched our understanding of the intrinsic G-quadrupex forming property and affinity of LNA and OMeNA modifications. This study demonstrates possible applications in the regulation of gene expression (i.e. manual intervention of gene therapy), genetic analyses, molecular diagnosis and the construction of nano-scale biostructures.
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Affiliation(s)
- Bo Liu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang 110001, China.
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Wu TC, Vasudev M, Dutta M, Stroscio MA. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer. IEEE Trans Nanobioscience 2013; 12:93-7. [PMID: 23694695 DOI: 10.1109/tnb.2013.2242484] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.
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Affiliation(s)
- Tsai-Chin Wu
- Bioengineering Department, University of Illinois, Chicago, IL 60607, USA.
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12
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Zhou W, Suntharalingam K, Brand NJ, Barton PJR, Vilar R, Ying L. Possible regulatory roles of promoter g-quadruplexes in cardiac function-related genes - human TnIc as a model. PLoS One 2013; 8:e53137. [PMID: 23326389 PMCID: PMC3541360 DOI: 10.1371/journal.pone.0053137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/23/2012] [Indexed: 12/15/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in oncogene promoters has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. We have explored the possible regulatory roles of promoter G4s in cardiac function-related genes using both computational and a wide range of experimental approaches. According to our bioinformatics results, it was found that potential G4-forming sequences are particularly enriched in the transcription regulatory regions (TRRs) of cardiac function-related genes. Subsequently, the promoter of human cardiac troponin I (TnIc) was chosen as a model, and G4s found in this region were subjected to biophysical characterisations. The chromosome 19 specific minisatellite G4 sequence (MNSG4) and near transcription start site (TSS) G4 sequence (−80 G4) adopt anti-parallel and parallel structures respectively in 100 mM KCl, with stabilities comparable to those of oncogene G4s. It was also found that TnIc G4s act cooperatively as enhancers in gene expression regulation in HEK293 cells, when stabilised by a synthetic G4-binding ligand. This study provides the first evidence of the biological significance of promoter G4s in cardiac function-related genes. The feasibility of using a single ligand to target multiple G4s in a particular gene has also been discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Nigel J. Brand
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
| | - Paul J. R. Barton
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Liming Ying
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- * E-mail:
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Yuminova AV, Spiridonova VA, Arutyunyan AM, Kopylov AM. Structural study of thrombin binding DNA aptamers by the circular dichroism. DOKL BIOCHEM BIOPHYS 2012; 442:36-8. [PMID: 22419092 DOI: 10.1134/s1607672912010115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Indexed: 11/22/2022]
Affiliation(s)
- A V Yuminova
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, Russia
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15
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Lane AN. The stability of intramolecular DNA G-quadruplexes compared with other macromolecules. Biochimie 2011; 94:277-86. [PMID: 21854828 DOI: 10.1016/j.biochi.2011.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/04/2011] [Indexed: 11/19/2022]
Abstract
DNA quadruplexes are often conceived as very stable structures. However, most of the free energy of stabilization derives from specific ion binding via inner sphere coordination of the GO6 of the guanine residues comprising the basic quartet. When compared with other nucleic acid structures such as DNA or RNA duplexes and hairpins, or proteins of the same number of atoms, metal-coordinated intramolecular quadruplexes are found to be of comparable or lower thermodynamic stability under similar solution conditions. Furthermore, intramolecular quadruplexes are actually less stable kinetically, than DNA duplexes or hairpins of the same size. Although the literature is incomplete, it is clear that polyelectrolyte ion effects, the influence of solvation and steric crowding on stability are qualitatively different between intramolecular quadruplexes and DNA duplexes. For example, decreasing water activity destabilizes DNA duplexes, whereas quadruplexes are stabilized. The variety of folded conformations accessible to a single sequence further implies strong sensitivity of the conformational ensemble to the solution conditions, compared with DNA duplexes or small single domain proteins. These considerations may have relevance to the conditions prevailing inside cell nuclei and therefore the structures that potentially might form in vivo.
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Affiliation(s)
- Andrew N Lane
- JG Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
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Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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Hong ES, Yoon HJ, Kim B, Yim YH, So HY, Shin SK. Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1245-1255. [PMID: 20434362 DOI: 10.1016/j.jasms.2010.03.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/09/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
The binding sites and consecutive binding constants of alkali metal ions, (M(+) = Na(+), K(+), Rb(+), and Cs(+)), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5-8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA-metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.
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Affiliation(s)
- Eun Sun Hong
- Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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Kendrick S, Hurley LH. The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements. ACTA ACUST UNITED AC 2010; 82:1609-1621. [PMID: 21796223 DOI: 10.1351/pac-con-09-09-29] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The nature of DNA has captivated scientists for more than fifty years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression.
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Trajkovski M, Sket P, Plavec J. Cation localization and movement within DNA thrombin binding aptamer in solution. Org Biomol Chem 2009; 7:4677-84. [PMID: 19865704 DOI: 10.1039/b914783g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The thrombin binding aptamer, 15-mer oligonucleotide d[G(2)T(2)G(2)TGTG(2)T(2)G(2)], was folded into the well known antiparallel unimolecular G-quadruplex in the presence of (15)NH(4)(+) ions. Although the formed G-quadruplex is thermodynamically less stable than in the presence of K(+) ions, the loop conformations and folding topology are the same. On the other hand, titration of Na(+) ions into an aqueous solution of TBA resulted in the formation of one major and several minor species of G-quadruplexes. Solution-state NMR was used to localize (15)NH(4)(+) ions between the two G-quartets within the core of the structure, and to determine the equilibrium binding constant, which equals 190 M(-1). No other potential cation binding sites were resolved on the time-scale of NMR spectrometer. Exchange of (15)NH(4)(+) ions between the inner binding site and bulk solution is characterized by the exchange rate constant of 1.0 s(-1) at 15 degrees C. T4 and T13 form a noncanonical base pair, which greatly affects access of bulk ions into the cation binding site in the G-quadruplex core. G2 and G11 exhibit out of plane bending towards the two TT loops away from the bound (15)NH(4)(+) ions, which in turn exposes them to more efficient chemical exchange processes with bulk ions and water.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Human telomeric G-quadruplex formed from duplex under near physiological conditions: Spectroscopic evidence and kinetics. Biochimie 2009; 91:1104-11. [DOI: 10.1016/j.biochi.2009.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022]
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Hall B, Cater S, Levy M, Ellington AD. Kinetic optimization of a protein-responsive aptamer beacon. Biotechnol Bioeng 2009; 103:1049-59. [PMID: 19431189 DOI: 10.1002/bit.22355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aptamers have been utilized as biosensors because they can be readily adapted to sensor platforms and signal transduction schemes through both rational design and selection. One highly generalizable scheme for the generation of the so-called aptamer beacons involves denaturing the aptamer with antisense oligonucleotides. For example, rational design methods have been utilized to adapt anti-thrombin aptamers to function as biosensors by hybridizing an antisense oligonucleotide containing a quencher to the aptamer containing a fluorescent label. In the presence of thrombin, the binding equilibrium is shifted, the antisense oligonucleotide dissociates, and the beacon lights up. By changing the affinity of the antisense oligonucleotide for the aptamer beacon, it has proven possible to change the extent of activation of the beacon. More importantly, modulating interactions between the antisense oligonucleotide and the aptamer strongly influences the kinetics of activation. Comparisons across multiple, designed aptamer beacons indicate that there is a strong inverse correlation between the thermodynamics of hybridization and the speed of activation, a finding that should prove to be generally useful in the design of future biosensors. By pre-organizing the thrombin-binding quadruplex within the aptamer the speed of response can be greatly increased. By integrating these various interactions, we were ultimately able to design aptamer beacons that were activated by threefold within 1 min of the addition of thrombin.
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Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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22
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Arora A, Nair DR, Maiti S. Effect of flanking bases on quadruplex stability and Watson-Crick duplex competition. FEBS J 2009; 276:3628-40. [PMID: 19490117 DOI: 10.1111/j.1742-4658.2009.07082.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Guanine-rich DNA sequences have the ability to fold into four-stranded structures called G-quadruplexes, and are considered as promising anticancer targets. Although the G-quadruplex structure is composed of quartets and interspersed loops, in the genome it is also flanked on each side by numerous bases. The effect of loop length and composition on quadruplex conformation and stability has been well investigated in the past, but the effect of flanking bases on quadruplex stability and Watson-Crick duplex competition has not been addressed. We have studied in detail the effect of flanking bases on quadruplex stability and on duplex formation by the G-quadruplex in the presence of complementary strands using the quadruplex-forming sequence located in the promoter region of the c-kit oncogene. The results obtained from CD, thermal difference spectrum and UV melting demonstrated the effect of flanking bases on quadruplex structure and stability. With the increase in flank length, the increase in the more favorable DeltaH(vH) is accompanied by a striking increase in the unfavorable DeltaS(vH), which resulted in a decrease in the overall DeltaG(vH) of quadruplex formation. Furthermore, CD, fluorescence and isothermal titration calorimetry studies demonstrated that the propensity to attain quadruplex structure decreases with increasing flank length.
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Affiliation(s)
- Amit Arora
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, Delhi, India
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23
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Kumar N, Basundra R, Maiti S. Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium. Nucleic Acids Res 2009; 37:3321-31. [PMID: 19324889 PMCID: PMC2691834 DOI: 10.1093/nar/gkp196] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The biological role of quadruplexes and polyamines has been independently associated with cancer. However, quadruplex-polyamine mediated transcriptional regulation remain unaddressed. Herein, using c-MYC quadruplex model, we have attempted to understand quadruplex–polyamine interaction and its role in transcriptional regulation. We initially employed biophysical approach involving CD, UV and FRET to understand the role of polyamines (spermidine and spermine) on conformation, stability, molecular recognition of quadruplex and to investigate the effect of polyamines on quadruplex–Watson Crick duplex transition. Our study demonstrates that polyamines affect the c-MYC quadruplex conformation, perturb its recognition properties and delays duplex formation. The relative free energy difference (ΔΔG°) between the duplex and quadruplex structure indicate that polyamines stabilize and favor c-MYC quadruplex over duplex. Further, we investigated the influence of polyamine mediated perturbation of this equilibrium on c-MYC expression. Our results suggest that polyamines induce structural transition of c-MYC quadruplex to a transcriptionally active motif with distinctive molecular recognition property, which drives c-MYC expression. These findings may allow exploiting quadruplex–polyamines interaction for developing antiproliferative strategies to combat aberrant gene expression.
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Affiliation(s)
| | | | - Souvik Maiti
- *To whom correspondence should be addressed. Tel: +91 11 2766 6156; Fax: +91 11 2766 7471; ,
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24
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Kumar N, Patowary A, Sivasubbu S, Petersen M, Maiti S. Silencing c-MYC expression by targeting quadruplex in P1 promoter using locked nucleic acid trap. Biochemistry 2009; 47:13179-88. [PMID: 19053274 DOI: 10.1021/bi801064j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nuclease hypersensitive element of P1 promoter in c-MYC gene harbors a potential of unusual structure called quadruplex, which is involved in molecular recognition and function. This Hoogsteen bonded structure is in dynamic equilibrium with the usual Watson-Crick duplex structure, and these competing secondary structures undergo interconversion for execution of their respective biological roles. Herein, we investigate the sensitivity of the c-MYC quadruplex-duplex equilibrium by employing a locked nucleic acid (LNA) modified complementary strand as a pharmacological agent. Our biophysical experiments indicate that the c-MYC quadruplex under physiological conditions is stable and dominates the quadruplex-WC duplex equilibrium in both sodium and potassium buffers. This equilibrium is perturbed upon introducing the LNA modified complementary strand, which demonstrates efficient invasion of stable c-MYC quadruplex and duplex formation in contrast to the unmodified complementary strand. Our data indicate that LNA modifications confer increased thermodynamic stability to the duplex and thus favor the predominance of the duplex population over that of the quadruplex. Further, we demonstrate that this perturbation of equilibrium by a pharmacological agent results in altered gene expression. Our in vivo experiment performed using the LNA modified complementary strand suggests the influence of the quadruplex-duplex structural switch in the modulation of gene expression. We believe that this exploratory approach utilizing the selectivity and specificity of Watson-Crick base pairing of LNA bases would allow the modulation of quadruplex regulated gene expression.
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Affiliation(s)
- Niti Kumar
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
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25
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Kumar N, Maiti S. A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes. Nucleic Acids Res 2008; 36:5610-22. [PMID: 18757890 PMCID: PMC2553590 DOI: 10.1093/nar/gkn543] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Loop length and its composition are important for the structural and functional versatility of quadruplexes. To date studies on the loops have mainly concerned model sequences compared with naturally occurring quadruplex sequences which have diverse loop lengths and compositions. Herein, we have characterized 36 quadruplex-forming sequences from the promoter regions of various proto-oncogenes using CD, UV and native gel electrophoresis. We examined folding topologies and determined the thermodynamic profile for quadruplexes varying in total loop length (5–18 bases) and composition. We found that naturally occurring quadruplexes have variable thermodynamic stabilities (ΔG37) ranging from −1.7 to −15.6 kcal/mol. Overall, our results suggest that both loop length and its composition affect quadruplex structure and thermodynamics, thus making it difficult to draw generalized correlations between loop length and thermodynamic stability. Additionally, we compared the thermodynamic stability of quadruplexes and their respective duplexes to understand quadruplex–duplex competition. Our findings invoke a discussion on whether biological function is associated with quadruplexes with lower thermodynamic stability which undergo facile formation and disruption, or by quadruplexes with high thermodynamic stability.
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Affiliation(s)
- Niti Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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26
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Kumar N, Sahoo B, Varun KAS, Maiti S, Maiti S. Effect of loop length variation on quadruplex-Watson Crick duplex competition. Nucleic Acids Res 2008; 36:4433-42. [PMID: 18599514 PMCID: PMC2490738 DOI: 10.1093/nar/gkn402] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The effect of loop length on quadruplex stability has been studied when the G-rich strand is present along with its complementary C-rich strand, thereby resulting in competition between quadruplex and duplex structures. Using model sequences with loop lengths varying from T to T5, we carried out extensive FRET to discover the influence of loop length on the quadruplex-Watson Crick duplex competition. The binding data show an increase in the binding affinity of quadruplexes towards their complementary strands upon increasing the loop length. Our kinetic data reveal that unfolding of the quadruplex in presence of a complementary strand involves a contribution from a predominant slow and a small population of fast opening conformer. The contribution from the fast opening conformer increases upon increasing the loop length leading to faster duplex formation. FCS data show an increase in the interconversion between the quadruplex conformers in presence of the complementary strand, which shifts the equilibrium towards the fast opening conformer with an increase in loop length. The relative free-energy difference (ΔΔG°) between the duplex and quadruplex indicates that an increase in loop length favors duplex formation and out competes the quadruplex.
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Affiliation(s)
- Niti Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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27
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Gong M, Nikcevic I, Wehmeyer KR, Limbach PA, Heineman WR. Protein-aptamer binding studies using microchip affinity capillary electrophoresis. Electrophoresis 2008; 29:1415-22. [PMID: 18324729 PMCID: PMC3529586 DOI: 10.1002/elps.200700777] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of traditional CE to detect weak binding complexes is problematic due to the fast-off rate resulting in the dissociation of the complex during the separation process. Additionally, proteins involved in binding interactions often nonspecifically stick to the bare-silica capillary walls, which further complicates the binding analysis. Microchip CE allows flexibly positioning the detector along the separation channel and conveniently adjusting the separation length. A short separation length plus a high electric field enables rapid separations thus reducing both the dissociation of the complex and the amount of protein loss due to nonspecific adsorption during the separation process. Thrombin and a selective thrombin-binding aptamer were used to demonstrate the capability of microchip CE for the study of relatively weak binding systems that have inherent limitations when using the migration shift method or other CE methods. The rapid separation of the thrombin-aptamer complex from the free aptamer was achieved in less than 10 s on a single-cross glass microchip with a relatively short detection length (1.0 cm) and a high electric field (670 V/cm). The dissociation constant was determined to be 43 nM, consistent with reported results. In addition, aptamer probes were used for the quantitation of standard thrombin samples by constructing a calibration curve, which showed good linearity over two orders of magnitude with an LOD for thrombin of 5 nM at a three-fold S/N.
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Affiliation(s)
- Maojun Gong
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Irena Nikcevic
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Kenneth R. Wehmeyer
- Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd, Mason, OH 45040, USA
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - William R. Heineman
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
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28
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Wilcox JM, Rempel DL, Gross ML. Method of measuring oligonucleotide-metal affinities: interactions of the thrombin binding aptamer with K+ and Sr2+. Anal Chem 2008; 80:2365-71. [PMID: 18318508 DOI: 10.1021/ac701903w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new, mass spectrometry-based method for measuring affinity constants for specific metal ion binding to DNA, particularly for quadruplex DNA. This method, which is applicable to other systems, utilizes the gas-phase signal fractions, as determined by mass spectrometry, from the bound and unbound species as input into a mathematical model that determines various parameters, one of which is the binding affinity constant. The system used to develop and test the model was the thrombin-binding aptamer, an appropriate quadruplex structure that binds both K+ and Sr2+ cations. Using this method, we measured the binding constants of potassium and strontium cations with the quadruplex structure to be 5000 and 240 nM, respectively. We then applied the method to measure the change in enthalpy of the binding of strontium cations to the thrombin binding aptamer. The DeltaH for this interaction is -71 kJ/mol (-17 kcal/mol). The binding constant measurements are consistent with earlier measurements on the same system, and the measured change in enthalpy is in excellent agreement with previous work.
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Affiliation(s)
- J Micah Wilcox
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, Missouri 63130, USA
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29
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Qin Y, Rezler EM, Gokhale V, Sun D, Hurley LH. Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4. Nucleic Acids Res 2007; 35:7698-713. [PMID: 17984069 PMCID: PMC2190695 DOI: 10.1093/nar/gkm538] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The proximal 5′-flanking region of the human platelet-derived growth factor A (PDGF-A) promoter contains one nuclease hypersensitive element (NHE) that is critical for PDGF-A gene transcription. On the basis of circular dichroism (CD) and electrophoretic mobility shift assay (EMSA), we have shown that the guanine-rich (G-rich) strand of the DNA in this region can form stable intramolecular parallel G-quadruplexes under physiological conditions. A Taq polymerase stop assay has shown that the G-rich strand of the NHE can form two major G-quadruplex structures, which are in dynamic equilibrium and differentially stabilized by three G-quadruplex-interactive drugs. One major parallel G-quadruplex structure of the G-rich strand DNA of NHE was identified by CD and dimethyl sulfate (DMS) footprinting. Surprisingly, CD spectroscopy shows a stable parallel G-quadruplex structure formed within the duplex DNA of the NHE at temperatures up to 100°C. This structure has been characterized by DMS footprinting in the double-stranded DNA of the NHE. In transfection experiments, 10 μM TMPyP4 reduced the activity of the basal promoter of PDGF-A ∼40%, relative to the control. On the basis of these results, we have established that ligand-mediated stabilization of G-quadruplex structures within the PDGF-A NHE can silence PDGF-A expression.
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Affiliation(s)
- Yong Qin
- College of Pharmacy, 1703 E. Mabel, University of Arizona, Tucson, Arizona 85721, USA
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30
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Kumar N, Maiti S. Role of locked nucleic acid modified complementary strand in quadruplex/Watson-Crick duplex equilibrium. J Phys Chem B 2007; 111:12328-37. [PMID: 17914789 DOI: 10.1021/jp072705u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the human genome, the G-rich sequences that form quadruplexes are present along with their C-rich complementary strands; this suggests the existence of equilibrium between a quadruplex and a Watson-Crick duplex which allows the execution of their respective biological functions. We have investigated the sensitivity of this equilibrium to pharmacological agents by employing locked nucleic acid (LNA) modified complementary strands, and demonstrated successful invasion of the stable telomeric quadruplex d[(G(3)TTA)(3)G(3)]. Fluorescence, UV, ITC, and SPR studies were performed to understand the binding process involving the preformed quadruplex and LNA-modified complementary strands compared with that involving the unmodified complementary strand. Our data indicate that LNA modifications in the complementary strand shift the equilibrium toward the duplex state. These modifications confer increased thermodynamic stability to the duplex and increase the magnitude of relative free energy (DeltaDeltaG degrees) difference between duplex and quadruplex, thus favoring the predominance of duplex population over quadruplex. This superior ability of LNA-modified complementary strand can be exploited to pave an exploratory approach in which it hybridizes to a telomeric quadruplex and drives duplex formation, and inhibits the recognition of 3' G-rich overhang by RNA template of telomerase which guides telomere extension.
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Affiliation(s)
- Niti Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
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31
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He F, Tang Y, Yu M, Feng F, An L, Sun H, Wang S, Li Y, Zhu D, Bazan GC. Quadruplex-to-duplex transition of G-rich oligonucleotides probed by cationic water-soluble conjugated polyelectrolytes. J Am Chem Soc 2007; 128:6764-5. [PMID: 16719437 DOI: 10.1021/ja058075w] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-quartet DNA converts to duplex form in the presence of its complementary strand. This conformational change can be detected in real time by a homogeneous assay method based on the signal amplification of conjugated polyelectrolytes and the specific interaction of intercalating dyes with double-stranded DNA (dsDNA). The probe solution contains a cationic, conjugated polymer (CCP), G-quadruplex labeled with a fluorescein at the 5'-terminus (G-quadruplex-Fl), and ethidium bromide (EB). The addition of a complementary target results in the transition from G-quadruplex to duplex (dsDNA-Fl) and EB intercalation within the duplex structure. Excitation of the CCP leads to energy transfer from CCP to dsDNA-Fl (FRET-1) and then energy transfer from dsDNA-Fl to EB (FRET-2). Increasing the number of mismatched bases discourages dsDNA formation, which is detected in the assay.
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Affiliation(s)
- Fang He
- Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China
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32
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Nagatoishi S, Nojima T, Galezowska E, Juskowiak B, Takenaka S. G quadruplex-based FRET probes with the thrombin-binding aptamer (TBA) sequence designed for the efficient fluorometric detection of the potassium ion. Chembiochem 2007; 7:1730-7. [PMID: 17009271 DOI: 10.1002/cbic.200600179] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The dual-labeled oligonucleotide derivative, FAT-0, carrying 6- carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA) labels at the 5' and 3' termini of the thrombin-binding aptamer (TBA) sequence 5'-GGT TGG TGT GGT TGG-3', and its derivatives, FAT-n (n=3, 5, and 7) with a spacer at the 5'-end of a TBA sequence of T(m)A (m=2, 4, and 6) have been designed and synthesized. These fluorescent probes were developed for monitoring K(+) concentrations in living organisms. Circular dichroism, UV-visible absorption, and fluorescence studies revealed that all FAT-n probes could form intramolecular tetraplex structures after binding K(+). Fluorescence resonance energy transfer and quenching results are discussed taking into account dye-dye contact interactions. The relationship between the fluorescence behavior of the probes and the spacer length in FAT-n was studied in detail and is discussed.
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Affiliation(s)
- Satoru Nagatoishi
- Department of Applied Chemistry, Kyushu University, Motooka, 819-0395, Japan
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33
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Nagatoishi S, Tanaka Y, Tsumoto K. Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions. Biochem Biophys Res Commun 2006; 352:812-7. [PMID: 17150180 DOI: 10.1016/j.bbrc.2006.11.088] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 11/17/2006] [Indexed: 11/20/2022]
Abstract
It is noteworthy that the formation of the DNA G-quadruplex is induced by factors other than stabilizing cations because this event probably occurs in living cells. Previous studies have shown that thrombin-binding DNA aptamer (TBA) forms a chair-type intramolecular G-quadruplex structure that binds with thrombin protein in the absence of stabilizing cations. Here, we used circular dichroism (CD) spectroscopy to confirm G-quadruplex formation in the presence of thrombin without stabilizing cations. We obtained characteristic CD spectra that demonstrated that TBA forms the distinctive G-quadruplex structure. Additionally, we investigated G-quadruplex formation induced by change of solvent environment: the influence of low-temperature conditions and molecular crowding.
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Affiliation(s)
- Satoru Nagatoishi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
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34
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Nagatoishi S, Nojima T, Juskowiak B, Takenaka S. A pyrene-labeled G-quadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew Chem Int Ed Engl 2006; 44:5067-70. [PMID: 16035025 DOI: 10.1002/anie.200501506] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoru Nagatoishi
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka 812-858, Japan
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35
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Nagatoishi S, Nojima T, Galezowska E, Gluszynska A, Juskowiak B, Takenaka S. Fluorescence energy transfer probes based on the guanine quadruplex formation for the fluorometric detection of potassium ion. Anal Chim Acta 2006; 581:125-31. [PMID: 17386435 DOI: 10.1016/j.aca.2006.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 08/02/2006] [Accepted: 08/08/2006] [Indexed: 10/24/2022]
Abstract
Dual-labeled oligonucleotide derivative, FAT-0, carrying 6-carboxyfluorescein (FAM) and 6-carboxy-tetramethylrhodamine (TAMRA) labels at 5'- and 3'-termini of thrombin-binding aptamer (TBA) sequence 5'-GGTTGGTGTGGTTGG-3' and its derivatives, FAT-n (n=3, 5, and 7) were designed and synthesized. FAT-n derivatives contained a T(m)A spacer (m=2, 4, and 6, respectively) at 5'-end of TBA sequence. The probes were developed to estimate the spacer effect on FRET efficiency and to identify the best probe for sensing of K(+). Circular dichroism (CD), UV-vis absorption, and fluorescence studies revealed that all FAT-n probes could form the intramolecular tetraplex structures after binding K(+). Association constants of particular K(+)/FAT-n complexes were determined using different experimental approaches. Suitability of particular probes for sensitive monitoring of K(+) in intra- and extracellular conditions was examined and discussed. Calibration graphs of fluorescence ratio were linear in the K(+) concentration range of 2-10 mM for extracellular conditions showing sensitivity of 1.2% mM(-1) K(+) and for intracellular conditions in the range of 100-200 mM with sensitivity of 0.49% mM(-1) K(+).
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Affiliation(s)
- Satoru Nagatoishi
- Department of Applied Chemistry, Kyushu University, Motooka 819-0395, Japan
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36
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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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37
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Juskowiak B. Analytical potential of the quadruplex DNA-based FRET probes. Anal Chim Acta 2006; 568:171-80. [PMID: 17761258 DOI: 10.1016/j.aca.2005.12.063] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 12/12/2005] [Accepted: 12/29/2005] [Indexed: 11/17/2022]
Abstract
DNA exhibits structural flexibility and may adopt also tetraplex structures known as guanine-quadruplexes or G-quadruplexes. These G-quadruplexes have recently received great attention because G-rich sequences are often found in genome and because of their potential links to mechanisms that relate to cancer, HIV, and other diseases. The unique structure of quadruplexes has also stimulated development of new analytical and bioanalytical assays based on fluorescence resonance energy transfer (FRET). Intramolecular folding of a flexible single-stranded DNA molecule into a compact G-quadruplex is a structural transition leading to closer proximity of its 5'- and 3'-ends. Thus, labeling both ends of a DNA strand with donor and acceptor fluorophores enables monitoring the quadruplex formation process by means of the FRET signal. This review shows how FRET technique contributes to G-quadruplex research and focuses mainly on analytical applications of FRET-labeled quadruplexes. Applications include studies of structural transitions of quadruplexes, FRET-based selection of ligands that bind to quadruplexes, design of molecular probes for protein recognition and development of sensors for detection of potassium ions in aqueous solution.
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Affiliation(s)
- Bernard Juskowiak
- Department of Analytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.
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38
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Fialová M, Kypr J, Vorlícková M. The thrombin binding aptamer GGTTGGTGTGGTTGG forms a bimolecular guanine tetraplex. Biochem Biophys Res Commun 2006; 344:50-4. [PMID: 16616893 DOI: 10.1016/j.bbrc.2006.03.144] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 03/21/2006] [Indexed: 11/29/2022]
Abstract
In the literature, the thrombin binding aptamer GGTTGGTGTGGTTGG is generally taken as a prototype of an intramolecular guanine tetraplex of DNA. Our results, however, show that this notion is not true in aqueous solutions. This conclusion is based on a dependence of the CD spectra on aptamer concentration, migration of the aptamer in polyacrylamide gels, and the Ferguson analysis of the gel migration data. The presented data document that the aptamer forms a bimolecular tetraplex. We furthermore show that only an extension of the aptamer by a sequence containing further guanines, or an elongation of loop regions, causes that its tetraplex folding is intramolecular.
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Affiliation(s)
- Markéta Fialová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
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39
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Rueda M, Luque FJ, Orozco M. G-Quadruplexes Can Maintain Their Structure in the Gas Phase. J Am Chem Soc 2006; 128:3608-19. [PMID: 16536534 DOI: 10.1021/ja055936s] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Several very extended (0.5-1 micros) molecular dynamics (MD) simulations of parallel and antiparallel G-quadruplex DNA strongly suggest that in the presence of suitable cations the quadruplex not only remains stable in the gas phase, but also displays a structure that closely resembles that found in extended (25-ns long) trajectories in aqueous solution. In the absence of the crucial cations, the trajectories become unstable and in general the quadruplex structure is lost. To our knowledge, this is the first physiologically relevant structure of DNA for which very large MD simulations suggest that the structure in water and in the gas phase are indistinguishable.
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Affiliation(s)
- Manuel Rueda
- Institut de Recerca Biomédica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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40
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Kumar N, Maiti S. The effect of osmolytes and small molecule on Quadruplex-WC duplex equilibrium: a fluorescence resonance energy transfer study. Nucleic Acids Res 2005; 33:6723-32. [PMID: 16321964 PMCID: PMC1301592 DOI: 10.1093/nar/gki961] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structural competition between the G-quadruplex and Watson-Crick duplex has been implicated for the repetitive DNA sequences, but the factors influencing this competitive equilibrium in the natural and pharmacological context need to be elucidated. Using a 21mer 5'-Fluorescein-d[(G3TTA)3G3]-TAMRA-3' as a model system, extensive fluorescence resonance energy transfer analysis was carried out to investigate sensitivity of this equilibrium to osmotic stress and quadruplex selective small molecule. The binding affinities and kinetics involved in the hybridization of quadruplex to its complementary strand in the absence and presence of different concentrations of osmolytes (ethylene glycol and glycerol) and a quadruplex selective ligand (cationic porphyrin-TMPyP4) were determined. The presence of osmolytes and cationic porphyrin decreased the binding affinity of quadruplex to its complementary strand and slowed the kinetics of the reaction by delaying the hybridization process. Our binding data analysis indicates that the presence of either osmolytes or porphyrin increase the amount of quadruplex in the equilibrium. In 100 mM KCl solution, when 30 nM of each of the components, i.e. quadruplex and the complementary strand, were mixed together, the amount of quadruplex present in the system under equilibrium were 17.6, 23.4, 23.1 and 19.6 nM in the absence and presence of 10% ethylene glycol, 10% glycerol and 150 nM TMPyP4, respectively. Fluorescence melting profile of quadruplex in the absence and presence of these perturbants confirm the findings that osmolytes and cationic porphyrin stabilize quadruplex, and thus, shift the equilibrium to quadruplex formation.
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Affiliation(s)
| | - Souvik Maiti
- To whom correspondence should be addressed. Tel: +91 11 2766 6156; Fax: +91 11 2766 7471;
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41
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Mao XA, Gmeiner WH. NMR study of the folding-unfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). Biophys Chem 2005; 113:155-60. [PMID: 15617822 DOI: 10.1016/j.bpc.2004.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Revised: 09/09/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Hydrogen exchange rates of the imino protons of the thrombin-binding 15 mer DNA aptamer d(G(1)G(2)T(3)T(4)G(5)G(6)T(7)G(8)T(9)G(10)G(11)T(12)T(13)G(14)G(15)) in the presence of Sr(2+) were measured. In the temperature range 15-35 degrees C, the exchange rates of the eight iminos in the quadruplex core were not uniform, with the G(2), G(11) and G(15) iminos exchanging faster, the G(1), G(5), G(10) and G(14) iminos exchanging slower, and the G(6) imino exchanging at a medium rate. In the quadruplex G(1), G(5), G(10) and G(14) adopted syn glycosidic conformation, while G(2), G(6), G(11) and G(15) adopted anti-conformation. It was found that the four slowly exchanging iminos, which were all the syn-iminos, happened to be located in the TT loops that were not easy to open to the solvent. The anti-iminos exchanged faster, but the G(6) imino exchanged slower than other anti-iminos, because its hydrogen bond with the G(10)O6 was stabilized by the TGT loop. The fact that the G(6) imino exchanged at a faster rate than those syn-iminos in the TT loops suggested that the TGT loop was less stable than the TT loops. Unfolding mechanism for the quadruplex was thus proposed: The quadruplex first uncoupled the three base pairs: G(1)-G(15), G(2)-G(14) and G(5)-G(11), which were not protected by any loops. Then it opened the TGT loop. Finally, it opened the TT loops and the sequence became an unstructured random coil that exchanged with the quadruplex conformation. The conformational exchange between the quadruplex and random coil had been detected.
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Affiliation(s)
- Xi-an Mao
- Biochemistry Department, Wake Forest University School of Medicine, Medical Center Blvd, Winston-Salem, NC 27157-1016, USA.
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42
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Nagatoishi S, Nojima T, Juskowiak B, Takenaka S. A Pyrene-Labeled G-Quadruplex Oligonucleotide as a Fluorescent Probe for Potassium Ion Detection in Biological Applications. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501506] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Brown NM, Rachwal PA, Brown T, Fox KR. Exceptionally slow kinetics of the intramolecular quadruplex formed by the Oxytricha telomeric repeat. Org Biomol Chem 2005; 3:4153-7. [PMID: 16267597 DOI: 10.1039/b511706b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We examined the stability and kinetics of folding of the Oxytricha telomeric repeat sequence (G4T4)4. Fluorescence melting experiments show that this intramolecular quadruplex, which is more stable in potassium- than sodium-containing buffers, shows considerable hysteresis between the melting and annealing profiles, even when heated at a rate of 0.05 degrees C min(-1). Quantitative analysis of this hysteresis, together with temperature-jump relaxation experiments show that the dissociation is exceptionally slow with a half-life of about 10 years at 37 degrees C in the presence of 50 mM K+. The association reaction has a half-life of a few seconds at 37 degrees C, but becomes slower at elevated temperatures consistent with the suggestion that association occurs by a nucleation-zipper mechanism.
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Affiliation(s)
- Nicholas M Brown
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, UKSO16 7PX
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Missailidis S, Thomaidou D, Borbas KE, Price MR. Selection of aptamers with high affinity and high specificity against C595, an anti-MUC1 IgG3 monoclonal antibody, for antibody targeting. J Immunol Methods 2005; 296:45-62. [PMID: 15680150 DOI: 10.1016/j.jim.2004.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 10/19/2004] [Accepted: 10/25/2004] [Indexed: 11/28/2022]
Abstract
Targeting of antibodies has found a number of applications in assays, anti-idiotypic therapies and vaccine design with a number of anti-idiotypic Abs generated and used in clinical applications, and some currently in clinical trials. Meanwhile, aptamers are a novel and particularly interesting targeting modality, with a unique ability to bind to a variety of targets. Aptamers offer unique benefits compared to other targeting agents, due to their high affinity and selectivity, relatively small size and in vitro synthesis, making them attractive alternatives to Abs and peptides. Aptamers have already been selected against a number of Abs for various applications. We now present a novel methodology for the selection of aptamers against Abs, which minimises the number of steps used and results in molecules that bind to the target Ab with high affinity and specificity. We have used the well-characterised anti-MUC1 monoclonal Ab C595 as an exemplar for raising aptamers against Abs. The methodology is based on the adsorption of the Ab to the surface of a PCR tube and the performance of SELEX selections in the PCR tube, based on elution steps resulting from the denaturation of the Ab on the first PCR amplification cycle. After 10 rounds of selection and amplification, selected aptamers have been characterised using a number of techniques, including fluorescence quenching, ELISA and competition ELISA procedures and a FRET type assay. Aptamers were found to bind their target Ab with a higher affinity than its natural antigenic peptide, as observed in fluorescent quenching and FRET experiments. Furthermore, they were able to displace the antigens from the antibody binding pocket in competition assays. This methodology offers the possibility of rapidly selecting aptamers for antibody targeting that could be used as diagnostic, imaging or therapeutic agents, or as recognition units in immunoassays, and can be potentially useful in raising aptamers against other protein targets.
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Affiliation(s)
- Sotiris Missailidis
- Chemistry Department, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
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