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Myres GJ, Kitt JP, Harris JM. Surface-Area Enhanced Raman Spectroscopy of DNA in Porous Silica: A Quantitative and Reproducible Alternative to Plasmonic-Based SERS. Anal Chem 2024; 96:7679-7686. [PMID: 38698534 DOI: 10.1021/acs.analchem.4c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Despite the success of surface-enhanced Raman spectroscopy (SERS) for detecting DNA immobilized on plasmonic metal surfaces, its quantitative response is limited by the rapid falloff of enhancement with distance from the metal surface and variations in sensitivity that depend on orientation and proximity to plasmonic "hot spots". In this work, we assess an alternative approach for enhancing detection by immobilizing DNA on the interior surfaces of porous silica particles. These substrates provide over a 1000-fold greater surface area for detection compared to a planar support. The porous silica substrate is a purely dielectric material with randomly oriented internal surfaces, where scattering is independent of proximity and orientation of oligonucleotides relative to the silica surface. We characterize the quantitative response of Raman scattering from DNA in porous silica particles with sequences used in previous SERS investigations of DNA for comparison. The results show that Raman scattering of DNA in porous silica is independent of distance of nucleotides from the silica surface, allowing detection of longer DNA strands with constant sensitivity. The surface area enhancement within particles is reproducible (<4% particle-to-particle variation) owing to the uniform internal pore structure and surface chemistry of the silica support. DNA immobilization with a bis-thiosuccinimide linker provides a Raman-active internal standard for quantitative interpretation of Raman scattering results. Despite the high (30 mM) concentrations of immobilized DNA within porous silica particles, they can be used to measure nanomolar binding affinities of target molecules to DNA by equilibrating a very small number of particles with a sufficiently large volume of low-concentration solution of target molecules.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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2
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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3
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Soenarjo AL, Lan Z, Sazanovich IV, Chan YS, Ringholm M, Jha A, Klug DR. The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy. J Am Chem Soc 2023; 145:19622-19632. [PMID: 37647128 PMCID: PMC10510320 DOI: 10.1021/jacs.3c04044] [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: 04/18/2023] [Indexed: 09/01/2023]
Abstract
A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the regulation of gene transcription and telomerase-mediated telomere maintenance and, therefore, is a target for drugs. The details of the molecular interactions that cause stacking of the guanine-tetrads are not well-understood, which limits a rational approach to the drugability of G4 sequences. To explore these interactions, we employed electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectroscopy to measure extended vibrational coupling spectra for a parallel-stranded G4-DNA formed by the Myc2345 nucleotide sequence. We also tracked the structural changes associated with G4-folding as a function of K+-ion concentration. To classify the structural elements that the folding process generates in terms of vibrational coupling characteristics, we used quantum-chemical calculations utilizing density functional theory to predict the coupling spectra associated with given structures, which are compared against the experimental data. Overall, 102 coupling peaks are experimentally identified and followed during the folding process. Several phenomena are noted and associated with formation of the folded form. This includes frequency shifting, changes in cross-peak intensity, and the appearance of new coupling peaks. We used these observations to propose a folding sequence for this particular type of G4 under our experimental conditions. Overall, the combination of experimental 2DIR data and DFT calculations suggests that guanine-quartets may already be present before the addition of K+-ions, but that these quartets are unstacked until K+-ions are added, at which point the full G4 structure is formed.
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Affiliation(s)
- A. Larasati Soenarjo
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Zhihao Lan
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton
Laboratory, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Yee San Chan
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - David R. Klug
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
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4
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D'Amico F, Graziano R, D'Aria F, Russomanno P, Di Fonzo S, Amato J, Pagano B. Cytosine epigenetic modifications and conformational changes in G-quadruplex DNA: An ultraviolet resonance Raman spectroscopy study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122901. [PMID: 37244027 DOI: 10.1016/j.saa.2023.122901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
Epigenetic modifications of DNA are known to play important regulatory roles in biological systems, especially in regulation of gene expression, and are associated with many types of human diseases, including cancer. Alternative DNA secondary structures, such as G-quadruplexes, can also influence gene transcription, thus suggesting that such structures may represent a distinctive layer of epigenetic information. G-quadruplex structures and DNA epigenetic modifications often go side by side, and recent evidence reveals that cytosine modifications within loops of G-quadruplexes can play a role in modulating their stability and structural polymorphism. Therefore, the development and validation of experimental techniques that can easily and reliably analyse G-quadruplex structures are highly desirable. In the present study, we propose to exploit the advantages of UV resonance Raman (UVRR) spectroscopy to investigate cytosine epigenetic modifications along with conformational changes in G-quadruplex-forming DNA. Our findings show that clear and specific spectral changes occur when there is a change in a G-quadruplex structure. Moreover, UVRR spectral analysis can indirectly distinguish the spectral variations occurring because of modifications in the guanine glycosidic conformations, as well as detect changes in the loops induced by H-bond formation or hydration of nitrogenous bases. The results further underscore the utility of UVRR spectroscopy for G-quadruplex structure elucidation under biologically relevant solution conditions.
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Affiliation(s)
- Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste I-34149, Italy
| | - Raffaele Graziano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste I-34149, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
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Myres GJ, Harris JM. Nanomolar Binding of an Antibiotic Peptide to DNA Measured with Raman Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4150-4160. [PMID: 36888905 DOI: 10.1021/acs.langmuir.3c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Immobilization of DNA to surfaces offers a convenient means of screening the binding affinity and selectivity of potential small-molecule therapeutic candidates. Unfortunately, most surface-sensitive methods for detecting these binding interactions are not informative of the molecular structure, information that is valuable for understanding the non-covalent interactions that stabilize binding. In this work, we report a method to meet this challenge by employing confocal Raman microscopy to quantify the association of a minor-groove-binding antimicrobial peptide, netropsin, to duplex DNA hairpin sequences immobilized on the interior surfaces of porous silica particles. To assess binding selectivity, particles functionalized with different sequences of DNA were equilibrated with solutions of 100 nM netropsin, and selective association was detected based on the presence of netropsin Raman scattering in the particles. The selectivity study revealed that netropsin binds to sequences of duplex DNA having AT-rich recognition regions. To quantify binding affinities, these AT-rich DNA sequences were equilibrated with a range of netropsin solution concentrations (1 to 100 nM). Raman scattering intensities of netropsin versus solution concentration were well described by single-binding-site Langmuir isotherms with nanomolar dissociation constants, in agreement with previous isothermal calorimetry and surface plasmon resonance results. Target sequence binding was accompanied with changes in netropsin and DNA vibrational modes consistent with the hydrogen bonding between the amide groups of netropsin and adenine and thymine bases in the DNA minor groove. The binding of netropsin to a control sequence lacking the AT-rich recognition region exhibited an affinity nearly 4 orders of magnitude weaker than found for the target sequences. The Raman spectrum of netropsin interacting with this control sequence showed broad pyrrole and amide mode vibrations at frequencies similar to a free solution, revealing less constrained conformations compared with the specific binding interactions observed with AT-rich sequences.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
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Liu L, Zhu L, Tong H, Su C, Wells JW, Chalikian TV. Distribution of Conformational States Adopted by DNA from the Promoter Regions of the VEGF and Bcl-2 Oncogenes. J Phys Chem B 2022; 126:6654-6670. [PMID: 36001297 DOI: 10.1021/acs.jpcb.2c04304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We employed a previously described procedure, based on circular dichroism (CD) spectroscopy, to quantify the distribution of conformational states adopted by equimolar mixtures of complementary G-rich and C-rich DNA strands from the promoter regions of the VEGF and Bcl-2 oncogenes. Spectra were recorded at different pHs, concentrations of KCl, and temperatures. The temperature dependences of the fractional populations of the duplex, G-quadruplex, i-motif, and coiled conformations of each promoter were then analyzed within the framework of a thermodynamic model to obtain the enthalpy and melting temperature of each folded-to-unfolded transition involved in the equilibrium. A comparison of the conformational data on the VEGF and Bcl-2 DNA with similar results on the c-MYC DNA, which we reported previously, reveals that the distribution of conformational states depends on the specific DNA sequence and is modulated by environmental factors. Under the physiological conditions of room temperature, neutral pH, and elevated concentrations of potassium ions, the duplex conformation coexists with the G-quadruplex conformation in proportions that depend on the sequence. This observed conformational diversity has biological implications, and it further supports our previously proposed thermodynamic hypothesis of gene regulation. In that hypothesis, a specific distribution of duplex and tetraplex conformations in a promoter region is fine-tuned to maintain the healthy level of gene expression. Any deviation from a healthy distribution of conformational states may result in pathology stemming from up- or downregulation of the gene.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Legeng Zhu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Haoyuan Tong
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Chongyu Su
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Yang N, Wang Y, Wang X, Zhang F, Xiao Y, Yan B, Zhang T, Liu X, Li Y. Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2022; 13:6208-6214. [PMID: 35770782 DOI: 10.1021/acs.jpclett.2c01461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.
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Affiliation(s)
- Ni Yang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yunpeng Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xiaotong Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Fenghai Zhang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Bingdi Yan
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Ting Zhang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xin Liu
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
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8
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Song Y, Ma Z, Zhang W. Manipulation of a Single Polymer Chain: From the Nanomechanical Properties to Dynamic Structure Evolution. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Ziwen Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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9
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Li P, Wang L, Sun M, Yao J, Li W, Lu W, Zhou Y, Zhang G, Hu C, Zheng W, Wei F. Binding affinity and conformation of a conjugated AS1411 aptamer at a cationic lipid bilayer interface. Phys Chem Chem Phys 2022; 24:9018-9028. [PMID: 35381056 DOI: 10.1039/d1cp05753g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamers have been widely used in the detection, diagnosis, and treatment of cancer. Owing to their special binding affinity toward cancer-related biomarkers, aptamers can be used for targeted drug delivery or bio-sensing/bio-imaging in various scenarios. The interfacial properties of aptamers play important roles in controlling the surface charge, recognition efficiency, and binding affinity of drug-delivering lipid-based carriers. In this research, the interfacial behaviors, such as surface orientation, molecular conformation, and adsorption kinetics of conjugated AS1411 molecules at different cationic lipid bilayer interfaces were investigated by sum frequency generation vibrational spectroscopy (SFG-VS) in situ and in real-time. It is shown that the conjugated AS1411 molecules at the DMTAP bilayer interface show a higher binding affinity but with slower binding kinetics compared to the DMDAP bilayer interface. The analysis results also reveal that the thymine residues of cholesteryl conjugated AS1411 molecules show higher conformational ordering compared to the thymine residues of the alkyl chain conjugated AS1411 molecules. These understandings provide unique molecular insight into the aptamer-lipid membrane interactions, which may help researchers to improve the efficiency and safety of aptamer-related drug delivery systems.
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Affiliation(s)
- Penghua Li
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Liqun Wang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Meng Sun
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Jiyuan Yao
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Wenhui Li
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China. .,Institution for Interdisciplinary Research, Jianghan University, Wuhan, Hubei, 430056, China
| | - Wangting Lu
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China. .,Institution for Interdisciplinary Research, Jianghan University, Wuhan, Hubei, 430056, China
| | - Youhua Zhou
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Geng Zhang
- Department of Chemistry, College of Science, Huazhong Agricultural University, No. 1, Shizishan Street, Wuhan 430070, China
| | - Chenglong Hu
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China.
| | - Wanquan Zheng
- Institution for Interdisciplinary Research, Jianghan University, Wuhan, Hubei, 430056, China.,Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Feng Wei
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, & School of Optoelectronic Materials and Technology, Jianghan University, Wuhan 430056, China. .,Institution for Interdisciplinary Research, Jianghan University, Wuhan, Hubei, 430056, China
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Kazarian AA, Barnhart W, Campuzano IDG, Cabrera J, Fitch T, Long J, Sham K, Wu B, Murray JK. Purification of guanine-quadruplex using monolithic stationary phase under ion-exchange conditions. J Chromatogr A 2020; 1634:461633. [PMID: 33189959 DOI: 10.1016/j.chroma.2020.461633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
The current study investigates a method for purification of the G-quadruplex secondary structure, naturally formed by a guanine-rich 21-mer oligonucleotide strand using a monolithic convective interaction media-quaternary amine (CIM-QA) column under ion-exchange conditions. The monolithic support was initially evaluated on a preparative scale against a highly efficient TSKgel SuperQ-5PW ion-exchange support designed for oligonucleotide purification. The CIM analogue demonstrated clear advantages over the particle-based support on the basis of rapid separation times, while also affording high purity of the G-quadruplex. Various parameters were investigated including the type of mobile phase anion, cation, pH and injection load to induce and control quadruplex formation, as well as enhance chromatographic separation and final purity. Potassium afforded the most prominent quadruplex formation, yet sodium allowed for the highest resolution and purity to be achieved with a 30 mg injection on an 8 ml CIM-QA monolithic column. This method was applied to purify in excess of 300 mg of the quadruplex, with excellent retention time precision of under 1% RSD. Native mass spectrometry was utilized to confirm the identity of the intact G-quadruplex under non-denaturing conditions, while ion-pairing reversed-phase methods confirmed the presence of the single-stranded oligonucleotide in high purity (92%) under denaturing conditions. The key advantage of the purification method enables isolation of the G-quadruplex in its native state on a milli-gram scale, allowing structural characterization to further our knowledge of its role and function. The G-quadruplex can also be subsequently denaturated at elevated temperature causing single strand formation if additional reactions are to be pursued, such as annealing to form a duplex, and evaluation in in vitro or in vivo studies.
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Affiliation(s)
| | - Wesley Barnhart
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Iain D G Campuzano
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Jeremy Cabrera
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Theodore Fitch
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Jason Long
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Kelvin Sham
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Bin Wu
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Justin K Murray
- Amgen Research, Amgen, Inc. One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
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11
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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13
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Liu L, Ma C, Wells JW, Chalikian TV. Conformational Preferences of DNA Strands from the Promoter Region of the c-MYC Oncogene. J Phys Chem B 2020; 124:751-762. [PMID: 31923361 DOI: 10.1021/acs.jpcb.9b10518] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized the conformational preferences of DNA in an equimolar mixture of complementary G-rich and C-rich strands from the promoter region of the c-MYC oncogene. Our CD-based approach presupposes that the CD spectrum of such a mixture is the spectral sum of the constituent duplex, G-quadruplex, i-motif, and coiled conformations. Spectra were acquired over a range of temperatures at different pHs and concentrations of KCl. Each spectrum was unmixed in terms of the predetermined spectra of the constituent conformational states to obtain the corresponding weighting factors for their fractional contributions to the total population of DNA. The temperature dependences of those contributions then were analyzed in concert according to a model based on a thermodynamic representation of the underlying equilibria. Fitted estimates of the melting enthalpy and temperature obtained for the duplex, G-quadruplex, and i-motif imply that the driving force behind dissociation of the duplex and the concomitant formation of tetrahelical structures is the folding of the G-strand into the G-quadruplex. The liberated C-strand adopts the i-motif conformation at acidic pH and exists in the coiled state at neutral pH. The i-motif alone cannot induce dissociation of the duplex even at pH 5.0, at which it is most stable. Under the physiological conditions of neutral pH, elevated potassium, and room temperature, the duplex and G-quadruplex conformations coexist with the C-strand in the coiled state. Taken together, our results suggest a novel, thermodynamically controlled mechanism for the regulation of gene expression.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Congshan Ma
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
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Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands. Molecules 2020; 25:molecules25030434. [PMID: 31972988 PMCID: PMC7037129 DOI: 10.3390/molecules25030434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
By substitution of natural nucleotides by their abasic analogs (i.e., 1',2'-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson-Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
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Hara T, Kodama T, Takegaki Y, Morihiro K, Ito KR, Obika S. Synthesis and Properties of 7-Deazapurine- and 8-Aza-7-deazapurine-Locked Nucleic Acid Analogues: Effect of the Glycosidic Torsion Angle. J Org Chem 2016; 82:25-36. [DOI: 10.1021/acs.joc.6b02525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Takashi Hara
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Kodama
- Graduate
School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yumi Takegaki
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kunihiko Morihiro
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate
School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
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Li H, Hai J, Zhou J, Yuan G. The formation and characteristics of the i-motif structure within the promoter of the c-myb proto-oncogene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:625-632. [PMID: 27487467 DOI: 10.1016/j.jphotobiol.2016.07.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 12/11/2022]
Abstract
C-myb proto-oncogene is a potential therapeutic target for some human solid tumors and leukemias. A long cytosine-rich sequence, which locates the downstream of the transcription initiation site, is demonstrated to fold into an intramolecular i-motif DNA using electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. Effects of factors, including the pH value, the number of C:C(+) dimers, the concentration of buffer, the molecular crowding condition, and the coexistence of the complementary DNA, on the formation and the structural stability of the i-motif DNA are systematically studied. We have demonstrated that the i-motif folding in the c-myb promoter could be accelerated upon synergistic physiological stimuli including intracellular molecular crowding and low pH values, as well as the large number of the i-motif C:C(+) dimers. Meanwhile, various inputs, such as acids/bases and metal ions, have exhibited their abilities in controlling the conformational switch of the c-myb GC-rich DNA. Acidic pH values and the presence of K(+) ions can induce the dissociation of the double helix. Our present strategy can greatly extend the potential usages of i-motif DNA molecules with specific sequences as conformational switch-controlled devices. Moreover, this work demonstrates the superiority of CD spectroscopy associated with ESI-MS as a rapid, more cost-effective and sensitive structural change responsive method in the research of DNA conformational switching.
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Affiliation(s)
- Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada.
| | - Jinhui Hai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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18
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König SLB, Evans AC, Huppert JL. Seven essential questions on G-quadruplexes. Biomol Concepts 2015; 1:197-213. [PMID: 25961997 DOI: 10.1515/bmc.2010.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.
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19
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Cao C, Zhang J, Li S, Xiong Q. Intelligent and ultrasensitive analysis of mercury trace contaminants via plasmonic metamaterial-based surface-enhanced Raman spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3252-6. [PMID: 24729476 DOI: 10.1002/smll.201400165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Indexed: 05/18/2023]
Abstract
Label-free molecular logic gates (AND, INHIBIT, and OR) are constructed based on specific conformation modulation of a guanine- and thymine-rich DNA, while the optical readout is enabled by the tunable metamaterials which serve as a substrate for surface enhanced Raman spectroscopy. The DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions down to 2 × 10(-4) ppb.
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Affiliation(s)
- Cuong Cao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371
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20
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Rehm C, Holder IT, Groß A, Wojciechowski F, Urban M, Sinn M, Drescher M, Hartig JS. A bacterial DNA quadruplex with exceptional K+ selectivity and unique structural polymorphism. Chem Sci 2014. [DOI: 10.1039/c4sc00440j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The G-quadruplex forming sequence d[(G4CT)3G4] shows complete and continuous quadruplex interconversion upon increasing K+-concentrations and pronounced K+ selectivity.
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Affiliation(s)
- Charlotte Rehm
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Isabelle T. Holder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Andreas Groß
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Filip Wojciechowski
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Maximilian Urban
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- 78457 Konstanz, Germany
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21
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Gracie K, Dhamodharan V, Pradeepkumar PI, Faulds K, Graham D. Qualitative SERS analysis of G-quadruplex DNAs using selective stabilising ligands. Analyst 2014; 139:4458-65. [DOI: 10.1039/c4an00551a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A SERS-based method has been developed for the analysis of G-quadruplex DNAs using three novel stabilising ligands.
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Affiliation(s)
- K. Gracie
- Centre of Molecular Nanometrology
- WestChem
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow, UK
| | - V. Dhamodharan
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400076, India
| | - K. Faulds
- Centre of Molecular Nanometrology
- WestChem
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow, UK
| | - D. Graham
- Centre of Molecular Nanometrology
- WestChem
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow, UK
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22
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Cao C, Zhang J, Wen X, Dodson SL, Dao NT, Wong LM, Wang S, Li S, Phan AT, Xiong Q. Metamaterials-based label-free nanosensor for conformation and affinity biosensing. ACS NANO 2013; 7:7583-91. [PMID: 23952283 DOI: 10.1021/nn401645t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that highly tunable plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g., G-quadruplexes, in different environments. We further demonstrate the use of the metamaterials for fingerprinting and detection of the arginine-glycine-glycine domain of nucleolin, a cancer biomarker that specifically binds to a G-quadruplex, with the picomolar sensitivity.
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Affiliation(s)
- Cuong Cao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371
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23
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Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. Nucleic Acids Res 2013; 41:1005-16. [PMID: 23193257 PMCID: PMC3553954 DOI: 10.1093/nar/gks1135] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/22/2012] [Indexed: 01/16/2023] Open
Abstract
DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K(+)-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. As Raman spectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G(3)(TTAG(3))(3) in the presence of K(+) and Na(+) ions throughout wide range of DNA concentrations. We demonstrate that the K(+)-structure of G(3)(TTAG(3))(3) at low DNA concentration is close to the antiparallel fold of Na(+)-stabilized quadruplex. On the increase of G(3)(TTAG(3))(3) concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K(+)-stabilized samples. The transition is synergically supported by increased K(+) concentration. However, even for extremely high G(3)(TTAG(3))(3) and K(+) concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K(+) ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na(+)-stabilized G(3)(TTAG(3))(3) retains its antiparallel folding regardless of the extremely high DNA and/or Na(+) concentrations, thermal destabilization or annealing.
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Affiliation(s)
- Jan Palacký
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Iva Kejnovská
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Peter Mojzeš
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
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24
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Abu-Ghazalah RM, Rutledge S, Lau LWY, Dubins DN, Macgregor RB, Helmy AS. Concentration-dependent structural transitions of human telomeric DNA sequences. Biochemistry 2012; 51:7357-66. [PMID: 22931349 DOI: 10.1021/bi300689t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)(n) can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5' or 3' end, and the sample preparation technique. In this work, we report our studies of the concentration dependence of the circular dichroism (CD) and the vibrational modes probed by Raman scattering of three previously characterized monomolecular G-quadruplexes: H-Tel, d[5'-A(GGGTTA)(3)GGG-3']; hybrid-1, d[5'-AAA(GGGTTA)(3)GGGAA-3']; and hybrid-2, d[5'-TTA(GGGTTA)(3)GGGTT-3']. At high (millimolar) ODN concentrations, we observed a transformation of the CD spectrum of H-Tel, with a relaxation time on the order of 10 h. Analysis of the kinetics of this process is consistent with the formation of an aggregated complex of folded H-Tel monomers. Upon dilution, the aggregates dissociate rapidly, yielding spectra identical to those of monomeric H-Tel. Both hybrid sequences undergo a similar transition under high-salt (1 M) conditions. The measurements suggest that for these ODN concentrations, which are typically used in high-resolution spectroscopies, the monomolecular G-quadruplex structures undergo a transition to multimolecular structures at room temperature. Guided by our findings, we propose that the terminal bases of the hybrid-1 and hybrid-2 ODNs impede the formation of these aggregates; however, in solutions containing 1 M salt, the hybrid oligonucleotides aggregate.
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Affiliation(s)
- Rashid M Abu-Ghazalah
- Edward S. Rogers Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
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25
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Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. The interaction of telomeric DNA and C-myc22 G-quadruplex with 11 natural alkaloids. Nucleic Acid Ther 2012; 22:127-36. [PMID: 22480315 DOI: 10.1089/nat.2012.0342] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Telomeric DNA and C-myc22 are DNA G-quadruplex (G4)-forming sequences associated with tumorigenesis. Ligands that can facilitate the formation and increase the stabilization of G4 can halt tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, we have investigated the interaction of 11 natural alkaloids with G4 formed by telomeric DNA and C-myc22 sequences. Our results indicated that sanguinarine (San), palmatine (Pal), and berberine (Beb) of the first series (S1) can induce the formation of G4 as well as increase the stabilization ability. Daurisoline (S2-1), O-methyldauricine (S2-2), O-diacetyldaurisoline (S2-3), daurinoline (S2-4), dauricinoline (S2-5), N,N'-dimethyldauricine iodide (S2-6), and N,N'-dimethyldaurisoline iodide (S2-7) of the second series (S2) showed similar stabilization ability. We found that unsaturated ring C, N(+) positively charged centers, and conjugated aromatic rings are key factors to increase the stabilization ability of S1, and we gave some advice on structure modification to S2 through structure-activity study. Besides, we found San and Pal to be cell cycle blocker in G(1). San was speculated to bind to G4 through intercalation or end stacking.
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Affiliation(s)
- Xiaohui Ji
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology College of Life Science, Beijing Normal University, Beijing, People's Republic of China
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Dhakal S, Yu Z, Konik R, Cui Y, Koirala D, Mao H. G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA. Biophys J 2012; 102:2575-84. [PMID: 22713573 DOI: 10.1016/j.bpj.2012.04.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 04/03/2012] [Accepted: 04/16/2012] [Indexed: 11/18/2022] Open
Abstract
G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.
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Affiliation(s)
- Soma Dhakal
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, USA
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Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. Following G-quadruplex formation by its intrinsic fluorescence. FEBS Lett 2011; 585:3969-77. [PMID: 22079665 DOI: 10.1016/j.febslet.2011.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/23/2011] [Accepted: 11/01/2011] [Indexed: 12/11/2022]
Abstract
We characterized and compared the fluorescence properties of various well-defined G-quadruplex structures. The increase of intrinsic fluorescence of G-rich DNA sequences when they form G-quadruplexes can be used to monitor the folding and unfolding of G-quadruplexes as a function of cations and temperature. The temperature-dependent fluorescence spectra of different G-quadruplexes also exhibit characteristic patterns. Thus, the stability and possibly also the structure of G-quadruplexes can be characterized and distinguished by their intrinsic fluorescence spectra.
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Affiliation(s)
- Nguyen Thuan Dao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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28
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Rusciano G, De Luca AC, Pesce G, Sasso A, Oliviero G, Amato J, Borbone N, D'Errico S, Piccialli V, Piccialli G, Mayol L. Label-free probing of G-quadruplex formation by surface-enhanced Raman scattering. Anal Chem 2011; 83:6849-55. [PMID: 21780762 DOI: 10.1021/ac201783h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, we establish the use of surface-enhanced Raman scattering (SERS) as a label-free analytical technique for the direct detection of G-quadruplex formation. In particular, we demonstrate that SERS analysis allows the evaluation of the relative stability of G quadruplexes that differ for the number of G tetrads and investigate several structural features of quadruplexes, such as the orientation of glycosidic bonds, the identification of distortions in the sugar-phosphate backbone, and the degree of hydrogen-bond solvation. Herein, the fluctuation of the SERS spectra, due to the specific interaction of vibrational modes with the SERS-active substrate, is quantitatively analyzed before and after quadruplex formation. The results of this study suggest a perpendicular orientation of the quadruplexes (with or without the 3'-tetra end linker) with respect to the silver colloidal surface, which opens new perspectives for the use of SERS as a label-free analytical tool for the study of the binding mode between quadruplexes and their ligands.
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Affiliation(s)
- Giulia Rusciano
- Dipartimento di Scienze Fisiche, Complesso Universitario, Universitá di Napoli Federico II, Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy.
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29
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Zhou W, Brand NJ, Ying L. G-quadruplexes-novel mediators of gene function. J Cardiovasc Transl Res 2011; 4:256-70. [PMID: 21302011 DOI: 10.1007/s12265-011-9258-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 01/24/2011] [Indexed: 11/30/2022]
Abstract
Since the famous double-helix model was proposed, chromosomal DNA has been regarded as a rigid molecule containing the genetic information of an organism. It is clear now that DNA can adopt many transient, complex structures that can perform different biological functions. The G4 DNA (also called DNA G-quadruplex or G-tetraplex), a four-stranded DNA structure composed of stacked G-tetrads (guanine tetrads), has attracted much attention during the past two decades due to its ability to adopt a variety of structures and its possible biological functions. This review gives a glimpse on the structural diversity and biophysical properties of these fascinating DNA structures. Common methods that are widely used in investigating biophysical properties and biological functions of G4 DNA are described briefly. Next, bioinformatics studies that indicate evidence of evolutionary selection and potential functions of G4 DNA are discussed. Finally, examples of various biological functions of different G4 DNA are given, and potential roles of G4 DNA in respect of cardiovascular science are discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, UK.
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30
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Li J, Huang YQ, Qin WS, Liu XF, Huang W. An optical-logic system based on cationic conjugated polymer/DNA/intercalating dyes assembly for label-free detection of conformational conversion of DNA i-motif structure. Polym Chem 2011. [DOI: 10.1039/c0py00375a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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31
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Pagba CV, Lane SM, Wachsmann-Hogiu S. Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2010; 2:207-17. [PMID: 21339867 PMCID: PMC3038437 DOI: 10.1364/boe.2.000207] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/07/2010] [Accepted: 12/18/2010] [Indexed: 05/02/2023]
Abstract
Quadruplex structures are higher order structures formed by guanine-rich oligonucleotides. In the present study, temperature-induced conformational changes in the quadruplex structures of aptamers and other guanine-rich oligonucleotides are probed by Raman spectroscopy. In particular, dramatic changes in the fingerprint region are observed in the spectra of thrombin binding aptamer at higher temperatures. These changes are accompanied by a decrease in the intensity of the 1480 cm(-1) peak (attributed to C8 = N7-H2), which is diagnostic of the quadruplex structure. We also show that these changes can be reversed (to a certain extent) by addition of K(+) ions.
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Affiliation(s)
- Cynthia V. Pagba
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
| | - Stephen M. Lane
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Neurological Surgery, University of California Davis, 4860 Y Street, Sacramento, CA 95817
| | - Sebastian Wachsmann-Hogiu
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Pathology and Internal Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817
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32
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Jarem DA, Huckaby LV, Delaney S. AGG interruptions in (CGG)(n) DNA repeat tracts modulate the structure and thermodynamics of non-B conformations in vitro. Biochemistry 2010; 49:6826-37. [PMID: 20695523 DOI: 10.1021/bi1007782] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The trinucleotide repeat sequence CGG/CCG is known to expand in the human genome. This expansion is the primary pathogenic signature of fragile X syndrome, which is the most common form of inherited mental retardation. It has been proposed that formation of non-B conformations by the repetitive sequence contributes to the expansion mechanism. It is also known that the CGG/CCG repeat sequence of healthy individuals, which is not prone to expansion, contains AGG/CCT interruptions every 8-11 CGG/CCG repeats. Using DNA containing 19 or 39 CGG repeats, we have found that both the position and number of interruptions modulate the non-B conformation adopted by the repeat sequence. Analysis by chemical probes revealed larger loops and the presence of bulges for sequences containing interruptions. Additionally, using optical analysis and calorimetry, the effect of these structural changes on the thermodynamic stability of the conformation has been quantified. Notably, changing even one nucleotide, as occurs when CGG is replaced with an AGG interruption, causes a measurable decrease in the stability of the conformation adopted by the repeat sequence. These results provide insight into the role interruptions may play in preventing expansion in vivo and also contribute to our understanding of the relationship between non-B conformations and trinucleotide repeat expansion.
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Affiliation(s)
- Daniel A Jarem
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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Pagba CV, Lane SM, Cho H, Wachsmann-Hogiu S. Direct detection of aptamer-thrombin binding via surface-enhanced Raman spectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:047006. [PMID: 20799837 DOI: 10.1117/1.3465594] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this study, we exploit the sensitivity offered by surface-enhanced Raman scattering (SERS) for the direct detection of thrombin using the thrombin-binding aptamer (TBA) as molecular receptor. The technique utilizes immobilized silver nanoparticles that are functionalized with thiolated thrombin-specific binding aptamer, a 15-mer (5'-GGTTGGTGTGGTTGG-3') quadruplex forming oligonucleotide. In addition to the Raman vibrational bands corresponding to the aptamer and blocking agent, new peaks (mainly at 1140, 1540, and 1635 cm(-1)) that are characteristic of the protein are observed upon binding of thrombin. These spectral changes are not observed when the aptamer-nanoparticle assembly is exposed to a nonbinding protein such as bovine serum albumin (BSA). This methodology could be further used for the development of label-free biosensors for direct detection of proteins and other molecules of interest for which aptamers are available.
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Affiliation(s)
- Cynthia V Pagba
- University of California, Davis, Sacramento, California 95817, USA.
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34
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Sannohe Y, Sugiyama H. Overview of formation of G-quadruplex structures. ACTA ACUST UNITED AC 2010; Chapter 17:Unit 17.2.1-17. [PMID: 20201027 DOI: 10.1002/0471142700.nc1702s40] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There are many structures that can be adopted by nucleic acids other than the Watson-Crick duplex. In particular, a noncanonical four-stranded topology, called a G-quadruplex, is of great interest because of its roles in key biological processes such as the maintenance of telomeres and regulation of gene transcription. This review describes the condition for forming the G-quadruplex structure, G-quadruplex-forming sequences, and methods for studying the structures.
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35
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Wang L, Liu X, Yang Q, Fan Q, Song S, Fan C, Huang W. A colorimetric strategy based on a water-soluble conjugated polymer for sensing pH-driven conformational conversion of DNA i-motif structure. Biosens Bioelectron 2010; 25:1838-42. [DOI: 10.1016/j.bios.2009.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
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36
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Abu-Ghazalah RM, Irizar J, Helmy AS, Macgregor RB. A study of the interactions that stabilize DNA frayed wires. Biophys Chem 2010; 147:123-9. [PMID: 20122787 DOI: 10.1016/j.bpc.2010.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
Abstract
Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine-guanine interactions. To probe the hydrogen bonding involved in the stabilization of d(A(15)G(15)) frayed wires, we used Raman spectroscopy in which the DNA sample is held in photonic crystal fibers. This technique significantly enhances the signals thus allowing the use of very low laser power. Based on our results for d(A(15)G(15)) and those of incorporating the isoelectronic guanine analog pyrazolo[3,4,-d]pyrimidine or PPG, into a frayed wire-forming sequence, we provide evidence that these structures are based on the G-quadruplex model. Furthermore, from the Raman spectrum, we observed markers that are consistent with the presence of deoxyguanosine residues in the syn conformation, this suggests the presence of anti-parallel G-quadruplexes. To identify the species that contain syn guanine residues, we used circular dichroism and gel electrophoresis to study an ODN in which all of the guanine residues were brominated, d(A(15)(8-Br)G(15)). In the presence of potassium, d(A(15)(8-Br)G(15)) forms what appears to be an anti-parallel dimeric G-quadruplex. To our knowledge, this is the first report of a DNA sequence having all its guanine residues replaced by 8-bromo-guanine and maintaining its ability to form a G-quadruplex structure.
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Affiliation(s)
- Rashid M Abu-Ghazalah
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario, Canada
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37
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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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38
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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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39
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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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40
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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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41
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Töhl J, Eimer W. Interaction of a G-DNA quadruplex with mono- and divalent cations. A force field calculation. Biophys Chem 2007; 67:177-86. [PMID: 17029896 DOI: 10.1016/s0301-4622(97)00037-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/1996] [Revised: 03/13/1997] [Accepted: 03/14/1997] [Indexed: 11/26/2022]
Abstract
The formation and stability of four-stranded DNA in solution is specifically dependent on the type of cations present. The interaction potential of a model quadruplex structure with different mono- and divalent ions was determined by force field calculations. Though the electrostatic contribution to the total energy is mainly responsible for the stabilisation of the cations within the quadruplex channel, it is the van der Waals interaction at short distances that determines the specific characteristics of the different cations. An explicit consideration of the solvent indicates that the position of water molecules in close proximity to the DNA channel have a strong influence on the form of the potential, and hence on the capability of the cations for leaving and re-entering the cavity. The effect of cation size, as expressed through their Lennard-Jones parameters, is discussed.
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Affiliation(s)
- J Töhl
- Department of Chemistry, University of Bielefeld, PO. Box 10 01 31, D-33 501 Bielefeld, Germany
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42
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Srivastava S, Srivastava S, Singh S, Gupta VP, Gupta VD. STABILITY AND TRANSITION IN A DNA TETRAPLEX: A MODEL FOR TELOMERES. J MACROMOL SCI B 2007. [DOI: 10.1081/mb-100000050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shinoo Srivastava
- a Division of Biopolymers , Central Drug Research Institute , Lucknow, 226 001, India
| | - Seema Srivastava
- a Division of Biopolymers , Central Drug Research Institute , Lucknow, 226 001, India
| | - Shyam Singh
- a Division of Biopolymers , Central Drug Research Institute , Lucknow, 226 001, India
| | - Vijai Prakash Gupta
- a Division of Biopolymers , Central Drug Research Institute , Lucknow, 226 001, India
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Kaushik M, Kukreti S. Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human beta-globin gene cluster. Nucleic Acids Res 2006; 34:3511-22. [PMID: 16855288 PMCID: PMC1524902 DOI: 10.1093/nar/gkl456] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 05/21/2006] [Accepted: 06/13/2006] [Indexed: 01/07/2023] Open
Abstract
Structural polymorphism of DNA is a widely accepted property. A simple addition to this perception has been our recent finding, where a single nucleotide polymorphism (SNP) site present in a quasipalindromic sequence of beta-globin LCR exhibited a hairpin-duplex equilibrium. Our current studies explore that secondary structures adopted by individual complementary strands compete with formation of a perfect duplex. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, circular dichroism (CD) techniques, we have demonstrated the structural transitions within a perfect duplex containing 11 bp quasipalindromic stretch (TGGGG(G/C)CCCCA), to hairpins and bulge duplex forms. The extended version of the 11 bp duplex, flanked by 5 bp on both sides also demonstrated conformational equilibrium between duplex and hairpin species. Gel-electrophoresis confirms that the duplex coexists with hairpin and bulge duplex/cruciform species. Further, in CD spectra of duplexes, presence of two overlapping positive peaks at 265 and 285 nm suggest the features of A- as well as B-type DNA conformation and show oligomer concentration dependence, manifested in A --> B transition. This indicates the possibility of an architectural switching at quasipalindromic region between linear duplex to a cruciform structure. Such DNA structural variations are likely to be found in the mechanics of molecular recognition and manipulation by proteins.
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Affiliation(s)
- Mahima Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi(North Campus), Delhi 110007, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi(North Campus), Delhi 110007, India
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44
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Alberti P, Bourdoncle A, Saccà B, Lacroix L, Mergny JL. DNA nanomachines and nanostructures involving quadruplexes. Org Biomol Chem 2006; 4:3383-91. [PMID: 17036128 DOI: 10.1039/b605739j] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA is an attractive component for molecular recognition, because of its self-assembly properties. Its three-dimensional structure can differ markedly from the classical double helix. For example, DNA or RNA strands carrying guanine or cytosine stretches associate into four-stranded structures called G-quadruplexes or i-DNA, respectively. Since 2002, several groups have described nanomachines that take advantage of this structural polymorphism. We first introduce the unusual structures that are involved in these devices (i.e., i-DNA and G-quadruplexes) and then describe the opening and closing steps that allow cycling. A quadruplex-duplex molecular machine is then presented in detail, together with the rules that govern its formation, its opening/closing kinetics and the various technical and physico-chemical parameters that play a role in the efficiency of this device. Finally, we review the few examples of nanostructures that involve quadruplexes.
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Affiliation(s)
- Patrizia Alberti
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153, 43 rue Cuvier, 75231, Paris cedex 05, France.
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45
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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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Vorlícková M, Chládková J, Kejnovská I, Fialová M, Kypr J. Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats. Nucleic Acids Res 2005; 33:5851-60. [PMID: 16221978 PMCID: PMC1253834 DOI: 10.1093/nar/gki898] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Secondary structures of the G-rich strand of human telomere DNA fragments G3(TTAG3)n, n = 1–16, have been studied by means of circular dichroism spectroscopy and PAGE, in solutions of physiological potassium cation concentrations. It has been found that folding of these fragments into tetraplexes as well as tetraplex thermostabilities and enthalpy values depend on the number of TTAG3 repeats. The suggested topologies include, e.g. antiparallel and parallel bimolecular tetraplexes, an intramolecular antiparallel tetraplex, a tetraplex consisting of three parallel chains and one antiparallel chain, a poorly stable parallel intramolecular tetraplex, and both parallel and antiparallel tetramolecular tetraplexes. G3(TTAG3)3 folds into a single, stable and very compact intramolecular antiparallel tetraplex. With an increasing repeat number, the fragment tetraplexes surprisingly are ever less thermostable and their migration and enthalpy decrease indicate increasing irregularities or domain splitting in their arrangements. Reduced stability and different topology of lengthy telomeric tails could contribute to the stepwise telomere shortening process.
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Affiliation(s)
- Michaela Vorlícková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
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Šket P, Črnugelj M, Plavec J. Identification of mixed di-cation forms of G-quadruplex in solution. Nucleic Acids Res 2005; 33:3691-7. [PMID: 15985684 PMCID: PMC1164438 DOI: 10.1093/nar/gki690] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Multinuclear NMR study has demonstrated that G-quadruplex adopted by d(G3T4G4) exhibits two cation binding sites between three of its G-quartets. Titration of tighter binding K+ ions into the solution of d(G3T4G4)2 folded in the presence of NH4+15 ions uncovered a mixed mono-K+-mono-NH4+15 form that represents intermediate in the conversion of di-NH4+15 into di-K+ form. Analogously, NH4+15 ions were found to replace Na+ ions inside d(G3T4G4)2 quadruplex. The preference of NH4+15 over Na+ ions for the two binding sites is considerably smaller than the preference of K+ over NH4+15 ions. The two cation binding sites within the G-quadruplex core differ to such a degree that NH4+15 ions bound to the site, which is closer to the edge-type loop, are always replaced first during titration by K+ ions. The second binding site is not taken up by K+ ion until K+ ion already resides at the first binding site. Quantitative analysis of concentrations of the three di-cation forms, which are in slow exchange on the NMR time scale, at 12 K+ ion concentrations afforded equilibrium binding constants. K+ ion binding to sites U and L within d(G3T4G4)2 is more favorable with respect to NH4+15 ions by Gibbs free energies of approximately −24 and −18 kJ mol−1 which includes differences in cation dehydration energies, respectively.
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Affiliation(s)
| | | | - Janez Plavec
- To whom correspondence should be addressed. Tel: +386 1 47 60 353; Fax: +386 1 47 60 300;
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Kumar N, Maiti S. Quadruplex to Watson-Crick duplex transition of the thrombin binding aptamer: a fluorescence resonance energy transfer study. Biochem Biophys Res Commun 2004; 319:759-67. [PMID: 15184048 DOI: 10.1016/j.bbrc.2004.05.052] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/17/2022]
Abstract
Thermodynamic parameters of closing up of guanine-rich thrombin binding element, upon binding to K(+) and Na(+) ions to form quadruplexes and opening up of these quadruplexes upon binding to its complementary strand, were investigated. For this purpose, 15mer deoxynucleotide, d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), labeled with 5'-fluorescein and 3'-tetramethylrhodamine was taken and fluorescence resonance energy transfer was monitored as a function of either metal ions or complementary strand concentrations. Equilibrium association constant obtained from FRET studies demonstrates that K(+) ions bind with higher affinity than the Na(+) ions. The enthalpy changes, DeltaH, obtained from temperature dependence of equilibrium association constant studies revealed that formation of quadruplex upon binding of metal ions is primarily enthalpy driven. Binding studies of complementary strand to the quadruplex suggest that opening of a quadruplex in NaCl buffer in presence of the complementary strand is enthalpic as well as entropic driven and can occur easily, whereas opening of the same quadruplex in KCl buffer suffers from enthalpic barrier. Comparison of overall thermodynamic parameters along with kinetics studies indicates that, although quadruplexes cannot efficiently compete with duplex formation at physiological pH, they delay the association of two strands.
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Affiliation(s)
- Niti Kumar
- Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Abstract
DNA conjugates containing adjacent duplex and guanine quadruplex assemblies have been designed to explore charge transport into quadruplex architectures. The quadruplex assemblies have been characterized structurally using circular dichroism and by assaying for chemical protection. Using an intercalating rhodium photooxidant, noncovalently bound or tethered to the duplex end, oxidizing radicals are found to be trapped in the folded quadruplex. Damage is observed almost exclusively at the external tetrads of the quadruplex. Little damage of the center tetrad is observed, due most likely to lowered efficiency of radical trapping within the quadruplex core. This pattern of damage is distinct from that observed for repetitive G sequences within duplex DNA. The data indicate, furthermore, that in the conjugates examined, the guanine quadruplex provides a more effective trap than a 5'-GG-3' guanine doublet within duplex DNA. Within these assemblies, sufficient base-base overlap must exist at the duplex/quadruplex junction to allow for charge migration. This funneling of damage to the quadruplex, as well as the unique pattern of damage within the quadruplex, requires consideration with respect to the analysis of oxidative DNA damage within the cell.
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Affiliation(s)
- Sarah Delaney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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