1
|
Marquevielle J, De Rache A, Vialet B, Morvan E, Mergny JL, Amrane S. G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C-T base-pair. Nucleic Acids Res 2022; 50:7134-7146. [PMID: 35736226 PMCID: PMC9262591 DOI: 10.1093/nar/gkac523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C-T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.
Collapse
Affiliation(s)
- Julien Marquevielle
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Aurore De Rache
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
- Department of Chemistry, UNamur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Brune Vialet
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Samir Amrane
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France
- Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| |
Collapse
|
2
|
Jarošová P, Hannig P, Kolková K, Mazzini S, Táborská E, Gargallo R, Borgonovo G, Artali R, Táborský P. Alkaloid Escholidine and Its Interaction with DNA Structures. BIOLOGY 2021; 10:1225. [PMID: 34943140 PMCID: PMC8698932 DOI: 10.3390/biology10121225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022]
Abstract
Berberine, the most known quaternary protoberberine alkaloid (QPA), has been reported to inhibit the SIK3 protein connected with breast cancer. Berberine also appears to reduce the bcl-2 and XIAP expression-proteins responsible for the inhibition of apoptosis. As some problems in the therapy with berberine arose, we studied the DNA binding properties of escholidine, another QPA alkaloid. CD, fluorescence, and NMR examined models of i-motif and G-quadruplex sequences present in the n-myc gene and the c-kit gene. We provide evidence that escholidine does not induce stabilization of the i-motif sequences, while the interaction with G-quadruplex structures appears to be more significant.
Collapse
Affiliation(s)
- Petra Jarošová
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Pavel Hannig
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Kateřina Kolková
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | - Eva Táborská
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, E-08028 Barcelona, Spain;
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | | | - Petr Táborský
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| |
Collapse
|
3
|
Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
Collapse
Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| |
Collapse
|
4
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
5
|
Pallan PS, Lybrand TP, Schlegel MK, Harp JM, Jahns H, Manoharan M, Egli M. Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Biochemistry 2020; 59:4627-4637. [PMID: 33275419 DOI: 10.1021/acs.biochem.0c00685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by GApGA, and the phosphate p stacks on G. We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2···G and Rp-PSO···G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 °C in melting temperature Tm and -4.7 kcal/mol in ΔΔG°. Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 Å longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 Å for S vs 1.52 Å for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.
Collapse
Affiliation(s)
| | | | - Mark K Schlegel
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Hartmut Jahns
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | |
Collapse
|
6
|
Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| |
Collapse
|
7
|
Maity A, Winnerdy FR, Chang WD, Chen G, Phan AT. Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs. Nucleic Acids Res 2020; 48:3315-3327. [PMID: 32100003 PMCID: PMC7102960 DOI: 10.1093/nar/gkaa008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
Collapse
Affiliation(s)
- Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Weili Denyse Chang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| |
Collapse
|
8
|
|
9
|
Sengar A, Vandana J, Chambers VS, Di Antonio M, Winnerdy F, Balasubramanian S, Phan AT. Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter. Nucleic Acids Res 2019; 47:1564-1572. [PMID: 30551210 PMCID: PMC6379715 DOI: 10.1093/nar/gky1179] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/02/2018] [Accepted: 12/12/2018] [Indexed: 01/08/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming sequence containing bulges within the PARP1 promoter. Structural features, like bulges, provide opportunities for selective chemical targeting of the non-canonical G-quadruplex structure within the PARP1 promoter, which could serve as an alternative therapeutic approach for the regulation of PARP1 expression. Here we report the G-quadruplex structure formed by a 23-nucleotide G-rich sequence in the PARP1 promoter. Our study revealed a three-layered intramolecular (3+1) hybrid G-quadruplex scaffold, in which three strands are oriented in one direction and the fourth in the opposite direction. This structure exhibits unique structural features such as an adenine bulge and a G·G·T base triple capping structure formed between the central edgewise loop, propeller loop and 5' flanking terminal. Given the highly important role of PARP1 in DNA repair and cancer intervention, this structure presents an attractive opportunity to explore the therapeutic potential of PARP1 inhibition via G-quadruplex DNA targeting.
Collapse
Affiliation(s)
- Anjali Sengar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - J Jeya Vandana
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Vicki S Chambers
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Marco Di Antonio
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| |
Collapse
|
10
|
Karg B, Weisz K. Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes. Chemistry 2018; 24:10246-10252. [PMID: 29756658 DOI: 10.1002/chem.201801851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/12/2018] [Indexed: 01/24/2023]
Abstract
A G-quadruplex forming sequence from the MYC promoter region was modified with syn-favoring 8-bromo-2'-deoxyguanosine residues. Depending on the number and position of modifications in the intramolecular parallel G-quadruplex, substitutions with the bromoguanosine analogue at the 5'-tetrad induce conformational rearrangements with concerted all-anti to all-syn transitions for all residues of the modified G-quartet. No unfavorable steric interactions of the C8-substituents in the medium grooves are apparent in the high-resolution structure as determined for a tetrasubstituted MYC quadruplex that exclusively forms the all-syn isomer. In contrast, considerable steric clashes with 5'-phosphate oxygen atoms for those analogues that follow a less flexible 1-nucleotide loop in the native all-anti conformation seem to constitute the major driving force for the tetrad inversion and allow for the rational design of appropriately substituted sequences. Correlations found between the population of species subjected to a tetrad flip and melting temperatures indicate that more effective conformational transitions are compromised by lower thermal stabilities of the modified parallel quadruplexes.
Collapse
Affiliation(s)
- Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| |
Collapse
|
11
|
Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
Collapse
Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
12
|
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: 31] [Impact Index Per Article: 3.4] [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.
Collapse
|
13
|
Lim KW, Jenjaroenpun P, Low ZJ, Khong ZJ, Ng YS, Kuznetsov VA, Phan AT. Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study. Nucleic Acids Res 2015; 43:5630-46. [PMID: 25958397 PMCID: PMC4477648 DOI: 10.1093/nar/gkv355] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/02/2015] [Indexed: 12/12/2022] Open
Abstract
Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters. Our analysis suggested that these should cover close to half of total SLQS in the entire genome. Among these, 48 508 SLQS were strand-specifically located in genic/promoter regions, with the majority of genes displaying a low number of SLQS. Notably, genes containing abundant SLQS clusters were strongly associated with brain tissues. Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. In vitro formation of diverse QDH by selective SLQS hits were successfully verified by nuclear magnetic resonance spectroscopy. Folding topologies of two SLQS were elucidated in detail. We also demonstrated that sequence changes at mutation/single-nucleotide polymorphism loci could affect the structural conformations adopted by SLQS. Thus, our predicted SLQS offer novel insights into the potential involvement of QDH in diverse (patho)biological processes and could represent novel regulatory signals.
Collapse
Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore
| | - Zhen Jie Low
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zi Jian Khong
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Yi Siang Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | | | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| |
Collapse
|
14
|
Zhang S, Wu Y, Zhang W. G-Quadruplex Structures and Their Interaction Diversity with Ligands. ChemMedChem 2014; 9:899-911. [DOI: 10.1002/cmdc.201300566] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Indexed: 12/22/2022]
|
15
|
Lim KW, Khong ZJ, Phan AT. Thermal Stability of DNA Quadruplex–Duplex Hybrids. Biochemistry 2013; 53:247-57. [DOI: 10.1021/bi401161a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kah Wai Lim
- School
of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zi Jian Khong
- School
of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Anh Tuân Phan
- School
of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| |
Collapse
|
16
|
Lim KW, Ng VCM, Martín-Pintado N, Heddi B, Phan AT. Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity. Nucleic Acids Res 2013; 41:10556-62. [PMID: 23999095 PMCID: PMC3905899 DOI: 10.1093/nar/gkt771] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K+ ions and only one in the presence of Na+ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K+ but not Na+. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na+ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na+-containing environment. These structures, together with the coexistence of other conformations in Na+ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K+ ions.
Collapse
Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Veronica Chinn Min Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Nerea Martín-Pintado
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +65 6514 1915; Fax: +65 6795 7981;
| |
Collapse
|
17
|
Karsisiotis AI, O'Kane C, Webba da Silva M. DNA quadruplex folding formalism--a tutorial on quadruplex topologies. Methods 2013; 64:28-35. [PMID: 23791747 DOI: 10.1016/j.ymeth.2013.06.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/04/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022] Open
Abstract
Quadruplexes of DNA adopt a large variety of topologies that are dependent on their environment. We have been developing a formalism for quadruplex folding based on the relationship between base and its sugar--as defined by the glycosidic bond angle. By reducing the quadruplex stem to a description based on two finite states of the range of angles the glycosidic bond angle may adopt, the description of the relationships of type of loop and groove widths of a quadruplex stem are possible. In its current form this formalism has allowed for the prediction of some unimolecular quadruplex topologies. Its rules, whilst developed for unimolecular quadruplexes of three loops, are of general utility in understanding the interdependency of structural characteristics of multimolecular folds, as well as unimolecular quadruplexes of more than three loops. Here we describe current understanding of the interdependent structural features that define the quadruplex fold, and provide a tutorial for the use and application of this formalism.
Collapse
Affiliation(s)
- Andreas Ioannis Karsisiotis
- School of Pharmacy & Pharmaceutical Sciences, Biomedical Sciences Research Institute, University of Ulster, Cromore Road, BT52 1SA, Coleraine, UK
| | | | | |
Collapse
|
18
|
Smestad J, Maher LJ. Ion-dependent conformational switching by a DNA aptamer that induces remyelination in a mouse model of multiple sclerosis. Nucleic Acids Res 2013; 41:1329-42. [PMID: 23175609 PMCID: PMC3553947 DOI: 10.1093/nar/gks1093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We recently reported that a guanosine-rich 40-mer DNA aptamer (LJM-3064) mediates remyelination in the Theiler's murine encephalomyelitis virus mouse model of multiple sclerosis. Here, we characterize the G-quadruplex forms of this aptamer in vitro, and demonstrate using circular dichroism spectroscopy that LJM-3064 undergoes a monovalent ion-dependent conformational switch. In the presence of sodium ions and no potassium ions, LJM-3064 adopts an antiparallel-stranded G-quadruplex structure. When presented with low concentrations of potassium ions in a buffer that mimics the composition of interstitial fluid and blood plasma, LJM-3064 rapidly switches to a parallel-stranded G-quadruplex conformation, which is presumably the physiologically active folded form. We characterize these conformational states using dimethyl sulfate reactivity studies and Bal 31 nuclease probing. Our analysis indicates that only the 5'-terminal 26 nucleotides are involved in G-quadruplex formation. Thermodynamic characterization of LJM-3064 at physiologically relevant ion concentrations reveals the G-quadruplex to be metastable at human body temperature. These data provide important structural and thermodynamic insights that may be valuable in optimizing LJM-3064 as a therapeutic remyelinating agent.
Collapse
Affiliation(s)
- John Smestad
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | |
Collapse
|
19
|
Structural probes in quadruplex nucleic acid structure determination by NMR. Molecules 2012; 17:13073-86. [PMID: 23128087 PMCID: PMC6268857 DOI: 10.3390/molecules171113073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/01/2012] [Accepted: 11/01/2012] [Indexed: 12/31/2022] Open
Abstract
Traditionally, isotope-labelled DNA and RNA have been fundamental to nucleic acid structural studies by NMR. Four-stranded nucleic acid architectures studies increasingly benefit from a plethora of nucleotide conjugates for resonance assignments, the identification of hydrogen bond alignments, and improving the population of preferred species within equilibria. In this paper, we review their use for these purposes. Most importantly we identify reasons for the failure of some modifications to result in quadruplex formation.
Collapse
|
20
|
Smith NM, Amrane S, Rosu F, Gabelica V, Mergny JL. Mercury-thymine interaction with a chair type G-quadruplex architecture. Chem Commun (Camb) 2012; 48:11464-6. [PMID: 23090661 DOI: 10.1039/c2cc36481f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The T-Hg-T bond was utilized to cross-link two lateral loops of chair-type G-quadruplex DNA (G4-DNA) structures. Two out of five cross-linking geometries are able to increase the melting temperature and simultaneously reduce the polymorphism of the G4-DNA conformations.
Collapse
|
21
|
Cang X, Šponer J, Cheatham TE. Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. J Am Chem Soc 2011; 133:14270-9. [PMID: 21761922 PMCID: PMC3168932 DOI: 10.1021/ja107805r] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence–structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT2, dT3, dTTA, and dT4] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The work also provides new insight into G-quadruplex folding and stability. This includes reporting the observed instability of the left propeller loop, which extends the rules for G-quadruplex folding. We also suggest a plausible explanation why human telomere sequences predominantly form hybrid-I and hybrid-II type structures in K+ solution. Overall, our calculation results indicate that short loops generally are less stable than longer loops, and we hypothesize that the extreme stability of sequences with very short loops could possibly derive from the formation of parallel multimers. The results suggest that free energy differences, estimated from MD and free energy analysis with current force fields and simulation protocols, are able to complement experiment and to help dissect and explain loop sequence, loop length, and G-tract length and orientation influences on G-quadruplex structure.
Collapse
Affiliation(s)
- Xiaohui Cang
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | |
Collapse
|
22
|
Cang X, Šponer J, Cheatham TE. Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res 2011; 39:4499-512. [PMID: 21296760 PMCID: PMC3105399 DOI: 10.1093/nar/gkr031] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 01/08/2023] Open
Abstract
Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)](4) models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.
Collapse
Affiliation(s)
- Xiaohui Cang
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, Brno, Czech Republic and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Jiří Šponer
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, Brno, Czech Republic and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, Brno, Czech Republic and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Fernando H, Sewitz S, Darot J, Tavaré S, Huppert JL, Balasubramanian S. Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nucleic Acids Res 2009; 37:6716-22. [PMID: 19745055 PMCID: PMC2777450 DOI: 10.1093/nar/gkp740] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex nucleic acids have been proposed to play a role in a number of fundamental biological processes that include transcription and translation. We have developed a single-chain antibody that is selective for G-quadruplex DNA over double-stranded DNA, and here show that when it is expressed in human cells, it significantly affects the expression of a wide variety of genes, in a manner that correlates with the presence of predicted G-quadruplexes. We observe cases where gene expression is increased or decreased, and that there are apparent interactions with G-quadruplex motifs at the beginning and end of the genes, and on either strand. The outcomes of this genome-wide study demonstrate that G-quadruplex recognition by the antibody has physiological consequences, and provides insights into some of the complexity associated with G-quadruplex-based regulation.
Collapse
Affiliation(s)
- Himesh Fernando
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | | | | | | | | |
Collapse
|
25
|
Lane AN, Chaires JB, Gray RD, Trent JO. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 2008; 36:5482-515. [PMID: 18718931 PMCID: PMC2553573 DOI: 10.1093/nar/gkn517] [Citation(s) in RCA: 571] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 07/26/2008] [Accepted: 07/29/2008] [Indexed: 12/30/2022] Open
Abstract
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
Collapse
Affiliation(s)
- Andrew N Lane
- Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA.
| | | | | | | |
Collapse
|
26
|
Webba da Silva M. NMR methods for studying quadruplex nucleic acids. Methods 2008; 43:264-77. [PMID: 17967697 DOI: 10.1016/j.ymeth.2007.05.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 05/16/2007] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.
Collapse
Affiliation(s)
- Mateus Webba da Silva
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine BT52 1SA, UK.
| |
Collapse
|
27
|
|
28
|
Patel DJ, Phan AT, Kuryavyi V. Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res 2007; 35:7429-55. [PMID: 17913750 PMCID: PMC2190718 DOI: 10.1093/nar/gkm711] [Citation(s) in RCA: 734] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Guanine-rich DNA sequences can form G-quadruplexes stabilized by stacked G–G–G–G tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent solution NMR-based G-quadruplex structures formed by the four-repeat human telomere in K+ solution and the guanine-rich strands of c-myc, c-kit and variant bcl-2 oncogenic promoters, as well as a bimolecular G-quadruplex that targets HIV-1 integrase. Such structure determinations have helped to identify unanticipated scaffolds such as interlocked G-quadruplexes, as well as novel topologies represented by double-chain-reversal and V-shaped loops, triads, mixed tetrads, adenine-mediated pentads and hexads and snap-back G-tetrad alignments. The review also highlights the recent identification of guanine-rich sequences positioned adjacent to translation start sites in 5′-untranslated regions (5′-UTRs) of RNA oncogenic sequences. The activity of the enzyme telomerase, which maintains telomere length, can be negatively regulated through G-quadruplex formation at telomeric ends. The review evaluates progress related to ongoing efforts to identify small molecule drugs that bind and stabilize distinct G-quadruplex scaffolds associated with telomeric and oncogenic sequences, and outlines progress towards identifying recognition principles based on several X-ray-based structures of ligand–G-quadruplex complexes.
Collapse
Affiliation(s)
- Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
| | | | | |
Collapse
|
29
|
Ikebukuro K, Yoshida W, Sode K. Aptameric enzyme subunit for homogeneous DNA sensing. Biotechnol Lett 2007; 30:243-52. [PMID: 17849085 PMCID: PMC7087721 DOI: 10.1007/s10529-007-9526-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 08/22/2007] [Accepted: 08/28/2007] [Indexed: 11/29/2022]
Abstract
We have developed an aptameric enzyme subunit (AES) which can detect the DNA in a homogeneous solution. The AES is an artificial enzyme subunit composed of an enzyme-inhibiting aptamer bearing a target-molecule binding site. We connected a probe DNA to a thrombin-inhibiting aptamer at its 5' or 3' end. The inhibitory activity of the thrombin-inhibiting aptamer bearing the probe DNA decreased compared to that of the original aptamer; however, it recovered upon hybridization with the target DNA. Using this AES, we were able to detect target DNAs by measuring the thrombin activity in a homogeneous solution.
Collapse
Affiliation(s)
- Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | | | | |
Collapse
|
30
|
Vorlícková M, Bednárová K, Kejnovská I, Kypr J. Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions. Biopolymers 2007; 86:1-10. [PMID: 17211886 DOI: 10.1002/bip.20672] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA guanine quadruplexes are all based on stacks of guanine tetrads, but they can be of many types differing by mutual strand orientation, topology, position and structure of loops, and the number of DNA molecules constituting their structure. Here we have studied a series of nine DNA fragments (G(3)Xn)(3)G(3), where X = A, C or T, and n = 1, 2 or 3, to find how the particular bases and their numbers enable folding of the molecule into quadruplex and what type of quadruplex is formed. We show that any single base between G(3) blocks gives rise to only four-molecular parallel-stranded quadruplexes in water solutions. In contrast to previous models, even two Ts in potential loops lead to tetramolecular parallel quadruplexes and only three consecutive Ts lead to an intramolecular quadruplex, which is antiparallel. Adenines make the DNA less prone to quadruplex formation. (G(3)A(2))(3)G(3) folds into an intramolecular antiparallel quadruplex. The same is true with (G(3)A(3))(3)G(3) but only in KCl. In NaCl or LiCl, (G(3)A(3))(3)G(3) prefers to generate homoduplexes. Cytosine still more interferes with the quadruplex, which only is generated by (G(3)C)(3)G(3), whereas (G(3)C(2))(3)G(3) and (G(3)C(3))(3)G(3) generate hairpins and/or homoduplexes. Ethanol is a more potent DNA guanine quadruplex inducer than are ions in water solutions. It promotes intramolecular folding and parallel orientation of quadruplex strands, which rather corresponds to quadruplex structures observed in crystals.
Collapse
Affiliation(s)
- Michaela Vorlícková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic.
| | | | | | | |
Collapse
|
31
|
Yoshida W, Sode K, Ikebukuro K. Aptameric enzyme subunit for biosensing based on enzymatic activity measurement. Anal Chem 2007; 78:3296-303. [PMID: 16689530 DOI: 10.1021/ac060254o] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aptameric enzyme subunit (AES), which is a DNA aptamer composed of an enzyme-inhibiting aptamer and a target molecule-binding aptamer, has been developed for the biosensing of target molecules. We used a thrombin-inhibiting aptamer as the aptamer that inhibits enzymatic activity. The thrombin-inhibiting aptamer folds into the G-quartet structure, which plays an important role in its inhibitory activity. As a target molecule-binding aptamer, an adenosine-binding aptamer was inserted into the G-quartet structure of the thrombin-inhibiting aptamer to enable the change of the G-quartet structure upon the recognition of adenosine. In the present study, the change in the G-quartet structure led to a change in the thrombin inhibition activity, and adenosine was successfully detected by measuring the thrombin activity in a homogeneous solution without bound/free separation. We constructed two kinds of AESs; one of the structures is universal and can be used for designing any target molecule-binding aptamer. Since the enzyme activity is measured, AESs enable the simple and high-sensitivity detection of target molecules in a homogeneous assay.
Collapse
Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-machi, Koganei, Tokyo 184-8588, Japan
| | | | | |
Collapse
|
32
|
Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 2006; 34:5402-15. [PMID: 17012276 PMCID: PMC1636468 DOI: 10.1093/nar/gkl655] [Citation(s) in RCA: 1824] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.
Collapse
Affiliation(s)
| | | | | | | | - Stephen Neidle
- To whom correspondence should be addressed. Tel: +44 207 753 5969; Fax: +44 207 753 5970;
| |
Collapse
|
33
|
Yoshida W, Sode K, Ikebukuro K. Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers. Biochem Biophys Res Commun 2006; 348:245-52. [PMID: 16876760 PMCID: PMC7092944 DOI: 10.1016/j.bbrc.2006.07.069] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 07/12/2006] [Indexed: 11/26/2022]
Abstract
A novel aptameric enzyme subunit (AES) which can detect target DNAs has been developed. AES is an enzyme-inhibiting aptamer bearing a target-molecule binding site which can allosterically control enzymatic activity. The thrombin-inhibiting aptamer bearing a G-quartet structure was chosen as the enzyme-inhibiting aptamer. The stem-and-loop structure, which contains a strand complementary to the target DNA, was inserted into the G-quartet structure of the thrombin-inhibiting aptamer to disrupt the G-quartet structure through the hybridization of the target DNA with the complementary strand in the AES. The disruption of the G-quartet structure led to a decrease of the inhibitory activity of the whole aptameric complex. Using this designed aptamer, we were able to detect target DNAs by measuring the thrombin activity in a homogeneous solution without bound/free separation, and the lower detection limit was 20 nM.
Collapse
|
34
|
Mergny JL, De Cian A, Amrane S, da Silva MW. Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes. Nucleic Acids Res 2006; 34:2386-97. [PMID: 16682446 PMCID: PMC1458523 DOI: 10.1093/nar/gkl098] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Repetitive 5′GGXGG DNA segments abound in, or near, regulatory regions of the genome and may form unusual structures called G-quadruplexes. Using NMR spectroscopy, we demonstrate that a family of 5′GCGGXGGY sequences adopts a folding topology containing double-chain reversals. The topology is composed of two bistranded quadruplex monomeric units linked by formation of G:C:G:C tetrads. We provide a complete thermodynamic and kinetic analysis of 13 different sequences using absorbance spectroscopy and DSC, and compare their kinetics with a canonical tetrameric parallel-stranded quadruplex formed by TG4T. We demonstrate large differences (up to 105-fold) in the association constants of these quadruplexes depending on primary sequence; the fastest samples exhibiting association rate equal or higher than the canonical TG4T quadruplex. In contrast, all sequences studied here unfold at a lower temperature than this quadruplex. Some sequences have thermodynamic stability comparable to the canonical TG4T tetramolecular quadruplex, but with faster association and dissociation. Sequence effects on the dissociation processes are discussed in light of structural data.
Collapse
Affiliation(s)
- Jean-Louis Mergny
- To whom correspondence should be addressed. Jean-Louis Mergny: Tel: +33 1 40 79 36 89; Fax: +33 1 40 79 37 05;
| | | | | | - Mateus Webba da Silva
- School of Biomedical Sciences, University of UlsterColeraine BT52 1SA, Northern Ireland, UK
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center1275 York Avenue, New York, NY 10021, USA
- Correspondance may also be addressed to M. Webba da Silva. Tel: +44 28 7032 4009; Fax: +44 28 7032 4375;
| |
Collapse
|
35
|
Hazel P, Parkinson GN, Neidle S. Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures. Nucleic Acids Res 2006; 34:2117-27. [PMID: 16641317 PMCID: PMC1449907 DOI: 10.1093/nar/gkl182] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405–16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93–102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dimer topology for sequences with T3 and T2 loops, which depend on the loop lengths, rather than only on G-quartet stability.
Collapse
Affiliation(s)
| | | | - Stephen Neidle
- To whom correspondence should be addressed. Tel: 44 207 753 5969; Fax: 44 207 753 5970;
| |
Collapse
|
36
|
Fialová M, Kypr J, Vorlícková M. The thrombin binding aptamer GGTTGGTGTGGTTGG forms a bimolecular guanine tetraplex. Biochem Biophys Res Commun 2006; 344:50-4. [PMID: 16616893 DOI: 10.1016/j.bbrc.2006.03.144] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 03/21/2006] [Indexed: 11/29/2022]
Abstract
In the literature, the thrombin binding aptamer GGTTGGTGTGGTTGG is generally taken as a prototype of an intramolecular guanine tetraplex of DNA. Our results, however, show that this notion is not true in aqueous solutions. This conclusion is based on a dependence of the CD spectra on aptamer concentration, migration of the aptamer in polyacrylamide gels, and the Ferguson analysis of the gel migration data. The presented data document that the aptamer forms a bimolecular tetraplex. We furthermore show that only an extension of the aptamer by a sequence containing further guanines, or an elongation of loop regions, causes that its tetraplex folding is intramolecular.
Collapse
Affiliation(s)
- Markéta Fialová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | | | | |
Collapse
|
37
|
Ikebukuro K, Okumura Y, Sumikura K, Karube I. A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm. Nucleic Acids Res 2005; 33:e108. [PMID: 16002787 PMCID: PMC1174901 DOI: 10.1093/nar/gni108] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Thrombin-inhibiting DNA aptamers have already been obtained through the systematic evolution of ligands by exponential enrichment (SELEX). However, SELEX is a method that screens DNA aptamers that bind to their target molecules, and it sometimes fails to screen good inhibitors. Therefore, it is necessary to develop a method of screening DNA aptamers based on their inhibitory effects on the target molecules. We developed a novel method of detecting aptamers using an evolution-mimicking algorithm, and we applied it to the search of new aptamers which inhibit thrombin. First, we randomly designed and synthesized ten 15mer oligonucleotides presumed to form G-quartet structures, and then measured their thrombin-inhibiting activities. The aptamers showing high inhibitory activity were selected, and we shuffled and mutated those sequences in silico to generate 10 new sequences of next-generation aptamers. After repeating the cycle five times, we successfully obtained the same aptamers reported previously, and they showed high inhibitory activity. In addition, we added 8mer oligonucleotides to both the 5' and the 3' end of the selected 15mer aptamers, and then repeated the evolution in silico. After two cycles, we were able to obtain aptamers with higher inhibitory activity than that of the 15mer aptamers.
Collapse
Affiliation(s)
- Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology 2-24-16 Naka-machi, Koganei, Tokyo 184-8588, Japan.
| | | | | | | |
Collapse
|
38
|
Webba da Silva M. Experimental demonstration of T:(G:G:G:G):T hexad and T:A:A:T tetrad alignments within a DNA quadruplex stem. Biochemistry 2005; 44:3754-64. [PMID: 15751952 DOI: 10.1021/bi0478190] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A template-based approach was used to design unprecedented architectural motifs into a known DNA framework. The structure formed by the sequence d(GCGGTTGGAT) in 0.1 M Na(+) solution has been determined using molecular dynamics simulations constrained by distance and dihedral restraints derived from NMR experiments. The molecular topology has been previously observed for the sequence d(GCGGTGGAT) (Webba da Silva, M. (2003) Biochemistry 42, 14356-65). Insertion of a single thymine into the double chain reversal formed by the segment GGTGG results in the unprecedented experimental demonstration of a T:(G:G:G:G):T hexad. The bi-stranded hexad results from the pairing alignment of two G(T-G) triads. Each triad results from recognition of the sheared edge of a guanine by the Watson-Crick edge of a thymine of the segment GGTTGG. The alignment is stabilized by base-stacking of the thymine to the sugar pucker of the preceding thymine. The latter is involved in formation of the T:A:A:T tetrad alignment by forming a hydrogen bond with the free amino proton of a Watson-Crick aligned A:A mispair. We have thus established that residues in double chain reversal loops linking juxtaposed tetrads of a quadruplex stem may facilitate formation of yet unknown hydrogen bond alignments. By employing a systematic approach analysis of sequence motifs appearing in double chain reversals, bridging tetrad layers should allow for the prediction of topologies and architectural motifs appearing in biologically relevant genomic regions.
Collapse
Affiliation(s)
- Mateus Webba da Silva
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.
| |
Collapse
|
39
|
Phan AT, Kuryavyi V, Ma JB, Faure A, Andréola ML, Patel DJ. An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase. Proc Natl Acad Sci U S A 2005; 102:634-9. [PMID: 15637158 PMCID: PMC545538 DOI: 10.1073/pnas.0406278102] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report on the NMR-based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit, which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel, and all guanines are anti with the exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G.G.G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A.(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.
Collapse
Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | | | | | | | | | | |
Collapse
|
40
|
Phan AT, Modi YS, Patel DJ. Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. J Am Chem Soc 2004; 126:8710-6. [PMID: 15250723 PMCID: PMC4692381 DOI: 10.1021/ja048805k] [Citation(s) in RCA: 426] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The nuclease-hypersensitivity element III1 in the c-myc promoter is a good anticancer target since it largely controls transcriptional activation of the important c-myc oncogene. Recently, the guanine-rich strand of this element has been shown to form an equilibrium between G-quadruplex structures built from two different sets of G-stretches; two models of intramolecular fold-back antiparallel-stranded G-quadruplexes, called "basket" and "chair" forms, were proposed. Here, we show by NMR that two sequences containing these two sets of G-stretches form intramolecular propeller-type parallel-stranded G-quadruplexes in K(+)-containing solution. The two structures involve a core of three stacked G-tetrads formed by four parallel G-stretches with all anti guanines and three double-chain-reversal loops bridging three G-tetrad layers. The central loop contains two or six residues, while the two other loops contain only one residue.
Collapse
Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
| | | | | |
Collapse
|
41
|
Phan AT, Modi YS, Patel DJ. Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) Sequence interconverts between asymmetric dimeric G-quadruplexes in solution. J Mol Biol 2004; 338:93-102. [PMID: 15050825 PMCID: PMC4690524 DOI: 10.1016/j.jmb.2004.02.042] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 02/17/2004] [Accepted: 02/18/2004] [Indexed: 10/26/2022]
Abstract
Recently, the two-repeat human telomeric d(TAGGGTTAGGGT) sequence has been shown to form interconverting parallel and antiparallel G-quadruplex structures in solution. Here, we examine the structures formed by the two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) sequence, which differs from the human sequence only by one G-for-A replacement in each repeat. We show by NMR that this sequence forms two novel G-quadruplex structures in Na+-containing solution. Both structures are asymmetric, dimeric G-quadruplexes involving a core of four stacked G-tetrads and two edgewise loops. The adjacent strands of the G-tetrad core are alternately parallel and antiparallel. All G-tetrads adopt syn.syn.anti.anti alignments, which occur with 5'-syn-anti-syn-anti-3' alternations along G-tracks. In the first structure (head-to-head), two loops are at one end of the G-tetrad core; in the second structure (head-to-tail), two loops are located on opposite ends of the G-tetrad core. In contrast to the human telomere counterpart, the proportions of the two forms here are similar for a wide range of temperatures; their unfolding rates are also similar, with an activation enthalpy of 153 kJ/mol.
Collapse
Affiliation(s)
- Anh Tuân Phan
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
| | | | | |
Collapse
|
42
|
Phan AT, Patel DJ. Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics. J Am Chem Soc 2004; 125:15021-7. [PMID: 14653736 PMCID: PMC4693644 DOI: 10.1021/ja037616j] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate by NMR that the two-repeat human telomeric sequence d(TAGGGTTAGGGT) can form both parallel and antiparallel G-quadruplex structures in K(+)-containing solution. Both structures are dimeric G-quadruplexes involving three stacked G-tetrads. The sequence d(TAGGGUTAGGGT), containing a single thymine-to-uracil substitution at position 6, formed a predominantly parallel dimeric G-quadruplex with double-chain-reversal loops; the structure was symmetric, and all guanines were anti. Another modified sequence, d(UAGGGT(Br)UAGGGT), formed a predominantly antiparallel dimeric G-quadruplex with edgewise loops; the structure was asymmetric with six syn guanines and six anti guanines. The two structures can coexist and interconvert in solution. For the latter sequence, the antiparallel form is more favorable at low temperatures (<50 degrees C), while the parallel form is more favorable at higher temperatures; at temperatures lower than 40 degrees C, the antiparallel G-quadruplex folds faster but unfolds slower than the parallel G-quadruplex.
Collapse
Affiliation(s)
- Anh Tuân Phan
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
| | | |
Collapse
|
43
|
Thorpe JH, Teixeira SCM, Gale BC, Cardin CJ. Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution. Nucleic Acids Res 2003; 31:844-9. [PMID: 12560479 PMCID: PMC149190 DOI: 10.1093/nar/gkg168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 11/21/2002] [Accepted: 11/21/2002] [Indexed: 11/13/2022] Open
Abstract
Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.
Collapse
Affiliation(s)
- James H Thorpe
- The University of Reading, School of Chemistry, Whiteknights, Reading, Berkshire RG6 6AD, UK
| | | | | | | |
Collapse
|
44
|
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Auxiliary elements of mammalian pre-mRNAs polyadenylation signals. ACTA ACUST UNITED AC 2002. [DOI: 10.7124/bc.00062e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, NAS of Ukraine
| |
Collapse
|
45
|
Liu H, Kugimiya A, Sakurai T, Katahira M, Uesugi S. A comparison of the properties and the solution structure for RNA and DNA quadruplexes which contain two GGAGG sequences joined with a tetranucleotide linker. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:785-801. [PMID: 12537021 DOI: 10.1081/ncn-120016481] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have determined solution structure of r(GGAGGUUUUGGAGG) (R14) by NMR; the RNA 14-mer forms an intra-strand parallel quadruplex with a G-tetrad and a hexad, in which a G-tetrad core is augmented by association of two A residues. The quadruplex further forms a dimer through stacking interaction between the hexads. In order to obtain insight into the difference between RNA and DNA quadruplexes, we synthesized the corresponding DNA 14-mer, d(GGAGGTTTTGGAGG) (D14), and examined its properties and structure by CD, gel electrophoresis, and NMR. K+ ions increased the thermal stability of both R14 and D14 structures. The binding affinity of K+ ions to R14 was much higher than that to D14. The CD and gel electrophoretic studies suggest that D14 forms a quadruplex entirely different from that of R14 in the presence of K+ ions; two molecules of D14 form a quadruplex with both antiparallel and parallel strand alignments and with diagonal loops at both ends of the stacked G-tetrads. The NMR study also gave results that are consistent with such structure: alternate glycosidic conformation, 5'G(syn)-G(anti)3', and characteristic chemical shift data observed for many quadruplexes containing diagonal TTTT loops.
Collapse
Affiliation(s)
- Hui Liu
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | | | | | | | | |
Collapse
|
46
|
Liu H, Matsugami A, Katahira M, Uesugi S. A dimeric RNA quadruplex architecture comprised of two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops. J Mol Biol 2002; 322:955-70. [PMID: 12367521 DOI: 10.1016/s0022-2836(02)00876-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using CD and NMR, we determined the structure of an RNA oligomer, r(GGAGGUUUUGGAGG) (R14), comprising two GGAGG segments joined by a UUUU segment. A modified quadruplex structure was observed for r(GGAGGUUUUGGAGG) in solution even in the absence of K(+). An unusually stable dimeric RNA quadruplex architecture formed from two strands of r(GGAGGUUUUGGAGG) at low K(+) concentration is reported here. In each strand of r(GGAGGUUUUGGAGG), two sets of successive turns in the GGAGG segments and turns at both ends of the UUUU loops drive four G-G steps to align in a parallel manner, a core with two stacked G-tetrads being formed. Two adenine bases bind to two edges of one G:G:G:G tetrad through the sheared G:A mismatch augmenting the tetrad into a G:G(:A):G:G(:A) hexad. Thus, one molecule of r(GGAGGUUUUGGAGG) folds into a modified quadruplex comprising a G:G:G:G tetrad, a UUUU double-chain reversal loop and a G:G(:A):G:G(:A) hexad. Two such molecules further associate by stacking through the dimeric hexad-hexad interface with a rotational symmetry. The ribose rings of most nucleotides take S (close to C2'-endo) puckering, which is unusual for an RNA. K(+) can increase the stability of this quadruplex structure; the number of bound K(+) was estimated from the results of the titration experiment. Besides G:G and G:A mismatches, a network of hydrogen bonds including O4'-NH(2) and C-H..O hydrogen bonds, and the extensive base stacking contribute to the high thermodynamic stability of R14. Our results could provide the stereochemical and thermodynamic basis for elucidating the biological role of the GGAGG-containing RNA segments abundantly existing in various RNAs. Relevance to quadruplex-mediated mRNA-FMRP binding and HIV-1 genome RNA dimerization is discussed.
Collapse
Affiliation(s)
- Hui Liu
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, Japan
| | | | | | | |
Collapse
|
47
|
Wen JD, Gray DM. The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry 2002; 41:11438-48. [PMID: 12234186 DOI: 10.1021/bi020276e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Ff gene 5 protein (g5p) is classified as a single-stranded DNA-binding protein. However, we previously showed that g5p binds with high affinity to a SELEX-selected G-rich 58-mer DNA oligomer, I-3, that forms an intramolecular G-quadruplex [Wen, J.-D., Gray, C. W., and Gray, D. M. (2001) Biochemistry 40, 9300-9310]. In 200 mM NaCl at 37 degrees C, g5p binds to I-3 in two stages, the first stage being the formation of a discrete intermediate complex that appears to be a precursor to a saturated g5p x I-3 complex. For the present paper, CD spectroscopy and DMS methylation techniques were used to investigate the binding of g5p to the I-3 oligomer and to the truncated 26-nucleotide core of the I-3 oligomer. The core sequence, called I-3c26, was d(GGGGTCAGGCTGGGGTTGTGCAGGTC). Results were the following: (1) The g5p binds in one stage to I-3c26 in 200 mM NaCl at 37 degrees C. (2) The intermediate complex of g5p.I-3 is formed by the binding of g5p to the core sequence. (3) G-quadruplex structures are maintained in both the g5p x I-3 and g5p x I-3c26 complexes, but the bound G-quadruplex structures are altered from their respective steady-state folded forms in 200 mM NaCl. (4) CD kinetics measurements showed that the I-3c26 quadruplex folds in two stages and that a transiently folded form is apparently the same as the altered structure to which g5p binds. (5) DMS methylation protection and interference experiments identified two guanines that are differentially involved in the steady-state folded and g5p-bound G-quadruplex structures. A model for a possible I-3c26 G-quadruplex structure is described.
Collapse
Affiliation(s)
- Jin-Der Wen
- Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688, USA
| | | |
Collapse
|
48
|
Crnugelj M, Hud NV, Plavec J. The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold. J Mol Biol 2002; 320:911-24. [PMID: 12126614 DOI: 10.1016/s0022-2836(02)00569-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The G-rich 11-mer oligonucleotide d(G(4)T(4)G(3)) forms a bimolecular G-quadruplex in the presence of sodium ions with a topology that is distinct from the folds of the closely related and well-characterized sequences d(G(4)T(4)G(4)) and d(G(3)T(4)G(3)). The solution structure of d(G(4)T(4)G(3))(2) has been determined using a combination of NMR spectroscopy and restrained molecular dynamics calculations. d(G(4)T(4)G(3))(2) forms an asymmetric dimeric fold-back structure consisting of three stacked G-quartets. The two T(4) loops that span diagonally across the outer faces of the G-quartets assume different conformations. The glycosidic torsion angle conformations of the guanine bases are 5'-syn-anti-syn-anti-(T(4) loop)-anti-syn-anti in one strand and 5'-syn-anti-syn-anti-(T(4) loop)-syn-anti-syn in the other strand. The guanine bases of the two outer G-quartets exhibit a clockwise donor-acceptor hydrogen-bonding directionality, while those of the middle G-quartet exhibit the anti-clockwise directionality. The topology of this G-quadruplex, like other bimolecular fold-back structures with diagonal loops, places each strand of the G-quartet region next to a neighboring parallel and an anti-parallel strand. The two guanine residues not involved in G-quartet formation, G4 and G12 (i.e. the fourth guanine base of one strand and the first guanine base of the other strand), adopt distinct conformations. G4 is stacked on top of an adjacent G-quartet, and this base-stacking continues along with the bases of the loop residues T5 and T6. G12 is orientated away from the core of G-quartets; stacked on the T7 base and apparently involved in hydrogen-bonding interactions with the phosphodiester group of this same residue. The cation-dependent folding of the d(G(4)T(4)G(3))(2) quadruplex structure is distinct from that observed for similar sequences. While both d(G(4)T(4)G(4)) and d(G(3)T(4)G(3)) form bimolecular, diagonally looped G-quadruplex structures in the presence of Na(+), K(+) and NH(4)(+), we have observed this folding to be favored for d(G(4)T(4)G(3)) in the presence of Na(+), but not in the presence of K(+) or NH(4)(+). The structure of d(G(4)T(4)G(3))(2) exhibits a "slipped-loop" element that is similar to what has been proposed for structural intermediates in the folding pathway of some G-quadruplexes, and therefore provides support for the feasibility of these proposed transient structures in G-quadruplex formation.
Collapse
Affiliation(s)
- Martin Crnugelj
- NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
| | | | | |
Collapse
|
49
|
Abstract
Hydrogen-bonded base pairs are an important determinant of nucleic acid structure and function. However, other interactions such as base-base stacking, base-backbone, and backbone-backbone interactions as well as effects exerted by the solvent and by metal or NH(4)(+) ions also have to be taken into account. In addition, hydrogen-bonded base complexes involving more than two bases can occur. With the rapidly increasing number and structural diversity of nucleic acid structures known at atomic detail higher-order hydrogen-bonded base complexes, base polyads, have attracted much interest. This review provides an overview on the occurrence of base polyads in nucleic acid structures and describes computational studies on these nucleic acid building blocks.
Collapse
Affiliation(s)
- J Sühnel
- Biocomputing Group, Institut für Molekulare Biotechnologie, Postfach 100813, D-07708 Jena, Germany
| |
Collapse
|
50
|
Zhang N, Gorin A, Majumdar A, Kettani A, Chernichenko N, Skripkin E, Patel DJ. Dimeric DNA quadruplex containing major groove-aligned A-T-A-T and G-C-G-C tetrads stabilized by inter-subunit Watson-Crick A-T and G-C pairs. J Mol Biol 2001; 312:1073-88. [PMID: 11580251 DOI: 10.1006/jmbi.2001.5002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report on an NMR study of unlabeled and uniformly 13C,15N-labeled d(GAGCAGGT) sequence in 1 M NaCl solution, conditions under which it forms a head-to-head dimeric quadruplex containing sequentially stacked G-C-G-C, G-G-G-G and A-T-A-T tetrads. We have identified, for the first time, a slipped A-T-A-T tetrad alignment, involving recognition of Watson-Crick A-T pairs along the major groove edges of opposing adenine residues. Strikingly, both Watson-Crick G-C and A-T pairings within the direct G-C-G-C and slipped A-T-A-T tetrads, respectively, occur between rather than within hairpin subunits of the dimeric d(GAGCAGGT) quadruplex. The hairpin turns in the head-to-head dimeric quadruplex involve single adenine residues and adds to our knowledge of chain reversal involving edgewise loops in DNA quadruplexes. Our structural studies, together with those from other laboratories, definitively establish that DNA quadruplex formation is not restricted to G(n) repeat sequences, with their characteristic stacked uniform G-G-G-G tetrad architectures. Rather, the quadruplex fold is a more versatile and robust architecture, accessible to a range of mixed sequences, with the potential to facilitate G-C-G-C and A-T-A-T tetrad through major and minor groove alignment, in addition to G-G-G-G tetrad formation. The definitive experimental identification of such major groove-aligned mixed A-T-A-T and G-C-G-C tetrads within a quadruplex scaffold, has important implications for the potential alignment of duplex segments during homologous recombination.
Collapse
Affiliation(s)
- N Zhang
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | | | | | | | | | | | | |
Collapse
|