1
|
Falanga AP, D'Urso A, Travagliante G, Gangemi CMA, Marzano M, D'Errico S, Terracciano M, Greco F, De Stefano L, Dardano P, Rea I, Piccialli G, Oliviero G, Borbone N. Higher-order G-quadruplex structures and porphyrin ligands: Towards a non-ambiguous relationship. Int J Biol Macromol 2024; 268:131801. [PMID: 38670185 DOI: 10.1016/j.ijbiomac.2024.131801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
Herein, we evaluated the interaction of the tetracationic porphyrin H2TCPPSpm4 with three distinct DNA G-quadruplex (G4) models, i.e., the tetramolecular G4 d(TGGGGT)4 (Q1), the 5'-5' stacked G4-dimer [d(CGGAGGT)4]2 (Q2), and a mixture of 5'-5' stacked G-wires [d(5'-CGGT-3'-3'-GGC-5')4]n (Qn). The combined data obtained from UV-Vis, CD, fluorescence, PAGE, RLS, AFM, NMR, and HPLC-SEC experiments allowed us to shed light on the binding mode of H2TCPPSpm4 with the three G4 models differing for the type and the number of available G4 ending faces, the length of the G4 units, and the number of stacked G4 building blocks. Specifically, we found that H2TCPPSpm4 interacted with the shortest Q1 as an end-stacking ligand, whereas the groove binding mode was ascertained in the case of the Q2 and Qn G4 models. In the case of the interaction with Q1 and Qn, we found that H2TCPPSpm4 induces the formation of supramolecular aggregates at porphyrin/G4 ratios higher than 2:1, whereas no significant aggregation was observed for the interaction with Q2 up to the 5:1 ratio. These results unambiguously demonstrated the suitability of porphyrins for the development of specific G4 ligands or G4-targeting diagnostic probes, being H2TCPPSpm4 capable to distinguish between different G4s.
Collapse
Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | - Gabriele Travagliante
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125 Catania, Italy
| | | | - Maria Marzano
- CESTEV, University of Naples Federico II, via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, Unit of Naples, National Research Council, via Pietro Castellino 111, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy.
| |
Collapse
|
2
|
Marzano M, D'Errico S, Greco F, Falanga AP, Terracciano M, Di Prisco D, Piccialli G, Borbone N, Oliviero G. Polymorphism of G-quadruplexes formed by short oligonucleotides containing a 3'-3' inversion of polarity: From G:C:G:C tetrads to π-π stacked G-wires. Int J Biol Macromol 2023; 253:127062. [PMID: 37748594 DOI: 10.1016/j.ijbiomac.2023.127062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
G-wires are supramolecular DNA structures based on the G-quadruplex (G4) structural motif obtained by the self-assembly of interlocked slipped G-rich oligonucleotide (ON) strands, or by end-to-end stacking of G4 units. Despite the increasing interest towards G-wires due to their potential applications in DNA nanotechnologies, the self-assembly process to obtain G-wires having a predefined length and stability is still neither completely understood nor controlled. In our previous studies, we demonstrated that the d(5'CG2-3'-3'-G2C5') ON, characterized by the presence of a 3'-3'-inversion of polarity site self-assembles into a G-wire structure when annealed in the presence of K+ ions. Herein, by using CD, PAGE, HPLC size exclusion chromatography, and NMR investigations we studied the propensity of shorter analogues having sequences 5'CGn-3'-3'-GmC5' (with n = 1 and 1 ≤ m ≤ 3) to form the corresponding G-quadruplexes and stacked G-wires. The results revealed that the formation of G-wires starting from d(5'CGn-3'-3'-GmC5') ONs is possible only for the sequences having n and m > 1 in which both guanosines flanking the 5'-ending cytosines are not involved into the 3'-3' phosphodiester bond.
Collapse
Affiliation(s)
- Maria Marzano
- CESTEV, University of Naples Federico II, Via Tommaso De Amicis 95, 80131 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Daria Di Prisco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy.
| | - Giorgia Oliviero
- ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| |
Collapse
|
3
|
Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
Collapse
Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
| |
Collapse
|
4
|
Nucleic Acids as Biotools at the Interface between Chemistry and Nanomedicine in the COVID-19 Era. Int J Mol Sci 2022; 23:ijms23084359. [PMID: 35457177 PMCID: PMC9031702 DOI: 10.3390/ijms23084359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appropriate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense- and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.
Collapse
|
5
|
Gabelica V. Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand. Acc Chem Res 2021; 54:3691-3699. [PMID: 34546031 DOI: 10.1021/acs.accounts.1c00396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.
Collapse
Affiliation(s)
- Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM,
ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
6
|
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: 34] [Impact Index Per Article: 11.3] [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
|
7
|
Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
Collapse
Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
| | | |
Collapse
|
8
|
Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd 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; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- 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; (E.N.); (D.M.); (D.M.)
| |
Collapse
|
9
|
Binas O, Bessi I, Schwalbe H. Structure Validation of G-Rich RNAs in Noncoding Regions of the Human Genome. Chembiochem 2020; 21:1656-1663. [PMID: 31943589 PMCID: PMC7318348 DOI: 10.1002/cbic.201900696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 12/22/2022]
Abstract
We present the rapid biophysical characterization of six previously reported putative G-quadruplex-forming RNAs from the 5'-untranslated region (5'-UTR) of silvestrol-sensitive transcripts for investigation of their secondary structures. By NMR and CD spectroscopic analysis, we found that only a single sequence-[AGG]2 [CGG]2 C-folds into a single well-defined G-quadruplex structure. Sequences with longer poly-G strands form unspecific aggregates, whereas CGG-repeat-containing sequences exhibit a temperature-dependent equilibrium between a hairpin and a G-quadruplex structure. The applied experimental strategy is fast and provides robust readout for G-quadruplex-forming capacities of RNA oligomers.
Collapse
Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue Strasse 760438FrankfurtGermany
| | - Irene Bessi
- Institute for Organic and Biomolecular ChemistryJulius Maximilians University WürzburgAm Hubland97074WürzburgGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue Strasse 760438FrankfurtGermany
| |
Collapse
|
10
|
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
|
11
|
Pavc D, Wang B, Spindler L, Drevenšek-Olenik I, Plavec J, Šket P. GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly. Nucleic Acids Res 2020; 48:2749-2761. [PMID: 31996902 PMCID: PMC7049726 DOI: 10.1093/nar/gkaa058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/22/2023] Open
Abstract
GCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5'-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3'-3' stacking of terminal G-quartets of GCn G-quadruplexes, while 3'-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.
Collapse
Affiliation(s)
- Daša Pavc
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Lea Spindler
- University of Maribor, Faculty of Mechanical Engineering, 2000 Maribor, Slovenia
- Department of Complex Matter, Jozef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Irena Drevenšek-Olenik
- Department of Complex Matter, Jozef Stefan Institute, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Mathematics and Physics, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia
- EN-FIST Center of Excellence, 1000 Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| |
Collapse
|
12
|
Marzano M, Falanga AP, Marasco D, Borbone N, D’Errico S, Piccialli G, Roviello GN, Oliviero G. Evaluation of an Analogue of the Marine ε-PLL Peptide as a Ligand of G-quadruplex DNA Structures. Mar Drugs 2020; 18:md18010049. [PMID: 31940851 PMCID: PMC7024349 DOI: 10.3390/md18010049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/04/2020] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
ε-poly-l-Lysine (ε-PLL) peptide is a product of the marine bacterium Bacillus subtilis with antibacterial and anticancer activity largely used worldwide as a food preservative. ε-PLL and its synthetic analogue α,ε-poly-l-lysine (α,ε-PLL) are also employed in the biomedical field as enhancers of anticancer drugs and for drug and gene delivery applications. Recently, several studies reported the interaction between these non-canonical peptides and DNA targets. Among the most important DNA targets are the DNA secondary structures known as G-quadruplexes (G4s) which play relevant roles in many biological processes and disease-related mechanisms. The search for novel ligands capable of interfering with G4-driven biological processes elicits growing attention in the screening of new classes of G4 binders. In this context, we have here investigated the potential of α,ε-PLL as a G4 ligand. In particular, the effects of the incubation of two different models of G4 DNA, i.e., the parallel G4 formed by the Pu22 (d[TGAGGGTGGGTAGGGTGGGTAA]) sequence, a mutated and shorter analogue of the G4-forming sequence known as Pu27 located in the promoter of the c-myc oncogene, and the hybrid parallel/antiparallel G4 formed by the human Tel22 (d[AGGGTTAGGGTTAGGGTTAGGG]) telomeric sequence, with α,ε-PLL are discussed in the light of circular dichroism (CD), UV, fluorescence, size exclusion chromatography (SEC), and surface plasmon resonance (SPR) evidence. Even though the SPR results indicated that α,ε-PLL is capable of binding with µM affinity to both the G4 models, spectroscopic and SEC investigations disclosed significant differences in the structural properties of the resulting α,ε-PLL/G4 complexes which support the use of α,ε-PLL as a G4 ligand capable of discriminating among different G4 topologies.
Collapse
Affiliation(s)
- Maria Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Biostructures and Bioimaging—CNR 1, Via Mezzocannone 16, 80134 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Stefano D’Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging—CNR 1, Via Mezzocannone 16, 80134 Naples, Italy
- Correspondence:
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| |
Collapse
|
13
|
Gonnelli A, Pieraccini S, Baldassarri EJ, Funari S, Masiero S, Ortore MG, Mariani P. Metallo-responsive self-assembly of lipophilic guanines in hydrocarbon solvents: a systematic SAXS structural characterization. NANOSCALE 2020; 12:1022-1031. [PMID: 31845695 DOI: 10.1039/c9nr08556d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipophilic guanines (LipoGs) in aprotic solvents undergo different self-assembly processes based on different H-bonded motifs. Cylindrical nanotubes made by π-π stacked guanine tetramers (G-quadruplexes) and flat, tape-like aggregates (G-ribbons) have been observed depending on the presence of alkali metal ions. To obtain information on the structural properties and stability of these LipoG aggregates, Small-Angle X-ray Scattering (SAXS) experiments have been performed in dodecane, both in the presence and in the absence of potassium ions. As a result, the occurrence of the two different metallo-responsive architectures (nanoribbons or columnar nanotubes) was confirmed and we reported here for the first time a systematic study on the dependence of the aggregate properties on composition, temperature and molecular unit structure. Even if dodecane was selected to favour LipoG solubility, a strong tendency to self-organize into ordered lyotropic phases was indeed detected.
Collapse
Affiliation(s)
- Adriano Gonnelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Biophysics Research Group, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | | | | | | | | | | | | |
Collapse
|
14
|
Marzano M, Falanga AP, Dardano P, D'Errico S, Rea I, Terracciano M, De Stefano L, Piccialli G, Borbone N, Oliviero G. π–π stacked DNA G-wire nanostructures formed by a short G-rich oligonucleotide containing a 3′–3′ inversion of polarity site. Org Chem Front 2020. [DOI: 10.1039/d0qo00561d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Rod-shaped G-wire assemblies potentially useful to obtain new hybrid and conducting materials were obtained by annealing short G-rich oligonucleotides incorporating a 3′–3′ inversion of polarity site in the presence of potassium or ammonium ions.
Collapse
Affiliation(s)
- Maria Marzano
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Andrea P. Falanga
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | | | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | - Monica Terracciano
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | - Gennaro Piccialli
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Nicola Borbone
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies
- University of Naples Federico II
- 80131 – Naples
- Italy
| |
Collapse
|
15
|
Moccia F, Riccardi C, Musumeci D, Leone S, Oliva R, Petraccone L, Montesarchio D. Insights into the G-rich VEGF-binding aptamer V7t1: when two G-quadruplexes are better than one! Nucleic Acids Res 2019; 47:8318-8331. [PMID: 31276595 PMCID: PMC6735921 DOI: 10.1093/nar/gkz589] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/20/2022] Open
Abstract
The G-quadruplex-forming VEGF-binding aptamer V7t1 was previously found to be highly polymorphic in a K+-containing solution and, to restrict its conformational preferences to a unique, well-defined form, modified nucleotides (LNA and/or UNA) were inserted in its sequence. We here report an in-depth biophysical characterization of V7t1 in a Na+-rich medium, mimicking the extracellular environment in which VEGF targeting should occur, carried out combining several techniques to analyse the conformational behaviour of the aptamer and its binding to the protein. Our results demonstrate that, in the presence of high Na+ concentrations, V7t1 behaves in a very different way if subjected or not to annealing procedures, as evidenced by native gel electrophoresis, size exclusion chromatography and dynamic light scattering analysis. Indeed, not-annealed V7t1 forms both monomeric and dimeric G-quadruplexes, while the annealed oligonucleotide is a monomeric species. Remarkably, only the dimeric aptamer efficiently binds VEGF, showing higher affinity for the protein compared to the monomeric species. These findings provide new precious information for the development of improved V7t1 analogues, allowing more efficient binding to the cancer-related protein and the design of effective biosensors or theranostic devices based on VEGF targeting.
Collapse
Affiliation(s)
- Federica Moccia
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy.,Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy.,Institute for Endocrinology and Oncology 'Gaetano Salvatore', CNR, Via Pansini 5, 80131 Napoli, Italy
| |
Collapse
|
16
|
D'Atri V, Gabelica V. DNA and RNA telomeric G-quadruplexes: what topology features can be inferred from ion mobility mass spectrometry? Analyst 2019; 144:6074-6088. [PMID: 31528871 DOI: 10.1039/c9an01216h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Maintenance of the telomeres is key to chromosome integrity and cell proliferation. The G-quadruplex structures formed by telomeric DNA and RNA (TTAGGG and UUAGGG repeats, respectively) are key to this process. However, because these sequences are particularly polymorphic, solving high-resolution structures is not always possible, and there is a need for new methodologies to characterize the multiple structures coexisting in solution. In this context, we evaluated whether ion mobility spectrometry coupled to native mass spectrometry could help separate and assign the G-quadruplex topologies. We explored the circular dichroism spectra, multimer formation, cation binding, and ion mobility spectra of several 4-repeat and 8-repeat telomeric DNA and RNA sequences, both in NH4+ and in K+. In 1 mM K+ and 100 mM trimethylammonium acetate, all RNAs fold intramolecularly (no multimer). In 8-repeat sequences, the subunits are not independent: in DNA the first subunit disfavors the folding of the second one, whereas in RNA the two subunits fold cooperatively via cation-mediated stacking. Ion mobility spectrometry shows that gas-phase structures keep a memory of - but are not identical to - the solution ones. At the native charge states, the loops can rearrange in a variety of ways (unless they are constrained by pre-formed hydrogen bonds), thereby wrapping the core and masking the strand arrangements. Our study highlights that, to progress towards structural assignment from IM-MS experiments, deeper understanding of the solution-to-gas-phase rearrangement mechanisms is warranted.
Collapse
Affiliation(s)
- Valentina D'Atri
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France.
| | | |
Collapse
|
17
|
Kolesnikova S, Curtis EA. Structure and Function of Multimeric G-Quadruplexes. Molecules 2019; 24:molecules24173074. [PMID: 31450559 PMCID: PMC6749722 DOI: 10.3390/molecules24173074] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.
Collapse
Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic.
| |
Collapse
|
18
|
Nici F, Oliviero G, Falanga AP, D'Errico S, Marzano M, Musumeci D, Montesarchio D, Noppen S, Pannecouque C, Piccialli G, Borbone N. Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides. Org Biomol Chem 2019. [PMID: 29543291 DOI: 10.1039/c7ob02346d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties. The here reported results demonstrate that only the DMT-substituted TEL-ODN 2 is effective in protecting human MT-4 cell cultures from HIV infection (76% max protection), notwithstanding all the three new aptamers proved to be capable of forming stable higher order dimeric G4s when annealed in K+-containing buffer, thus suggesting that the recognition of a hydrophobic pocket on the target glycoprotein by the aptamers represents a main structural feature for triggering their anti-HIV activity.
Collapse
Affiliation(s)
- F Nici
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli, Italy
| | - A P Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - S D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - M Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - D Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - D Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - S Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - C Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| |
Collapse
|
19
|
Marzano M, Falanga AP, D'Errico S, Pinto B, Roviello GN, Piccialli G, Oliviero G, Borbone N. New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes. Molecules 2019; 24:molecules24030654. [PMID: 30759875 PMCID: PMC6384581 DOI: 10.3390/molecules24030654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/13/2023] Open
Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG₄T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG₄T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC⁻size-exclusion chromatography (HPLC⁻SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG₄T)₄. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.
Collapse
Affiliation(s)
- Maria Marzano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Brunella Pinto
- Dipartimento di Chimica, Università degli Studi di Milano, via Camillo Golgi 19, 20133 Milano, Italy.
| | | | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, via Sergio Pansini 5, 80131 Napoli, Italy.
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| |
Collapse
|
20
|
Falanga AP, Cerullo V, Marzano M, Feola S, Oliviero G, Piccialli G, Borbone N. Peptide Nucleic Acid-Functionalized Adenoviral Vectors Targeting G-Quadruplexes in the P1 Promoter of Bcl-2 Proto-Oncogene: A New Tool for Gene Modulation in Anticancer Therapy. Bioconjug Chem 2019; 30:572-582. [PMID: 30620563 DOI: 10.1021/acs.bioconjchem.8b00674] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The B-cell lymphoma 2 (Bcl-2) gene encodes for an antiapoptotic protein associated with the onset of many human tumors. Several oligonucleotides (ONs) and ON analogues are under study as potential tools to counteract the Bcl-2 expression. Among these are Peptide Nucleic Acids (PNAs). The absence of charges on PNA backbones allows the formation of PNA/DNA complexes provided with higher stability than the corresponding natural DNA/DNA counterparts. To date, the use of PNAs in antigene or antisense strategies is strongly limited by their inability to efficiently cross the cellular membranes. With the aim of downregulating the expression of Bcl-2, we propose here a novel antigene approach which uses oncolytic adenoviral vectors (OAds) as a new cancer cell-targeted PNA delivery system. The ability of oncolytic Ad5D24 vectors to selectively infect and kill cancer cells was exploited to transfect with high efficiency and selectivity a short cytosine-rich PNA complementary to the longest loop of the main G-quadruplex formed by the 23-base-long bcl2midG4 sequence located 52-30 bp upstream of the P1 promoter of Bcl-2 gene. Physico-chemical and biological investigations confirmed the ability of the PNA-conjugated Ad5D24 vectors to load and transfect their PNA cargo into human A549 and MDA-MB-436 cancer cell lines, as well as the synergistic (OAd+PNA) cytotoxic effect against the same cell lines. This approach holds promise for safer chemotherapy because of reduced toxicity to healthy tissues and organs.
Collapse
Affiliation(s)
- Andrea Patrizia Falanga
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | - Vincenzo Cerullo
- Department of Molecular Medicine and Medical Biotechnologies , University of Naples Federico II , Via Sergio Pansini 5 , 80131 Naples , Italy
| | - Maria Marzano
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | | | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies , University of Naples Federico II , Via Sergio Pansini 5 , 80131 Naples , Italy
| | - Gennaro Piccialli
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| | - Nicola Borbone
- Department of Pharmacy , University of Naples Federico II , Via Domenico Montesano 49 , 80131 Naples , Italy
| |
Collapse
|
21
|
Varizhuk AM, Protopopova AD, Tsvetkov VB, Barinov NA, Podgorsky VV, Tankevich MV, Vlasenok MA, Severov VV, Smirnov IP, Dubrovin EV, Klinov DV, Pozmogova GE. Polymorphism of G4 associates: from stacks to wires via interlocks. Nucleic Acids Res 2018; 46:8978-8992. [PMID: 30107602 PMCID: PMC6158749 DOI: 10.1093/nar/gky729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 01/16/2023] Open
Abstract
We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1',2'-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.
Collapse
Affiliation(s)
- Anna M Varizhuk
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Anna D Protopopova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Vladimir B Tsvetkov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Nikolay A Barinov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Victor V Podgorsky
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Maria V Tankevich
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Maria A Vlasenok
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Vyacheslav V Severov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Igor P Smirnov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Evgeniy V Dubrovin
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Dmitry V Klinov
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Galina E Pozmogova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| |
Collapse
|
22
|
Benito S, Ferrer A, Benabou S, Aviñó A, Eritja R, Gargallo R. Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:185-195. [PMID: 29448171 DOI: 10.1016/j.saa.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/16/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105M-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.
Collapse
Affiliation(s)
- S Benito
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Ferrer
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - S Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain.
| |
Collapse
|
23
|
Chaudhary S, Kaushik M, Kukreti R, Kukreti S. Structural switch from a multistranded G-quadruplex to single strands as a consequence of point mutation in the promoter of the human GRIN1 gene. MOLECULAR BIOSYSTEMS 2018; 13:1805-1816. [PMID: 28702665 DOI: 10.1039/c7mb00360a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A huge number of G-rich sequences forming quadruplexes are found in the human genome, especially in telomeric regions, UTRs, and the promoter regions of a number of genes. One such gene is GRIN1 encoding the NR1 subunit of the N-methyl-d-aspartate receptor (NMDA). Several lines of reports have implicated that attenuated function of NMDA results in schizophrenia, a genetic disorder characterized by hallucinations, delusions, and psychosis. Involvement of the GRIN1 gene in the pathogenesis of schizophrenia has been extensively analysed. Recent reports have demonstrated that polymorphism in the promoter region of GRIN1 at position -855 (G/C) has a possible association with schizophrenia. The binding site for the NF-κB transcription factor gets altered due to this mutation, resulting in reduced gene expression as well as NMDA activity. By combining gel electrophoresis (PAGE), circular dichroism (CD) and CD melting techniques, the G → C single nucleotide polymorphism (SNP) at the G-rich sequence (d-CTTAGCCCGAGGAG[combining low line]GGGGGTCCCAAGT; GRIN1) was investigated. We report that the GRIN1 sequence can form an octameric/multistranded quadruplex structure with parallel conformation in the presence of K+ as well as Na+. CD and gel studies are in good correlation in order to detect molecularity and strand conformation. The parallel G-quadruplex species was hypothesized to be octameric in K+/Na+ salts. The mutated sequence (d-CTTAGCCCGAGGAC[combining low line]GGGGGTCCCAAGT; GRIN1M) remained single stranded under physiological conditions. CD melting studies support the formation of an interstranded G-quadruplex structure by the GRIN1 sequence. Two structural models are propounded for a multistranded parallel G-quadruplex conformation which might be responsible for regulating the gene expression normally underlying memory and learning.
Collapse
Affiliation(s)
- Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.
| | | | | | | |
Collapse
|
24
|
Park Y, Kim KT, Kim BH. G-Quadruplex formation using fluorescent oligonucleotides as a detection method for discriminating AGG trinucleotide repeats. Chem Commun (Camb) 2018; 52:12757-12760. [PMID: 27722273 DOI: 10.1039/c6cc06566j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have developed a simple and sensitive system for detecting AGG trinucleotide repeats through the formation of intermolecular G-quadruplexes using a fluorescent oligonucleotide. The fluorescence signal increased rapidly and dramatically by 44.7-fold with respect to the low background signal in the presence of RNA agg repeats and by 35.0-fold in the presence of DNA AGG repeats.
Collapse
Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Ki Tae Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTEH), Pohang 37673, Republic of Korea.
| |
Collapse
|
25
|
Kolesnikova S, Hubálek M, Bednárová L, Cvacka J, Curtis EA. Multimerization rules for G-quadruplexes. Nucleic Acids Res 2017; 45:8684-8696. [PMID: 28911118 PMCID: PMC5587800 DOI: 10.1093/nar/gkx637] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
G-quadruplexes can multimerize under certain conditions, but the sequence requirements of such structures are not well understood. In this study, we investigated the ability of all possible variants of the central tetrad in a monomeric, parallel-strand G-quadruplex to form higher-order structures. Although most of these 256 variants existed primarily as monomers under the conditions of our screen, ∼10% formed dimers or tetramers. These structures could form in a wide range of monovalent and divalent metal ions, and folding was highly cooperative in both KCl and MgCl2. As was previously shown for G-quadruplexes that bind GTP and promote peroxidase reactions, G-quadruplexes that form dimers and tetramers have distinct sequence requirements. Some mutants could also form heteromultimers, and a second screen was performed to characterize the sequence requirements of these structures. Taken together, these experiments provide new insights into the sequence requirements and structures of both homomultimeric and heteromultimeric G-quadruplexes.
Collapse
Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Martin Hubálek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Josef Cvacka
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| |
Collapse
|
26
|
Manukyan A, Tekin A. The intermolecular dimer potential for guanine. J Chem Phys 2017; 147:154311. [DOI: 10.1063/1.4998792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artür Manukyan
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| |
Collapse
|
27
|
D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
Collapse
Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Oliviero G, D'Errico S, Pinto B, Nici F, Dardano P, Rea I, De Stefano L, Mayol L, Piccialli G, Borbone N. Self-Assembly of G-Rich Oligonucleotides Incorporating a 3'-3' Inversion of Polarity Site: A New Route Towards G-Wire DNA Nanostructures. ChemistryOpen 2017; 6:599-605. [PMID: 28794955 PMCID: PMC5542749 DOI: 10.1002/open.201700024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Indexed: 01/20/2023] Open
Abstract
Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions. Our results expand the repertoire of synthetic methodologies to obtain new tailored DNA G-wire nanostructures.
Collapse
Affiliation(s)
- Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies Via S. Pansini 5 80131 Napoli Italy
| | - Stefano D'Errico
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Brunella Pinto
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Fabrizia Nici
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Principia Dardano
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Ilaria Rea
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Luca De Stefano
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Luciano Mayol
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Gennaro Piccialli
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Nicola Borbone
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| |
Collapse
|
29
|
Kulikov K, Nozinovic S, Kath-Schorr S. The 5'-AG 5 CC-3' Fragment from the Human CPEB3 Ribozyme Forms an Ultrastable Parallel RNA G-Quadruplex. Chembiochem 2017; 18:969-973. [PMID: 28296179 DOI: 10.1002/cbic.201700028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 11/07/2022]
Abstract
An unusually thermostable G-quadruplex is formed by a sequence fragment of a naturally occurring ribozyme, the human CPEB3 ribozyme. Strong evidence is provided for the formation of a uniquely stable intermolecular G-quadruplex structure consisting of five tetrad layers, by using CD spectroscopy, UV melting curves, 2D NMR spectroscopy, and gel shift analysis. The cationic porphyrin TMPyP4 destabilizes the complex.
Collapse
Affiliation(s)
- Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Senada Nozinovic
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| |
Collapse
|
30
|
Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
Collapse
Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
| | | | | |
Collapse
|
31
|
Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
| |
Collapse
|
32
|
Romanucci V, Marchand A, Mendoza O, D’Alonzo D, Zarrelli A, Gabelica V, Di Fabio G. Kinetic ESI-MS Studies of Potent Anti-HIV Aptamers Based on the G-Quadruplex Forming Sequence d(TGGGAG). ACS Med Chem Lett 2016; 7:256-60. [PMID: 26985311 DOI: 10.1021/acsmedchemlett.5b00408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/24/2022] Open
Abstract
To investigate what properties make tetramolecular G-quadruplex ODNs good anti-HIV aptamers, we studied the stoichiometry and the self-assembly kinetics of the highly active 5'-end modified G-quadruplexes based on the d(TGGGAG) sequence. Our results demonstrate that the 5'-end conjugation does not necessarily increase the folding rate of the G-quadruplex; indeed, it ascribes anti-HIV activity. Unexpectedly, the G4-folding kinetics of the inactive G4 is similar to that of the 5'-end modified sequences. ESI-MS studies also revealed the formation of higher order G4 structures identified as octameric complexes along with tetramolecular G-quadruplexes.
Collapse
Affiliation(s)
- Valeria Romanucci
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Adrien Marchand
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Oscar Mendoza
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Daniele D’Alonzo
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Armando Zarrelli
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| | - Valérie Gabelica
- IECB,
ARNA Laboratory, University of Bordeaux, 33600 Pessac, France
- Inserm,
U869, ARNA Laboratory, Institut National de la Santé et de la Recherche Médicale, 33000 Bordeaux, France
| | - Giovanni Di Fabio
- Department
of Chemical Sciences, University of Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
| |
Collapse
|
33
|
Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
Collapse
Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| |
Collapse
|
34
|
Manukyan A, Tekin A. First principles potential for the cytosine dimer. Phys Chem Chem Phys 2015; 17:14685-701. [DOI: 10.1039/c5cp00553a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new first principles potential for the cytosine dimer.
Collapse
Affiliation(s)
- Artür Manukyan
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| | - Adem Tekin
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| |
Collapse
|
35
|
Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
Collapse
|
36
|
Malgowska M, Gudanis D, Kierzek R, Wyszko E, Gabelica V, Gdaniec Z. Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats. Nucleic Acids Res 2014; 42:10196-207. [PMID: 25081212 PMCID: PMC4150804 DOI: 10.1093/nar/gku710] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trinucleotide repeats are microsatellite sequences that are polymorphic in length. Their expansion in specific genes underlies a number of neurodegenerative disorders. Using ultraviolet-visible, circular dichroism, nuclear magnetic resonance (NMR) spectroscopies and electrospray ionization mass spectrometry, the structural preferences of RNA molecules composed of two and four repeats of AGG, CGG and UGG in the presence of K+, Na+ and NH4+ were analysed. (AGG)2A, (AGG)4A, p(UGG)2U and p(UGG)4U strongly prefer folding into G-quadruplexes, whereas CGG-containing sequences can adopt different types of structure depending on the cation and on the number of repeats. In particular, the two-repeat CGG sequence folds into a G-quadruplex in potassium buffer. We also found that each G-quadruplex fold is different: A:(G:G:G:G)A hexads were found for (AGG)2A, whereas mixed G:C:G:C tetrads and U-tetrads were observed in the NMR spectra of G(CGG)2C and p(UGG)2U, respectively. Finally, our NMR study highlights the influence of the strand sequence on the structure formed, and the influence of the intracellular environment on the folding. Importantly, we highlight that although potassium ions are prevalent in cells, the structures observed in the HeLa cell extract are not always the same as those prevailing in biophysical studies in the presence of K+ ions.
Collapse
Affiliation(s)
- Magdalena Malgowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Valérie Gabelica
- Laboratoire de Spectrométrie de Masse, Institut de Chimie, Bat. B6c, Université de Liège, B-4000 Liège, Belgium Inserm, U869 ARNA Laboratory, F-33000 Bordeaux, France University of Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| |
Collapse
|
37
|
Zhou J, Rosu F, Amrane S, Korkut DN, Gabelica V, Mergny JL. Assembly of chemically modified G-rich sequences into tetramolecular DNA G-quadruplexes and higher order structures. Methods 2014; 67:159-68. [DOI: 10.1016/j.ymeth.2014.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/20/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022] Open
|
38
|
Martadinata H, Phan AT. Formation of a stacked dimeric G-quadruplex containing bulges by the 5'-terminal region of human telomerase RNA (hTERC). Biochemistry 2014; 53:1595-600. [PMID: 24601523 DOI: 10.1021/bi4015727] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the structure formed by the first 18-nt of the 5'-terminal region of the human telomerase RNA (hTERC or hTR) using gel electrophoresis and UV, CD, and NMR spectroscopy. Our data suggest that this 18-nt sequence, r(GGGUUGCGGAGGGUGGGC), can form a stacked dimeric G-quadruplex in potassium solution. The two subunits, each being a three-layer parallel-stranded G-quadruplex with a cytosine bulge, are stacked at their 5'-end. The formation of this stacked dimeric G-quadruplex containing bulges could be biologically relevant for the dimerization and other interactions of the active human telomerase.
Collapse
Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371
| | | |
Collapse
|
39
|
Ho MC, Chang CW. Cationic and anionic reverse micelles as the molecular crowding container for G-quadruplex structure. RSC Adv 2014. [DOI: 10.1039/c4ra02141j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The d[AG3(T2AG3)3] sequence shows different molecular crowding effects in AOT and CTAB reverse micelles (RMs). Our result indicates that the CTAB RMs are ideal molecular crowding containers for G-quadruplex structure.
Collapse
Affiliation(s)
- Meng-Chieh Ho
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| | - Chih-Wei Chang
- Department of Chemistry
- National Changhua University of Education
- Changhua 50058, Taiwan
| |
Collapse
|
40
|
D'Atri V, Borbone N, Amato J, Gabelica V, D'Errico S, Piccialli G, Mayol L, Oliviero G. DNA-based nanostructures: The effect of the base sequence on octamer formation from d(XGGYGGT) tetramolecular G-quadruplexes. Biochimie 2013; 99:119-28. [PMID: 24316277 DOI: 10.1016/j.biochi.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]
Abstract
In a previous work we have demonstrated that the DNA sequence CGGTGGT folds into a higher order G-quadruplex structure (2Q), obtained by the 5'-5' stacking of two unusual G(:C):G(:C):G(:C):G(:C) planar octads belonging to two identical tetra-stranded parallel quadruplexes, when annealed in the presence of ammonium or potassium ions. In the present paper, we discuss the role played by the title nucleosides X and Y (where X and Y stand for A, C, G, or T) on the formation and stability of 2Q structures formed by the XGGYGGT oligodeoxynucleotides. We found that the above mentioned dimerization pathway is not peculiar to the CGGTGGT sequence, but is possible for all the remaining CGGYGGT sequences (with Y = A, C, or G). Furthermore, we have found that the TGGAGGT sequence, despite the absence of the 5'-ending C, is also capable of forming a 2Q-like higher order quadruplex by using a slightly different dimerization interface, as characterized by NMR spectroscopy. To the best of our knowledge, this is the first characterization of a quadruplex multimer formed by an oligodeoxynucleotide presenting a thymine at its 5'-end. Examples of such structures were observed previously only in crystals and in the presence of non-physiological cations. Our results expand the repertoire of DNA quadruplex nanostructures of chosen length and add further complexity to the structural polymorphism of G-rich DNA sequences.
Collapse
Affiliation(s)
- Valentina D'Atri
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Jussara Amato
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Valérie Gabelica
- Univ. Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France; INSERM, U869, ARNA laboratory, F-33000 Bordeaux, France
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| |
Collapse
|
41
|
Abstract
This review summarizes the results of structural studies carried out with analogs of G-quadruplexes built from natural nucleotides. Several dozens of base-, sugar-, and phosphate derivatives of the biological building blocks have been incorporated into more than 50 potentially quadruplex forming DNA and RNA oligonucleotides and the stability and folding topology of the resultant intramolecular, bimolecular and tetramolecular architectures characterized. The TG4T, TG5T, the 15 nucleotide-long thrombin binding aptamer, and the human telomere repeat AG3(TTAG3)3 sequences were modified in most cases, and four guanine analogs can be noted as being particularly useful in structural studies. These are the fluorescent 2-aminopurine, the 8-bromo-, and 8-methylguanines, and the hypoxanthine. The latter three analogs stabilize a given fold in a mixture of structures making possible accurate structural determinations by circular dichroism and nuclear magnetic resonance measurements.
Collapse
Affiliation(s)
- Janos Sagi
- a Rimstone Laboratory , RLI, 29 Lancaster Way, Cheshire , CT , 06410 , USA
| |
Collapse
|
42
|
|