1
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Huynh M, Vinck R, Gibert B, Gasser G. Strategies for the Nuclear Delivery of Metal Complexes to Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311437. [PMID: 38174785 DOI: 10.1002/adma.202311437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The nucleus is an essential organelle for the function of cells. It holds most of the genetic material and plays a crucial role in the regulation of cell growth and proliferation. Since many antitumoral therapies target nucleic acids to induce cell death, tumor-specific nuclear drug delivery could potentiate therapeutic effects and prevent potential off-target side effects on healthy tissue. Due to their great structural variety, good biocompatibility, and unique physico-chemical properties, organometallic complexes and other metal-based compounds have sparked great interest as promising anticancer agents. In this review, strategies for specific nuclear delivery of metal complexes are summarized and discussed to highlight crucial parameters to consider for the design of new metal complexes as anticancer drug candidates. Moreover, the existing opportunities and challenges of tumor-specific, nucleus-targeting metal complexes are emphasized to outline some new perspectives and help in the design of new cancer treatments.
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Affiliation(s)
- Marie Huynh
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Robin Vinck
- Orano, 125 avenue de Paris, Châtillon, 92320, France
| | - Benjamin Gibert
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
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2
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Zoli M. Twist-stretch relations in nucleic acids. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:641-650. [PMID: 37357224 DOI: 10.1007/s00249-023-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/15/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the base pairs. Using path integral techniques which sum over the ensemble of the base pair fluctuations, I compute the average helical repeat of the molecules as a function of the load. The obtained twist-stretch relations and stretching properties, for short A- and B-helical fragments, are consistent with the opposite behaviors observed in kilo-base long molecules.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
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3
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Mattioli R, Maggiore A, Di Risola D, Federico R, D'Erme M, Francioso A, Mosca L. Natural deep eutectic solvents protect RNA from thermal-induced degradation. Arch Biochem Biophys 2023; 745:109714. [PMID: 37549802 DOI: 10.1016/j.abb.2023.109714] [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: 05/02/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
RNA is a fundamental nucleic acid for life and it plays important roles in the regulation of gene transcription, post-transcriptional regulation, and epigenetic regulation. Recently, the focus on this nucleic acid has significantly increased due to the development of mRNA vaccines and RNA-based gene therapy protocols. Unfortunately, RNA based products show constrains mainly owing to instability and easy degradability of the RNA molecules. Indeed, unlike the DNA molecule which has a great intrinsic stability, RNA is more prone to degradation and this process is accelerated under thermal treatment. Here we describe a method that involves the use of Natural Deep Eutectic Solvents (NaDES) capable of slowing down RNA degradation process. Our results show that this technology seems suitable for improving the stability of specific RNA molecules particularly susceptible to thermal-induced degradation. Therefore, this technique represents a valuable tool to stabilize RNA molecules used in gene therapy and mRNA vaccines.
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Affiliation(s)
- Roberto Mattioli
- Department of Biochemical Sciences, Sapienza University of Rome, 00185, Rome, Italy.
| | - Anna Maggiore
- Department of Biochemical Sciences, Sapienza University of Rome, 00185, Rome, Italy; Department of Brain Sciences, Imperial College London, London, W12 0NN, United Kingdom
| | - Daniel Di Risola
- Department of Biochemical Sciences, Sapienza University of Rome, 00185, Rome, Italy
| | | | - Maria D'Erme
- Department of Biochemical Sciences, Sapienza University of Rome, 00185, Rome, Italy
| | - Antonio Francioso
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100, Teramo, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University of Rome, 00185, Rome, Italy
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4
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Harp JM, Lybrand TP, Pallan PS, Coates L, Sullivan B, Egli M. Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Nucleic Acids Res 2022; 50:7721-7738. [PMID: 35819202 PMCID: PMC9303348 DOI: 10.1093/nar/gkac577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2′-OH orientation (H2′-C2′-O2′-HO2′ torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2′-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3′, 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2′-OD backbone-orientation. GAGA-tetraloop riboses display a 2′-OD base-orientation. An atypical C2′-endo sugar pucker is strictly correlated with a 2′-OD sugar-orientation. Neutrons reveal the strong preference of the 2′-OH to donate in H-bonds and that 2′-OH orientation affects both backbone geometry and ribose pucker. We discuss 2′-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Terry P Lybrand
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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5
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Dutta N, Deb I, Sarzynska J, Lahiri A. Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives. J Comput Aided Mol Des 2022; 36:205-224. [PMID: 35338419 PMCID: PMC8956458 DOI: 10.1007/s10822-022-00447-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
Pseudouridine is one of the most abundant post-transcriptional modifications in RNA. We have previously shown that the FF99-derived parameters for pseudouridine and some of its naturally occurring derivatives in the AMBER distribution either alone or in combination with the revised γ torsion parameters (parmbsc0) failed to reproduce their conformational characteristics observed experimentally (Deb et al. in J Chem Inf Model 54:1129–1142, 2014; Deb et al. in J Comput Chem 37:1576–1588, 2016; Dutta et al. in J Chem Inf Model 60:4995–5002, 2020). However, the application of the recommended bsc0 correction did lead to an improvement in the description not only of the distribution in the γ torsional space but also of the sugar pucker distributions. In an earlier study, we examined the transferability of the revised glycosidic torsion parameters (χIDRP) for Ψ to its derivatives. We noticed that although these parameters in combination with the AMBER FF99-derived parameters and the revised γ torsional parameters resulted in conformational properties of these residues that were in better agreement with experimental observations, the sugar pucker distributions were still not reproduced accurately. Here we report a new set of partial atomic charges for pseudouridine, 1-methylpseudouridine, 3-methylpseudouridine and 2′-O-methylpseudouridine and a new set of glycosidic torsional parameters (χND) based on chosen glycosidic torsional profiles that most closely corresponded to the NMR data for conformational propensities and studied their effect on the conformational distributions using REMD simulations at the individual nucleoside level. We have also studied the effect of the choice of water model on the conformational characteristics of these modified nucleosides. Our observations suggest that the current revised set of parameters and partial atomic charges describe the sugar pucker distributions for these residues more accurately and that the choice of a suitable water model is important for the accurate description of their conformational properties. We have further validated the revised sets of parameters by studying the effect of substitution of uridine with pseudouridine within single stranded RNA oligonucleotides on their conformational and hydration characteristics.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, West Bengal, 700009, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, West Bengal, 700009, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, West Bengal, 700009, India.
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6
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Wang Z, Liu J, Zhang Y, Qi J, Han X, Zhao X, Bai D, Zhao H, Chen Q. Intrinsic Contributions of 2'-Hydroxyl to the Hydration of Nucleosides at the Monomeric Level. Chemistry 2020; 26:17046-17055. [PMID: 32786015 DOI: 10.1002/chem.202002835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 02/05/2023]
Abstract
Although many reports have revealed structural differences between DNA and RNA at the polymeric level, there are no comparative studies with 2'-deoxyribonucleoside and ribonucleoside to explore the role of the 2'-OH group at the monomeric level under the same conditions. Inspired by this, herein, the intrinsic contributions of the 2'-OH group in the nucleoside have been systematically investigated by directly solving the single-crystal structures of 2'-deoxy-2-aminoadenosine (1), 2-aminoadenosine (2), and 2-aminoarabinofuranosyladenine (3) in water. The 2'-OH group not only influenced the conformation and base-pair pattern of the single-nucleoside molecule, but also played a fundamental role in the entire supramolecular structure. Interestingly, compound 1, which did not contain the 2'-OH group, displayed strong hydration, whereas 2 and 3 (with the 2'-OH group in the opposite direction) exhibited no hydration, which was completely different from that observed in nucleic acids. Meanwhile, compound 1 trapped water molecules to form unique trihydrol moieties, which further served as the backbone to construct the simplest double-chain DNA-like structures. To this end, to investigate the effect of the biological environment on these unique structures, the solvent was changed from water to phosphate-buffered saline (PBS). Surprisingly, such a subtle adjustment led to entirely different superstructures, consisting of 2D lamellar structures in water and 3D porous structures in PBS. These large morphological differences could be attributed to delicate ion hydration, which was also confirmed through variable-temperature X-ray analysis, SEM, and intermolecular interaction energy calculations. In summary, this study comprehensively investigated the intrinsic contributions of 2'-hydroxyl to the hydration of nucleosides at the monomeric level; this is helpful to further understand the differences in DNA/RNA and the impact of their surrounding environment.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Jiang Liu
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Yanan Zhang
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Jiajia Qi
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Xianglong Han
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Xuefeng Zhao
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical, Research Center for Oral Diseases, Chinese Academy of Medical Sciences, Research Unit of Oral Carcinogenesis and Management, West China, Hospital of Stomatology, Sichuan University, 610041, Chengdu, P.R. China
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7
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Xu J, Tojo S, Fujitsuka M, Kawai K. Dynamics of Single‐Stranded RNA Looping Probed and Photoregulated by Sulfonated Pyrene. ChemistrySelect 2020. [DOI: 10.1002/slct.202002231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8–1 Ibaraki Osaka 567-0047 Japan
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8–1 Ibaraki Osaka 567-0047 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8–1 Ibaraki Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8–1 Ibaraki Osaka 567-0047 Japan
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8
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Yu B, Pletka CC, Iwahara J. NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups. J Phys Chem B 2020; 124:1065-1070. [PMID: 31958014 PMCID: PMC7021563 DOI: 10.1021/acs.jpcb.9b10987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Channing C. Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
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9
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Towards Self-Transfecting Nucleic Acid Nanostructures for Gene Regulation. Trends Biotechnol 2019; 37:983-994. [DOI: 10.1016/j.tibtech.2019.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 01/06/2023]
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10
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Rangadurai A, Zhou H, Merriman DK, Meiser N, Liu B, Shi H, Szymanski ES, Al-Hashimi HM. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Res 2019; 46:11099-11114. [PMID: 30285154 PMCID: PMC6237737 DOI: 10.1093/nar/gky885] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022] Open
Abstract
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson–Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2′-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5–4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3–4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.
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Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | | | - Nathalie Meiser
- Goethe University, Institute for Organic Chemistry and Chemical Biology, Frankfurt am Main, Germany
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.,Department of Chemistry, Duke University, Durham, NC, USA
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11
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Alcolea Palafox M, Franklin Benial AM, K Rastogi V. Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes. Int J Mol Sci 2019; 20:E3477. [PMID: 31311161 PMCID: PMC6678171 DOI: 10.3390/ijms20143477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2'-OH group. The weaker Watson-Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química-Física, Facultad de CienciasQuímicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | | | - V K Rastogi
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201002, India
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12
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Malicki S, Ksiazek M, Majewski P, Pecak A, Mydel P, Grudnik P, Dubin G. Development of a novel, high-affinity ssDNA trypsin inhibitor. J Enzyme Inhib Med Chem 2019; 34:638-643. [PMID: 30727784 PMCID: PMC6366424 DOI: 10.1080/14756366.2019.1569648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Inhibitors of serine proteases are not only extremely useful in the basic research but are also applied extensively in clinical settings. Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) approach we developed a family of novel, single-stranded DNA aptamers capable of specific trypsin inhibition. Our most potent candidate (T24) and its short version (T59) were thoroughly characterised in terms of efficacy. T24 and T59 efficiently inhibited bovine trypsin with Ki of 176 nM and 475 nM, respectively. Interestingly, in contrast to the majority of known trypsin inhibitors, the selected aptamers have superior specificity and did not interact with porcine trypsin or any human proteases tested. These included plasmin and thrombin characterised by trypsin-like substrate specificity. Our results demonstrate that SELEX may be successfully employed in the development of potent and specific DNA based protease inhibitors.
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Affiliation(s)
- Stanislaw Malicki
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Miroslaw Ksiazek
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland.,c Department of Oral Immunology and Infectious Diseases , University of Louisville School of Dentistry , Kentucky , USA
| | - Pawel Majewski
- b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Aleksandra Pecak
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Piotr Mydel
- b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland.,d Department of Clinical Science , Broegelmann Research Laboratory, University of Bergen , Bergen , Norway
| | - Przemyslaw Grudnik
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland
| | - Grzegorz Dubin
- a Malopolska Centre of Biotechnology , Jagiellonian University , Krakow , Poland.,b Department of Microbiology, Faculty of Biochemistry , Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
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13
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Alcolea Palafox M. Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers 2019; 110:e23247. [PMID: 30676643 DOI: 10.1002/bip.23247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
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14
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Andrałojć W, Małgowska M, Sarzyńska J, Pasternak K, Szpotkowski K, Kierzek R, Gdaniec Z. Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus. RNA (NEW YORK, N.Y.) 2019; 25:121-134. [PMID: 30341177 PMCID: PMC6298561 DOI: 10.1261/rna.068163.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/16/2018] [Indexed: 05/24/2023]
Abstract
Uridine tetrads (U-tetrads) are a structural element encountered in RNA G-quadruplexes, for example, in the structures formed by the biologically relevant human telomeric repeat RNA. For these molecules, an unexpectedly strong stabilizing influence of a U-tetrad forming at the 3' terminus of a quadruplex was reported. Here we present the high-resolution solution NMR structure of the r(UGGUGGU)4 quadruplex which, in our opinion, provides an explanation for this stabilization. Our structure features a distinctive, abrupt chain reversal just prior to the 3' uridine tetrad. Similar "reversed U-tetrads" were already observed in the crystalline phase. However, our NMR structure coupled with extensive explicit solvent molecular dynamics (MD) simulations identifies some key features of this motif that up to now remained overlooked. These include the presence of an exceptionally stable 2'OH to phosphate hydrogen bond, as well as the formation of an additional K+ binding pocket in the quadruplex groove.
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Affiliation(s)
- Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Małgowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kamil Szpotkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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15
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Lemkul JA, MacKerell AD. Polarizable force field for RNA based on the classical drude oscillator. J Comput Chem 2018; 39:2624-2646. [PMID: 30515902 PMCID: PMC6284239 DOI: 10.1002/jcc.25709] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/01/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022]
Abstract
RNA molecules are highly dynamic and capable of adopting a wide range of complex, folded structures. The factors driving the folding and dynamics of these structures are dependent on a balance of base pairing, hydration, base stacking, ion interactions, and the conformational sampling of the 2'-hydroxyl group in the ribose sugar. The representation of these features is a challenge for empirical force fields used in molecular dynamics simulations. Toward meeting this challenge, the inclusion of explicit electronic polarization is important in accurately modeling RNA structure. In this work, we present a polarizable force field for RNA based on the classical Drude oscillator model, which represents electronic degrees of freedom via negatively charged particles attached to their parent atoms by harmonic springs. Beginning with parametrization against quantum mechanical base stacking interaction energy and conformational energy data, we have extended the Drude-2017 nucleic acid force field to include RNA. The conformational sampling of a range of RNA sequences were used to validate the force field, including canonical A-form RNA duplexes, stem-loops, and complex tertiary folds that bind multiple Mg2+ ions. Overall, the Drude-2017 RNA force field reproduces important properties of these structures, including the conformational sampling of the 2'-hydroxyl and key interactions with Mg2+ ions. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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16
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Lewis acidity of benzene in half-sandwich ruthenium arene complex. A computational study. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.05.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Dzowo YK, Wolfbrandt C, Resendiz MJE, Wang H. Modeling of canonical and C2′- O-thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability. NEW J CHEM 2018. [DOI: 10.1039/c8nj01739e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal stabilization of the duplex. Predicting the effects that modifications will have on structure of RNA is of importance in the development of new RNA technologies.
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Affiliation(s)
| | | | | | - Haobin Wang
- Department of Chemistry
- University of Colorado Denver
- Denver
- USA
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18
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein. J Am Chem Soc 2017; 140:339-345. [PMID: 29227646 DOI: 10.1021/jacs.7b10595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl proton resonances of uniformly 13C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man3) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man3 and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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19
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Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study. JOURNAL OF BIOPHYSICS 2017; 2017:1059216. [PMID: 28321253 PMCID: PMC5340175 DOI: 10.1155/2017/1059216] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/15/2017] [Indexed: 11/20/2022]
Abstract
The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.
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20
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Darré L, Ivani I, Dans PD, Gómez H, Hospital A, Orozco M. Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA. J Am Chem Soc 2016; 138:16355-16363. [DOI: 10.1021/jacs.6b09471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Leonardo Darré
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Ivan Ivani
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Pablo D. Dans
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Hansel Gómez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
- Department
of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
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21
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Ball R, Brindley J. The Life Story of Hydrogen Peroxide III: Chirality and Physical Effects at the Dawn of Life. ORIGINS LIFE EVOL B 2016; 46:81-93. [PMID: 26399407 DOI: 10.1007/s11084-015-9465-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022]
Abstract
It is a remarkable observed fact that all life on Earth is homochiral, its biology using exclusively the D-enantiomer of ribose, the sugar moiety of the ribonucleic acids, and the L-enantiomers of the chiral amino acids. Motivated by concurrent work that elaborates further the role of hydrogen peroxide in providing an oscillatory drive for the RNA world (Ball & Brindley 2015a, J. R. Soc. Interface 12, 20150366, and Ball & Brindley 2015b, this journal, in press), we reappraise the structure and physical properties of this small molecule within this context. Hydrogen peroxide is the smallest, simplest molecule to exist as a pair of non-superimposable mirror images, or enantiomers, a fact which leads us to develop the hypothesis that its enantiospecific interactions with ribonucleic acids led to enantioselective outcomes. We propose a mechanism by which these chiral interactions may have led to amplification of D-ribonucleic acids and extinction of L-ribonucleic acids.
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Affiliation(s)
- Rowena Ball
- Mathematical Sciences Institute and Research School of Chemistry, The Australian National University, Canberra, 2602, Australia.
| | - John Brindley
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
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22
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Zhu Q, Liu G, Kai M. DNA Aptamers in the Diagnosis and Treatment of Human Diseases. Molecules 2015; 20:20979-97. [PMID: 26610462 PMCID: PMC6332121 DOI: 10.3390/molecules201219739] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility of generation and synthesis. To better understand the specific potential of DNA aptamers, an overview of the progress in the generation and application of DNA aptamers in human disease diagnosis and therapy are presented in this review. Special attention is given to researches that are relatively close to practical application. DNA aptamers are expected to have great potential in the diagnosis and treatment of human diseases.
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Affiliation(s)
- Qinchang Zhu
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Ge Liu
- Department of Genomic Epidemiology, Research Center for Environment and Developmental Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Masaaki Kai
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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23
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Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
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Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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24
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Bazzi S, Novotný J, Yurenko YP, Marek R. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. Chemistry 2015; 21:9414-25. [PMID: 26032561 DOI: 10.1002/chem.201500743] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 01/13/2023]
Abstract
A new class of quadruplex nucleobases, derived from 3-deazaguanine, has been designed for various applications as smart quadruplex ligands as well as quadruplex-based aptamers, receptors, and sensors. An efficient strategy for modifying the guanine quadruplex core has been developed and tested by using quantum chemistry methods. Several potential guanine derivatives modified at the 3- or 8-position or both are analyzed, and the results compared to reference systems containing natural guanine. Analysis of the formation energies (BLYP-D3(BJ)/def2-TZVPP level of theory, in combination with the COSMO model for water) in model systems consisting of two and three stacked tetrads with Na(+) /K(+) ion(s) inside the internal channel indicates that the formation of structures with 3-halo-3-deazaguanine bases leads to a substantial gain in energy, as compared to the corresponding reference guanine complexes. The results cast light on changes in the noncovalent interactions (hydrogen bonding, stacking, and ion coordination) in a quadruplex stem upon modification of the guanine core. In particular, the enhanced stability of the modified quadruplexes was shown to originate mainly from increased π-π stacking. Our study suggests the 3-halo-3-deazaguanine skeleton as a potential building unit for quadruplex systems and smart G-quadruplex ligands.
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Affiliation(s)
- Sophia Bazzi
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Jan Novotný
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Yevgen P Yurenko
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
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25
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Zou T, Liu J, Lum CT, Ma C, Chan RCT, Lok CN, Kwok WM, Che CM. Luminescent Cyclometalated Platinum(II) Complex Forms Emissive Intercalating Adducts with Double-Stranded DNA and RNA: Differential Emissions and Anticancer Activities. Angew Chem Int Ed Engl 2014; 53:10119-23. [DOI: 10.1002/anie.201405384] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/21/2022]
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26
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Zou T, Liu J, Lum CT, Ma C, Chan RCT, Lok CN, Kwok WM, Che CM. Luminescent Cyclometalated Platinum(II) Complex Forms Emissive Intercalating Adducts with Double-Stranded DNA and RNA: Differential Emissions and Anticancer Activities. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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27
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Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J Chem Theory Comput 2013; 10:463-80. [PMID: 26579924 DOI: 10.1021/ct400837p] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.
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Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC, Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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28
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Fonville JM, Swart M, Vokáčová Z, Sychrovský V, Šponer JE, Šponer J, Hilbers CW, Bickelhaupt FM, Wijmenga SS. Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Chemistry 2012; 18:12372-87. [PMID: 22899588 DOI: 10.1002/chem.201103593] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/10/2022]
Abstract
NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1)H and (13)C NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13)C and (1)H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.
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Affiliation(s)
- Judith M Fonville
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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29
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Denning EJ, MacKerell AD. Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity. J Am Chem Soc 2012; 134:2800-6. [PMID: 22242623 DOI: 10.1021/ja211328g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.
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Affiliation(s)
- Elizabeth J Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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30
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Denning EJ, Priyakumar UD, Nilsson L, MacKerell AD. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem 2011; 32:1929-43. [PMID: 21469161 PMCID: PMC3082605 DOI: 10.1002/jcc.21777] [Citation(s) in RCA: 288] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 01/24/2011] [Accepted: 01/30/2011] [Indexed: 01/02/2023]
Abstract
Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick base pair opening which is not consistent with experiment, whereas analysis of molecular dynamics (MD) simulations show the 2'-hydroxyl moiety to almost exclusively sample the O3' orientation. Quantum mechanical (QM) studies of RNA related model compounds indicate the energy minimum associated with the O3' orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2'-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3' orientations of the 2'-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2'-hydroxyl moiety and support a model whereby the 2'-hydroxyl can enhance the probability of conformational transitions in RNA.
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Affiliation(s)
- Elizabeth J. Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, Baltimore, MD 21201
| | - U. Deva Priyakumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, Baltimore, MD 21201
| | - Lennart Nilsson
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University
of Maryland, Baltimore, MD 21201
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31
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Nozinovic S, Gupta P, Fürtig B, Richter C, Tüllmann S, Duchardt-Ferner E, Holthausen MC, Schwalbe H. Determination of the Conformation of the 2′OH Group in RNA by NMR Spectroscopy and DFT Calculations. Angew Chem Int Ed Engl 2011; 50:5397-400. [DOI: 10.1002/anie.201007844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 01/04/2023]
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Nozinovic S, Gupta P, Fürtig B, Richter C, Tüllmann S, Duchardt-Ferner E, Holthausen MC, Schwalbe H. Konformationsbestimmung der 2′OH-Gruppe in RNA durch NMR-Spektroskopie und Dichtefunktionalrechnungen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Kloiber K, Spitzer R, Tollinger M, Konrat R, Kreutz C. Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label. Nucleic Acids Res 2011; 39:4340-51. [PMID: 21252295 PMCID: PMC3105391 DOI: 10.1093/nar/gkq1361] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The refolding kinetics of bistable RNA sequences were studied in unperturbed equilibrium via 13C exchange NMR spectroscopy. For this purpose a straightforward labeling technique was elaborated using a 2′-13C-methoxy uridine modification, which was prepared by a two-step synthesis and introduced into RNA using standard protocols. Using 13C longitudinal exchange NMR spectroscopy the refolding kinetics of a 20 nt bistable RNA were characterized at temperatures between 298 and 310 K, yielding the enthalpy and entropy differences between the conformers at equilibrium and the activation energy of the refolding process. The kinetics of a more stable 32 nt bistable RNA could be analyzed by the same approach at elevated temperatures, i.e. at 314 and 316 K. Finally, the dynamics of a multi-stable RNA able to fold into two hairpin- and a pseudo-knotted conformation was studied by 13C relaxation dispersion NMR spectroscopy.
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Affiliation(s)
- Karin Kloiber
- Institute of Organic Chemistry, Leopold Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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Global transcriptome analysis of the Escherichia coli O157 response to Houttuynia Cordata Thunb. BIOCHIP JOURNAL 2010. [DOI: 10.1007/s13206-010-4312-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Hänsel R, Foldynová-Trantírková S, Löhr F, Buck J, Bongartz E, Bamberg E, Schwalbe H, Dötsch V, Trantírek L. Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy. J Am Chem Soc 2010; 131:15761-8. [PMID: 19824671 DOI: 10.1021/ja9052027] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In-cell NMR spectroscopy of proteins in different cellular environments is a well-established technique that, however, has not been applied to nucleic acids so far. Here, we show that isotopically labeled DNA and RNA can be observed inside the eukaryotic environment of Xenopus laevis oocytes by in-cell NMR spectroscopy. One limiting factor for the observation of nucleic acids in Xenopus oocytes is their reduced stability. We demonstrate that chemical modification of DNA and RNA can protect them from degradation and can significantly enhance their lifetime. Finally, we show that the imino region of the NMR spectrum is devoid of any oocyte background signals enabling the detection even of isotopically nonlabeled molecules.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry, Goethe-University, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
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Nozinovic S, Fürtig B, Jonker HRA, Richter C, Schwalbe H. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res 2009; 38:683-94. [PMID: 19906714 PMCID: PMC2811024 DOI: 10.1093/nar/gkp956] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 A) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.
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Affiliation(s)
- Senada Nozinovic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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37
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Keene FR, Smith JA, Collins JG. Metal complexes as structure-selective binding agents for nucleic acids. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2009.01.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Gkionis K, Platts JA, Hill JG. Insights into DNA Binding of Ruthenium Arene Complexes: Role of Hydrogen Bonding and π Stacking. Inorg Chem 2008; 47:3893-902. [DOI: 10.1021/ic702459h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - J. Grant Hill
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
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Abstract
This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.
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40
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Ying J, Bax A. 2'-hydroxyl proton positions in helical RNA from simultaneously measured heteronuclear scalar couplings and NOEs. J Am Chem Soc 2007; 128:8372-3. [PMID: 16802782 DOI: 10.1021/ja0606226] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 2'-hydroxyl group in RNA plays an important structural role; it defines hydration in the minor groove, impacts thermodynamic stability of RNA, and often participates in RNA catalysis. To better study this important functional group in RNA, we describe a constant-time HMQC-IPAP-NOESY 3D NMR experiment. It simultaneously yields highly resolved 13C-separated NOEs from ribose protons to the 2'OH proton, as well as E.COSY-type measurement of JC-OH couplings, thereby permitting a quantitative study of the orientation of the 2'OH proton in RNA. The observed NOE patterns indicate that the 2'OH bonds in A-form helical RNA are primarily oriented toward the base domain, as further supported by small (1.3 +/- 0.7 Hz) 3JC1'-2'OH and relatively large (4.2 +/- 0.7 Hz) 3JC3'-2'OH couplings. The constant-time HMQC-IPAP-NOESY is suitable for measurement of interactions of rapidly exchanging protons in proteins and nucleic acids.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Fohrer J, Reinscheid U, Hennig M, Carlomagno T. Calculation of the Dependence of Homo- and Heteronuclear3J and2J Scalar Couplings for the Determination of the 2′-Hydroxy Conformation in RNA. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Fohrer J, Reinscheid U, Hennig M, Carlomagno T. Calculation of the Dependence of Homo- and Heteronuclear3J and2J Scalar Couplings for the Determination of the 2′-Hydroxy Conformation in RNA. Angew Chem Int Ed Engl 2006; 45:7033-6. [PMID: 17006869 DOI: 10.1002/anie.200602583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jörg Fohrer
- Abteilung 030, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany
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Cornish PV, Giedroc DP, Hennig M. Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots. JOURNAL OF BIOMOLECULAR NMR 2006; 35:209-23. [PMID: 16865417 DOI: 10.1007/s10858-006-9033-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/08/2006] [Accepted: 05/17/2006] [Indexed: 05/11/2023]
Abstract
A variety of powerful NMR experiments have been introduced over the last few years that allow for the direct identification of different combinations of donor and acceptor atoms involved in hydrogen bonds in biomolecules. This ability to directly observe tertiary structural hydrogen bonds in solution tremendously facilitates structural studies of nucleic acids. We show here that an adiabatic HNN-COSY pulse scheme permits observation and measurement of J(N,N) couplings for nitrogen sites that are separated by up to 140 ppm in a single experiment at a proton resonance frequency of 500 MHz. Crucial hydrogen bond acceptor sites in nucleic acids, such as cytidine N3 nitrogens, can be unambiguously identified even in the absence of detectable H41 and H42 amino protons using a novel triple-resonance two-dimensional experiment, denoted H5(C5C4)N3. The unambiguous identification of amino nitrogen donor and aromatic nitrogen acceptor sites associated with both major groove as well as minor groove triple base pairs reveal the details of hydrogen bonding networks that stabilize the complex architecture of frameshift-stimulating mRNA pseudoknots. Another key tertiary interaction involving a 2'-OH hydroxyl proton that donates a hydrogen bond to an aromatic nitrogen acceptor in a cis Watson-Crick/sugar edge interaction can also be directly detected using a quantitative J(H,N) 1H,15N-HSQC experiment.
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Affiliation(s)
- Peter V Cornish
- Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, TX 77843-2128, USA
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