51
|
Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach. Int J Mol Sci 2019; 20:ijms20205190. [PMID: 31635135 PMCID: PMC6834124 DOI: 10.3390/ijms20205190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 30–50% of malignant growths can be prevented by avoiding risk factors and implementing evidence-based strategies. Colorectal cancer (CRC) accounted for the second most common cancer and the third most common cause of cancer death worldwide. This cancer subtype can be reduced by early detection and patients’ management. In this study, the functional roles of the identified microRNAs were determined using an in silico pipeline. Five microRNAs identified using an in silico approach alongside their seven target genes from our previous study were used as datasets in this study. Furthermore, the secondary structure and the thermodynamic energies of the microRNAs were revealed by Mfold algorithm. The triplex binding ability of the oligonucleotide with the target promoters were analyzed by Trident. Finally, evolutionary stage-specific somatic events and co-expression analysis of the target genes in CRC were analyzed by SEECancer and GeneMANIA plugin in Cytoscape. Four of the five microRNAs have the potential to form more than one secondary structure. The ranges of the observed/expected ratio of CpG dinucleotides of these genes range from 0.60 to 1.22. Three of the candidate microRNA were capable of forming multiple triplexes along with three of the target mRNAs. Four of the total targets were involved in either early or metastatic stage-specific events while three other genes were either a product of antecedent or subsequent events of the four genes implicated in CRC. The secondary structure of the candidate microRNAs can be used to explain the different degrees of genetic regulation in CRC due to their conformational role to modulate target interaction. Furthermore, due to the regulation of important genes in the CRC pathway and the enrichment of the microRNA with triplex binding sites, they may be a useful diagnostic biomarker for the disease subtype.
Collapse
|
52
|
Nguyen TJD, Manuguerra I, Kumar V, Gothelf KV. Toehold-Mediated Strand Displacement in a Triplex Forming Nucleic Acid Clamp for Reversible Regulation of Polymerase Activity and Protein Expression. Chemistry 2019; 25:12303-12307. [PMID: 31373735 DOI: 10.1002/chem.201903496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 12/31/2022]
Abstract
Triplex forming oligonucleotides are used as a tool for gene regulation and in DNA nanotechnology. By incorporating artificial nucleic acids, target affinity and biological stability superior to that of natural DNA may be obtained. This work demonstrates how a chimeric clamp consisting of acyclic (L)-threoninol nucleic acid (aTNA) and DNA can bind DNA and RNA by the formation of a highly stable triplex structure. The (L)-aTNA clamp is released from the target again by the addition of a releasing strand in a strand displacement type of reaction. It is shown that the clamp efficiently inhibits Bsu and T7 RNA polymerase activity and that polymerase activity is reactivated by displacing the clamp. The clamp was successfully applied to the regulation of luciferase expression by reversible binding to the mRNA. When targeting a sequence in the double stranded plasmid, 40 % downregulation of protein expression is achieved.
Collapse
Affiliation(s)
- Thuy J D Nguyen
- Center for Multifunctional Biomolecular Drug Design (CEMBID) at the, Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Ilenia Manuguerra
- Center for Multifunctional Biomolecular Drug Design (CEMBID) at the, Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Vipin Kumar
- Center for Multifunctional Biomolecular Drug Design (CEMBID) at the, Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| | - Kurt V Gothelf
- Center for Multifunctional Biomolecular Drug Design (CEMBID) at the, Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark
| |
Collapse
|
53
|
Zhao H, Yang Q, Wang Z, Zhao H, Liu B, Chen Q, Dong M. Fabrication of 2D Hetero-Complexes With Nucleic-Acid-Base Adenine and Fatty-Acid Stearic Acid at Liquid/Solid Interface. Front Chem 2019; 7:513. [PMID: 31403041 PMCID: PMC6669938 DOI: 10.3389/fchem.2019.00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/04/2019] [Indexed: 02/05/2023] Open
Abstract
Designing and fabricating hetero-complexes composed of organic and biological compounds had become an exciting area referring to biological recognition, molecular devices etc. Here, hydrogen-bonded complex of nucleic-acid-base (adenine, A) and fatty-acid (stearic acid, SA) was designed, fabricated and investigated at liquid/solid interface. The interesting striped-shaped structure composed of SA-A-SA trimers was formed after introducing adenine molecules. Meanwhile, the primary lamella-shape characteristic of the assembly of SA molecules was kept because of the collaboration of non-covalent interactions of molecule-molecule and molecule-substrate. With a series of experimental characterization and theoretical simulation, the origination of the as-prepared 2D hetero-complexes was gradually exhibited from the assembled structures of two building blocks of stearic acid and adenine. Our study provides a blueprint for designing additional multi-component complexes based on the existing molecular assembled architectures.
Collapse
Affiliation(s)
- Huiling Zhao
- School of Physics and Electronics, Henan University, Kaifeng, China.,Interdisciplinary Nanoscience Centre (iNANO), Sino-Danish Center for Education and Research (SDC), Aarhus University, Aarhus, Denmark
| | - Qian Yang
- Interdisciplinary Nanoscience Centre (iNANO), Sino-Danish Center for Education and Research (SDC), Aarhus University, Aarhus, Denmark
| | - Zegao Wang
- Interdisciplinary Nanoscience Centre (iNANO), Sino-Danish Center for Education and Research (SDC), Aarhus University, Aarhus, Denmark.,College of Materials Science and Engineering, Sichuan University, Chengdu, China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bo Liu
- School of Physics and Electronics, Henan University, Kaifeng, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Centre (iNANO), Sino-Danish Center for Education and Research (SDC), Aarhus University, Aarhus, Denmark
| |
Collapse
|
54
|
Osman AMA, Pedersen EB. Conjugation of N-(3-(9-Ethynyl-6 H-indolo[2,3- b]quinoxalin-6-yl)propyl)-2,2,2-trifluoroacetamide Intercalator to a Triplex Forming Oligonucleotide, a Three-Way Junction, and a G-Quadruplex. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Amany M. A. Osman
- Nucleic Acid Center; Department of Physics; Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
- Chemistry Department; Faculty of Science; Menoufia University; Shebin El-Koam Egypt
| | - Erik B. Pedersen
- Nucleic Acid Center; Department of Physics; Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
| |
Collapse
|
55
|
Wu G, Liu Y, Yang Z, Katakam N, Rouh H, Ahmed S, Unruh D, Surowiec K, Li G. Multilayer 3D Chirality and Its Synthetic Assembly. RESEARCH 2019; 2019:6717104. [PMID: 31549078 PMCID: PMC6750085 DOI: 10.34133/2019/6717104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/23/2019] [Indexed: 12/31/2022]
Abstract
3D chirality of sandwich type of organic molecules has been discovered. The key element of this chirality is characterized by three layers of structures that are arranged nearly in parallel fashion with one on top and one down from the center plane. Individual enantiomers of these molecules have been fully characterized by spectroscopies with their enantiomeric purity measured by chiral HPLC. The absolute configuration was unambiguously assigned by X-ray diffraction analysis. This is the first multilayer 3D chirality reported and is anticipated to lead to a new research area of asymmetric synthesis and catalysis and to have a broad impact on chemical, medicinal, and material sciences in future.
Collapse
Affiliation(s)
- Guanzhao Wu
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Yangxue Liu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Zhen Yang
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Nandakumar Katakam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Hossein Rouh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Sultan Ahmed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Daniel Unruh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Kazimierz Surowiec
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Guigen Li
- Institute of Chemistry and BioMedical Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| |
Collapse
|
56
|
Sasaki S. Development of Novel Functional Molecules Targeting DNA and RNA. Chem Pharm Bull (Tokyo) 2019; 67:505-518. [PMID: 31155555 DOI: 10.1248/cpb.c19-00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleic acid therapeutics such as antisense and small interfering RNA (siRNA) have attracted increasing attention as innovative medicines that interfere with and/or modify gene expression systems. We have developed new functional oligonucleotides that can target DNA and RNA with high efficiency and selectivity. This review summarizes our achievements, including (1) the formation of non-natural triplex DNA for sequence-specific inhibition of transcription; (2) artificial receptor molecules for 8-oxidized-guanosine nucleosides; and (3) reactive oligonucleotides with a cross-linking agent or a functionality-transfer nucleoside for RNA pinpoint modification.
Collapse
Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
| |
Collapse
|
57
|
Taniguchi Y, Wang L, Okamura H, Sasaki S. Synthesis of 2'-deoxy-4-aminopyridinylpseudocytidine Derivatives for Incorporation Into Triplex Forming Oligonucleotides. ACTA ACUST UNITED AC 2019; 77:e80. [PMID: 30884181 DOI: 10.1002/cpnc.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes the detailed synthetic protocol for the preparation of the phosphoramidite units of the 2'-deoxy-4-aminopyridinylpseudocytidine derivatives. These C-nucleoside derivatives are useful units for the incorporation into triplex forming oligonucleotides (TFOs) to form the stable triplex DNA containing the CG interrupting sites. Commercially available 1-methyl-2'-deoxypseudouridine is prepared from thymidine and 5-iodo-uracil by a simple method, that is, coupling of glycal and 5-iodo-1-methyluracil by the Heck reaction, followed by desilylation and diastereoselective reduction. The carbonyl group at the 4 position of the pseudouridine derivative is activated by 3-nitorotriazole and treated with the corresponding aromatic amine compounds to produce the 2'-deoxy-4-aminopyridinylpseudocytidine derivatives. These derivatives are then successfully converted to the phosphoramidite units and incorporated into the oligodeoxynucleotides. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Lei Wang
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hidenori Okamura
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| |
Collapse
|
58
|
Affiliation(s)
- Peter B. Dervan
- Division of Chemistry & Chemical EngineeringCalifornia Institute of Technology 1200 E. California Blvd. Pasadena, CA 91125 USA
| |
Collapse
|
59
|
Li J, Begbie A, Boehm BJ, Button A, Whidborne C, Pouferis Y, Huang DM, Pukala TL. Ion Mobility-Mass Spectrometry Reveals Details of Formation and Structure for GAA·TCC DNA and RNA Triplexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:103-112. [PMID: 30341580 DOI: 10.1007/s13361-018-2077-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
DNA and RNA triplexes are thought to play key roles in a range of cellular processes such as gene regulation and epigenetic remodeling and have been implicated in human disease such as Friedreich's ataxia. In this work, ion mobility-mass spectrometry (IM-MS) is used with supporting UV-visible spectroscopy to investigate DNA triplex assembly, considering stability and specificity, for GAA·TTC oligonucleotide sequences of relevance to Friedreich's ataxia. We demonstrate that, contrary to other examples, parallel triplex structures are favored for these sequences and that stability is enhanced by increasing oligonucleotide length and decreasing pH. We also provide evidence for the self-association of these triplexes, consistent with a proposed model of higher order DNA structures formed in Friedreich's ataxia. By comparing triplex assembly using DNA- and RNA-based triplex-forming oligonucleotides, we demonstrate more favorable formation of RNA triplexes, suggesting a role for their formation in vivo. Finally, we interrogate the binding properties of netropsin, a known polyamide triplex destabilizer, with RNA-DNA hybrid triplexes, where preference for duplex binding is evident. We show that IM-MS is able to report on relevant solution-phase populations of triplex DNA structures, thereby further highlighting the utility of this technology in structural biology. Our data therefore provides new insights into the possible DNA and RNA assemblies that may form as a result of GAA triplet repeats. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Jiawei Li
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Alexander Begbie
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Belinda J Boehm
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Alexander Button
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Charles Whidborne
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Yannii Pouferis
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - David M Huang
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
| |
Collapse
|
60
|
Swasey SM, Rosu F, Copp SM, Gabelica V, Gwinn EG. Parallel Guanine Duplex and Cytosine Duplex DNA with Uninterrupted Spines of Ag I-Mediated Base Pairs. J Phys Chem Lett 2018; 9:6605-6610. [PMID: 30380874 DOI: 10.1021/acs.jpclett.8b02851] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes, and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can introduce new functionalities and enhanced stabilities. Here we demonstrate, using mass spectrometry (MS), ion mobility spectrometry (IMS), and fluorescence resonance energy transfer (FRET), that parallel-stranded structures consisting of up to 20 G-AgI-G contiguous base pairs are formed when natural DNA sequences are mixed with silver cations in aqueous solution. FRET indicates that duplexes formed by poly(cytosine) strands with 20 contiguous C-AgI-C base pairs are also parallel. Silver-mediated G-duplexes form preferentially over G-quadruplexes, and the ability of Ag+ to convert G-quadruplexes into silver-paired duplexes may provide a new route to manipulating these biologically relevant structures. IMS indicates that G-duplexes are linear and more rigid than B-DNA. DFT calculations were used to propose structures compatible with the IMS experiments. Such inexpensive, defect-free, and soluble DNA-based nanowires open new directions in the design of novel metal-mediated DNA nanotechnology.
Collapse
Affiliation(s)
- Steven M Swasey
- Department of Chemistry and Biochemistry , Univerisity of California Santa Barbara , Santa Barbara , California 93117 , United States
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie , Université de Bordeaux, CNRS & Inserm (IECB, UMS3033, US001) , 2 rue Robert Escarpit , 33607 Pessac , France
| | - Stacy M Copp
- Center for Integrated Nanotechnologies , Los Alamos National Laboratories , Los Alamos , New Mexico 87545 , United States
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle , Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB , 2 rue Robert Escarpit , 33607 Pessac , France
| | - Elisabeth G Gwinn
- Department of Physics , Univerisity of California Santa Barbara , Santa Barbara , California 93117 , United States
| |
Collapse
|
61
|
Walsh S, El-Sagheer AH, Brown T. Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above. Chem Sci 2018; 9:7681-7687. [PMID: 30393529 PMCID: PMC6182420 DOI: 10.1039/c8sc02418a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
The instability of DNA triplexes particularly at neutral pH and above severely limits their applications. Here, we demonstrate that the introduction of a thiazole orange (TO) intercalator onto a thymine nucleobase in triplex forming oligonucleotides (TFOs) resolves this problem. The stabilising effects are additive; multiple TO units produce nanomolar duplex binding and triplex stability can surpass that of the underlying duplex. In one example, a TFO containing three TO units increased the triplex melting temperature at pH 7 by a remarkable 50 °C relative to the unmodified triplex. Notably, TO intercalation promotes TFO binding to target sequences other than pure polypurine tracts by the use of 5-(1-propynyl)cytosine (pC) against C:G inversions. By overcoming the instability of triplexes across a broad range of pH and sequence contexts, these very simple 'TOTFO' probes could expand triplex applications into many areas including diagnostics and cell imaging.
Collapse
Affiliation(s)
- Sarah Walsh
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- ATDBio Ltd. , Oxford Science Park , Oxford , UK
| | - Afaf Helmy El-Sagheer
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
| |
Collapse
|
62
|
Abstract
Oligonucleotides (ONs) can interfere with biomolecules representing the entire extended central dogma. Antisense gapmer, steric block, splice-switching ONs, and short interfering RNA drugs have been successfully developed. Moreover, antagomirs (antimicroRNAs), microRNA mimics, aptamers, DNA decoys, DNAzymes, synthetic guide strands for CRISPR/Cas, and innate immunity-stimulating ONs are all in clinical trials. DNA-targeting, triplex-forming ONs and strand-invading ONs have made their mark on drug development research, but not yet as medicines. Both design and synthetic nucleic acid chemistry are crucial for achieving biologically active ONs. The dominating modifications are phosphorothioate linkages, base methylation, and numerous 2'-substitutions in the furanose ring, such as 2'-fluoro, O-methyl, or methoxyethyl. Locked nucleic acid and constrained ethyl, a related variant, are bridged forms where the 2'-oxygen connects to the 4'-carbon in the sugar. Phosphorodiamidate morpholino oligomers, carrying a modified heterocyclic backbone ring, have also been commercialized. Delivery remains a major obstacle, but systemic administration and intrathecal infusion are used for treatment of the liver and brain, respectively.
Collapse
Affiliation(s)
- C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden; .,Stellenbosch Institute for Advanced Study, Wallenberg Research Centre, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden; .,Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| |
Collapse
|
63
|
Jayarathna DR, Stout HD, Achim C. Metal Coordination to Ligand-Modified Peptide Nucleic Acid Triplexes. Inorg Chem 2018; 57:6865-6872. [PMID: 29845860 DOI: 10.1021/acs.inorgchem.8b00442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A challenging goal in nanotechnology is the precise and programmable arrangement of specific elements in nanosystems in the three-dimensional space. The use of ligand-modified nucleic acids represents an accurate and selective tool to achieve this goal when it comes to metal ion organization. The synthesis of peptide nucleic acid (PNA) monomers that contain ligands instead of nucleobases makes possible the creation of metal-mediated alternative base pairs and triplets at specific locations in PNA duplexes and triplexes, respectively. We report the formation of four- and six-coordinate metal complexes between PNA triplexes modified with 2,2'-bipyridine (Bpy) or 8-hydroxyquinoline (Q) ligands and 3d metal ions. These metal complexes function as alternative base triplets or pairs in that they increase the thermal stability of the triplexes if the stability constants of the metal complexes are relatively high. The increase in the triplex melting temperature correlates with the stability constants of the metal complexes with ligand-containing PNA determined by UV-vis titrations. The metal complexes coordinate two or three ligands although three bidentate ligands are in close proximity of each other within a triplex. Metal coordination to ligand-modified PNA triplexes was further studied by electron paramagnetic resonance (EPR) spectroscopy and circular dichrosim (CD) spectroscopy. EPR spectroscopy indicated the formation of a square planar [CuQ2] complex between Cu2+ and Q-containing PNA triplex. Taken together, the spectroscopic results indicate that in the presence of 1 equiv of Fe2+ or Ni2+ the majority, but not all, of the Bpy-containing PNA triplexes contain [MBpy3] complexes, with a minority of them being metal free. We attribute this behavior to a supramolecular chelate effect exerted by the triplex, which favors the formation of tris-ligand complexes, that is balanced by the steric interactions between the metal complex and the adjacent nucleobase triplets, which decrease the stability of the complex and triplex. In contrast, the very high stability of square planar [MQ2] complexes of Cu2+ and Ni2+ leads to formation of bis-ligand complexes instead of tris-ligand complexes with Q3-containing PNA triplexes. The metal-containing PNA triplexes have a terminal l-lysine and adopt a left-handed chiral structure in solution. The handedness of the PNA triplex determines that of the metal complexes formed with the Bpy-containing PNA triplexes.
Collapse
Affiliation(s)
- Dilhara R Jayarathna
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Heather D Stout
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Catalina Achim
- Department of Chemistry , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| |
Collapse
|
64
|
|
65
|
Non-canonical DNA structures: Comparative quantum mechanical study. Biophys Chem 2018; 235:19-28. [DOI: 10.1016/j.bpc.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 11/21/2022]
|
66
|
Hartono YD, Xu Y, Karshikoff A, Nilsson L, Villa A. Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids. J Chem Inf Model 2018. [PMID: 29537270 DOI: 10.1021/acs.jcim.7b00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (LNA), is widely used in triplex forming oligonucleotides to target sites in the human genome. In this study, the parameters for LNA are developed in line with the CHARMM nucleic acid force field and validated toward the available structural experimental data. In conjunction, two computational methods were used to calculate the protonation state of the third strand cytidine in various DNA triplex environments: λ-dynamics and multiple pH regime. Both approaches predict p K of this cytidine shifted above physiological pH when cytidine is in the third strand in a triplex environment. Both methods show an upshift due to cytidine methylation, and a small downshift when the sugar configuration is locked. The predicted p K values for cytidine in DNA triplex environment can inform the design of better-binding oligonucleotides.
Collapse
Affiliation(s)
- Yossa Dwi Hartono
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden.,Division of Structural Biology and Biochemistry, School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - You Xu
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Andrey Karshikoff
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| |
Collapse
|
67
|
Maldonado R, Filarsky M, Grummt I, Längst G. Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus. RNA (NEW YORK, N.Y.) 2018; 24:371-380. [PMID: 29222118 PMCID: PMC5824356 DOI: 10.1261/rna.063800.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 05/04/2023]
Abstract
Triplexes are noncanonical DNA structures, which are functionally associated with regulation of gene expression through ncRNA targeting to chromatin. Based on the rules of Hoogsteen base-pairing, polypurine sequences of a duplex can potentially form triplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyses have revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers, suggesting a potential function of RNA-DNA triplexes in transcriptional regulation. Here, we have quantitatively evaluated the potential of different sequences of human and mouse ribosomal RNA genes (rDNA) to form triplexes at different salt and pH conditions. We show by biochemical and biophysical approaches that some of these predicted sequences form triplexes with high affinity, following the canonical rules for triplex formation. We further show that RNA triplex-forming oligos (TFOs) are more stable than their DNA counterpart, and point mutations strongly affect triplex formation. We further show differential sequence requirements of pyrimidine and purine TFO sequences for efficient binding, depending on the G-C content of the TTS. The unexpected sequence specificity, revealing distinct sequence requirements for purine and pyrimidine TFOs, shows that in addition to the Hoogsteen pairing rules, a sequence code and mutations have to be taken into account to predict genomic TTS.
Collapse
Affiliation(s)
- Rodrigo Maldonado
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
| | - Michael Filarsky
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), Universität Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
68
|
Aravalli RN, Steer CJ. CRISPR/Cas9 therapeutics for liver diseases. J Cell Biochem 2018; 119:4265-4278. [PMID: 29266637 DOI: 10.1002/jcb.26627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
Abstract
The development of innovative genome editing techniques in recent years has revolutionized the field of biomedicine. Among the novel approaches, the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas9) technology has become the most popular, in part due to its matchless ability to carry out gene editing at the target site with great precision. With considerable successes in animal and preclinical studies, CRISPR/Cas9-mediated gene editing has paved the way for its use in human trials, including patients with a variety of liver diseases. Gene editing is a logical therapeutic approach for liver diseases because many metabolic and acquired disorders are caused by mutations within a single gene. In this review, we provide an overview on current and emerging therapeutic strategies for the treatment of liver diseases using the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Clifford J Steer
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
69
|
Chandrasekaran AR, Rusling DA. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res 2018; 46:1021-1037. [PMID: 29228337 PMCID: PMC5814803 DOI: 10.1093/nar/gkx1230] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/30/2017] [Indexed: 11/14/2022] Open
Abstract
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
Collapse
Affiliation(s)
| | - David A Rusling
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| |
Collapse
|
70
|
Heiderscheit EA, Eguchi A, Spurgat MC, Ansari AZ. Reprogramming cell fate with artificial transcription factors. FEBS Lett 2018; 592:888-900. [PMID: 29389011 DOI: 10.1002/1873-3468.12993] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
Abstract
Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states. Here, we compare the unique strengths and limitations of different ATF platforms, highlight the advantages of cooperative assembly, and present the potential of ATF libraries in revealing gene regulatory networks that govern cell fate choices.
Collapse
Affiliation(s)
- Evan A Heiderscheit
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Mackenzie C Spurgat
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| |
Collapse
|
71
|
Ma B, Lu M, Yu BY, Tian J. A galactose-mediated targeting nanoprobe for intracellular hydroxyl radical imaging to predict drug-induced liver injury. RSC Adv 2018; 8:22062-22068. [PMID: 35541760 PMCID: PMC9081097 DOI: 10.1039/c8ra01424h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/04/2018] [Indexed: 11/21/2022] Open
Abstract
Drug-induced liver injury (DILI) is a serious concern in modern medicine due to its unpredictability. Currently, biochemical serum markers are being used in DILI detection. However, these biomarker-based methods lack sensitivity and specificity. A high intracellular level of hydroxyl radicals (˙OH) has been regarded as an early indicator of DILI. Therefore, we proposed an ˙OH-responsive and hepatocyte-targeted nanoprobe via conjugation of carboxyfluorescein-labeled DNA and pegylated galactose on the surface of gold nanoparticles. The nanoprobe could bind to a hepatocyte-specific asialoglycoprotein receptor through galactose, and it could be internalized into liver cells. In the presence of high levels of ˙OH in DILI, the DNA could be cleaved to release carboxyfluorescein, leading to remarkable fluorescence enhancement for ˙OH detection. Confocal fluorescence imaging demonstrated that the nanoprobe could be successfully applied in monitoring high ˙OH levels resulting from acetaminophen or triptolide-induced liver injury, which may provide a simple but powerful protocol for the prediction of DILI. A galactose-mediated targeting nanoprobe has been developed for the accurate imaging of ˙OH to predict drug-induced hepatotoxicity at an early stage.![]()
Collapse
Affiliation(s)
- Bailing Ma
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 211198
| | - Mi Lu
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 211198
| | - Bo-Yang Yu
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 211198
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research
- School of Traditional Chinese Pharmacy
- China Pharmaceutical University
- Nanjing 211198
| |
Collapse
|
72
|
Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
Collapse
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| |
Collapse
|
73
|
Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| |
Collapse
|
74
|
Nguyen TQN, Lim KW, Phan AT. A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs. Sci Rep 2017; 7:11969. [PMID: 28931822 PMCID: PMC5607247 DOI: 10.1038/s41598-017-10583-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022] Open
Abstract
Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.
Collapse
Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
75
|
Pabon-Martinez YV, Xu Y, Villa A, Lundin KE, Geny S, Nguyen CH, Pedersen EB, Jørgensen PT, Wengel J, Nilsson L, Smith CIE, Zain R. LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures. Sci Rep 2017; 7:11043. [PMID: 28887512 PMCID: PMC5591256 DOI: 10.1038/s41598-017-09147-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/20/2017] [Indexed: 12/19/2022] Open
Abstract
The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked nucleic acid (LNA) substitutions in the ON when targeting a c-MYC or FXN (Frataxin) sequence. We found that LNA-containing single strand TFOs are conformationally pre-organized for major groove binding. Reduced content of LNA at consecutive positions at the 3'-end of a TFO destabilizes the triplex structure, whereas the presence of Twisted Intercalating Nucleic Acid (TINA) at the 3'-end of the TFO increases the rate and extent of triplex formation. A triplex-specific intercalating benzoquinoquinoxaline (BQQ) compound highly stabilizes LNA-containing triplex structures. Moreover, LNA-substitution in the duplex pyrimidine strand alters the double helix structure, affecting x-displacement, slide and twist favoring triplex formation through enhanced TFO major groove accommodation. Collectively, these findings should facilitate the design of potent anti-gene ONs.
Collapse
Affiliation(s)
- Y Vladimir Pabon-Martinez
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Sylvain Geny
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Institut Curie, PSL Research University, UMR 9187-U 1196, CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
| |
Collapse
|
76
|
D'Souza DJ, Kool ET. Solvent, pH, and Ionic Effects on the Binding of Single-Stranded DNA by Circular Oligodeoxynucleotides. Bioorg Med Chem Lett 2017; 4:965-970. [PMID: 27840561 DOI: 10.1016/s0960-894x(01)80664-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The effects of changing solution conditions on the strength of triple helical complexes formed between pyrimidine-rich circular DNA oligonucleotides and their homopurine complements are examined. The complexes display properties different from those seen for other types of DNA triplexes.
Collapse
Affiliation(s)
- David J D'Souza
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Eric T Kool
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| |
Collapse
|
77
|
Patro LPP, Kumar A, Kolimi N, Rathinavelan T. 3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-Dimensional Nucleic Acid Structures. J Mol Biol 2017; 429:2438-2448. [PMID: 28652006 DOI: 10.1016/j.jmb.2017.06.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information. Furthermore, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by X-ray crystallography or NMR techniques, are essential to establish their biological function(s). A web server, namely 3D-NuS (http://iith.ac.in/3dnus/), has been developed to generate energy-minimized models of 80 different types of triplexes, 64 types of G-quadruplexes, left-handed Z-DNA/RNA duplexes, and RNA-DNA hybrid duplex along with inter- and intramolecular DNA or RNA duplexes comprising a variety of mismatches and their chimeric forms for any user-defined sequence and length. It also generates an ensemble of conformations corresponding to the modeled structure. These structures may serve as good starting models for docking proteins and small molecules with nucleic acids, NMR structure determination, cryo-electron microscope modeling, DNA/RNA nanotechnology applications and molecular dynamics simulation studies.
Collapse
Affiliation(s)
- L Ponoop Prasad Patro
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Abhishek Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | | |
Collapse
|
78
|
Mulla RS, Pitarch-Jarque J, García-España E, Desa T, Lurie-Luke E, Williams JAG. Monoamide Derivatives of EDTA Incorporating Pendent Carboxylates or Pyridyls: Synthesis, Metal Binding, and Crystal Structure of a Dinuclear Ca2+
Complex Featuring Bridging Na+
Ions. ChemistrySelect 2017. [DOI: 10.1002/slct.201700995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Javier Pitarch-Jarque
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; C/ Catedrático José Beltrán, 2 46980, Paterna Valencia Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; C/ Catedrático José Beltrán, 2 46980, Paterna Valencia Spain
| | - Tanya Desa
- Procter and Gamble Technical Centres Limited, Rusham Park; Whitehall Lane, Egham Surrey TW20 9NW
| | - Elena Lurie-Luke
- Procter and Gamble Technical Centres Limited, Rusham Park; Whitehall Lane, Egham Surrey TW20 9NW
| | | |
Collapse
|
79
|
Zhu Y, Hamlow LA, He CC, Lee JK, Gao J, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue. J Phys Chem B 2017; 121:4048-4060. [PMID: 28355483 DOI: 10.1021/acs.jpcb.7b02906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
Collapse
Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J K Lee
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| |
Collapse
|
80
|
Yamayoshi A, Miyoshi D, Zouzumi YK, Matsuyama Y, Ariyoshi J, Shimada N, Murakami A, Wada T, Maruyama A. Selective and Robust Stabilization of Triplex DNA Structures Using Cationic Comb-type Copolymers. J Phys Chem B 2017; 121:4015-4022. [DOI: 10.1021/acs.jpcb.7b01926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Asako Yamayoshi
- The
Hakubi Center for Advanced Research, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daisuke Miyoshi
- Faculty
of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yu-ki Zouzumi
- Faculty
of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Yohei Matsuyama
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Jumpei Ariyoshi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Naohiko Shimada
- Department
of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57
Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Akira Murakami
- Department
of Biomolecular Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takehiko Wada
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1,
Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsushi Maruyama
- Department
of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57
Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| |
Collapse
|
81
|
Solé A, Delagoutte E, Ciudad CJ, Noé V, Alberti P. Polypurine reverse-Hoogsteen (PPRH) oligonucleotides can form triplexes with their target sequences even under conditions where they fold into G-quadruplexes. Sci Rep 2017; 7:39898. [PMID: 28067256 PMCID: PMC5220335 DOI: 10.1038/srep39898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 11/28/2016] [Indexed: 02/03/2023] Open
Abstract
Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. In this work, we provide an in vitro characterization (UV and fluorescence spectroscopy, gel electrophoresis and nuclease assays) of the structure and stability of two repair-PPRH oligonucleotides and of the complexes they form with their single-stranded targets. We show that one PPRH oligonucleotide forms a hairpin, while the other folds, in potassium, into a guanine-quadruplex (G4). However, the hairpin-prone oligonucleotide does not form a triplex with its single-stranded target, while the G4-prone oligonucleotide converts from a G4 into a reverse-Hoogsteen hairpin forming a triplex with its target sequence. Our work proves, in particular, that folding of a PPRH oligonucleotide into a G4 does not necessarily impair sequence-specific DNA recognition by triplex formation. It also illustrates an original example of DNA structural conversion of a G4 into a reverse-Hoogsteen hairpin driven by triplex formation; this kind of conversion might occur at particular loci of genomic DNA.
Collapse
Affiliation(s)
- Anna Solé
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Emmanuelle Delagoutte
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Carlos J. Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Patrizia Alberti
- Structure et Instability of Genomes, Sorbonne Universités, Muséum National d’Histoire Naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France
| |
Collapse
|
82
|
Yang H, Yao W, Wang Y, Shi L, Su R, Wan D, Xu N, Lian W, Chen C, Liu S. High-throughput screening of triplex DNA binders from complicated samples by 96-well pate format in conjunction with peak area-fading UHPLC-Orbitrap MS. Analyst 2017; 142:670-675. [DOI: 10.1039/c6an01974a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Screening triplex DNA binders from complicated samples in a high-throughput fashion with good reproducibility without the requirement of an extra releasing step.
Collapse
Affiliation(s)
- Hongmei Yang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| | - Wenbin Yao
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Yihan Wang
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Lei Shi
- High Temperature Reactor Holdings Co
- Ltd
- China Nuclear Engineering Group Co
- Beijing 100037
- China
| | - Rui Su
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Debin Wan
- Department of Entomology and Comprehensive Cancer Center
- University of California
- Davis
- USA
| | - Niusheng Xu
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- China
| | - Wenhui Lian
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Changbao Chen
- Changchun University of Chinese Medicine
- Changchun 130117
- China
| | - Shuying Liu
- Changchun University of Chinese Medicine
- Changchun 130117
- China
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
| |
Collapse
|
83
|
Mukherjee A, Vasquez KM. Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks. J Vis Exp 2016. [PMID: 27911399 DOI: 10.3791/54678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic. While ICL-forming agents show preferences for certain base sequences (e.g., 5'-TA-3' is the preferred crosslinking site for psoralen), they largely induce DNA damage in an indiscriminate fashion. However, by covalently coupling the ICL-inducing agent to a triplex-forming oligonucleotide (TFO), which binds to DNA in a sequence-specific manner, targeted DNA damage can be achieved. Here, we use a TFO covalently conjugated on the 5' end to a 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) psoralen to generate a site-specific ICL on a mutation-reporter plasmid to use as a tool to study the architectural modification, processing, and repair of complex DNA lesions by HMGB1 in human cells. We describe experimental techniques to prepare TFO-directed ICLs on reporter plasmids, and to interrogate the association of HMGB1 with the TFO-directed ICLs in a cellular context using chromatin immunoprecipitation assays. In addition, we describe DNA supercoiling assays to assess specific architectural modification of the damaged DNA by measuring the amount of superhelical turns introduced on the psoralen-crosslinked plasmid by HMGB1. These techniques can be used to study the roles of other proteins involved in the processing and repair of TFO-directed ICLs or other targeted DNA damage in any cell line of interest.
Collapse
Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin;
| |
Collapse
|
84
|
Li Y, Syed J, Sugiyama H. RNA-DNA Triplex Formation by Long Noncoding RNAs. Cell Chem Biol 2016; 23:1325-1333. [DOI: 10.1016/j.chembiol.2016.09.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/29/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023]
|
85
|
Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| |
Collapse
|
86
|
Sharma C, Awasthi SK. Versatility of peptide nucleic acids (PNAs): role in chemical biology, drug discovery, and origins of life. Chem Biol Drug Des 2016; 89:16-37. [PMID: 27490868 DOI: 10.1111/cbdd.12833] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/03/2016] [Accepted: 07/28/2016] [Indexed: 12/16/2022]
Abstract
This review briefly discussed nomenclature, synthesis, chemistry, and biophysical properties of a plethora of PNA derivatives reported since the discovery of aegPNA. Different synthetic methods and structural analogs of PNA synthesized till date were also discussed. An insight was gained into various chemical, physical, and biological properties of PNA which make it preferable over all other classes of modified nucleic acid analogs. Thereafter, various approaches with special attention to the practical constraints, characteristics, and inherent drawbacks leading to the delay in the development of PNA as gene therapeutic drug were outlined. An explicit account of the successful application of PNA in different areas of research such as antisense and antigene strategies, diagnostics, molecular probes, and so forth was described along with the current status of PNA as gene therapeutic drug. Further, the plausibility of the existence of PNA and its role in primordial chemistry, that is, origin of life was explored in an endeavor to comprehend the mystery and open up its deepest secrets ever engaging and challenging the human intellect. We finally concluded it with a discussion on the future prospects of PNA technology in the field of therapeutics, diagnostics, and origin of life.
Collapse
Affiliation(s)
- Chiranjeev Sharma
- Chemical Biology Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Satish Kumar Awasthi
- Chemical Biology Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| |
Collapse
|
87
|
Okamura H, Taniguchi Y, Sasaki S. Aminopyridinyl-Pseudodeoxycytidine Derivatives Selectively Stabilize Antiparallel Triplex DNA with Multiple CG Inversion Sites. Angew Chem Int Ed Engl 2016; 55:12445-9. [DOI: 10.1002/anie.201606136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hidenori Okamura
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| |
Collapse
|
88
|
Okamura H, Taniguchi Y, Sasaki S. Aminopyridinyl-Pseudodeoxycytidine Derivatives Selectively Stabilize Antiparallel Triplex DNA with Multiple CG Inversion Sites. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hidenori Okamura
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| |
Collapse
|
89
|
Wang M, Yu Y, Liang C, Lu A, Zhang G. Recent Advances in Developing Small Molecules Targeting Nucleic Acid. Int J Mol Sci 2016; 17:ijms17060779. [PMID: 27248995 PMCID: PMC4926330 DOI: 10.3390/ijms17060779] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/01/2016] [Accepted: 05/09/2016] [Indexed: 12/19/2022] Open
Abstract
Nucleic acids participate in a large number of biological processes. However, current approaches for small molecules targeting protein are incompatible with nucleic acids. On the other hand, the lack of crystallization of nucleic acid is the limiting factor for nucleic acid drug design. Because of the improvements in crystallization in recent years, a great many structures of nucleic acids have been reported, providing basic information for nucleic acid drug discovery. This review focuses on the discovery and development of small molecules targeting nucleic acids.
Collapse
Affiliation(s)
- Maolin Wang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Chao Liang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Aiping Lu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| | - Ge Zhang
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China.
| |
Collapse
|
90
|
Zhao HQ, Qiu GH, Liang Z, Li MM, Sun B, Qin L, Yang SP, Chen WH, Chen JX. A zinc(II)-based two-dimensional MOF for sensitive and selective sensing of HIV-1 ds-DNA sequences. Anal Chim Acta 2016; 922:55-63. [DOI: 10.1016/j.aca.2016.03.054] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/21/2016] [Accepted: 03/26/2016] [Indexed: 12/16/2022]
|
91
|
An overview on the interaction of phenazinium dye phenosafranine to RNA triple and double helices. Int J Biol Macromol 2016; 86:345-51. [DOI: 10.1016/j.ijbiomac.2016.01.078] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 12/22/2022]
|
92
|
Yamagata Y, Emura T, Hidaka K, Sugiyama H, Endo M. Triple Helix Formation in a Topologically Controlled DNA Nanosystem. Chemistry 2016; 22:5494-8. [PMID: 26938310 DOI: 10.1002/chem.201505030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/11/2022]
Abstract
In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.
Collapse
Affiliation(s)
- Yutaro Yamagata
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan. .,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
| |
Collapse
|
93
|
Wirth-Hamdoune D, Ullrich S, Scheffer U, Radanović T, Dürner G, Göbel MW. A Bis(guanidinium)alcohol Attached to a Hairpin Polyamide: Synthesis, DNA Binding, and Plasmid Cleavage. Chembiochem 2016; 17:506-14. [DOI: 10.1002/cbic.201500566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Daniela Wirth-Hamdoune
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Ute Scheffer
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Toni Radanović
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Gerd Dürner
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| |
Collapse
|
94
|
Aviñó A, Mazzini S, Gargallo R, Eritja R. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA. Int J Mol Sci 2016; 17:211. [PMID: 26861295 PMCID: PMC4783943 DOI: 10.3390/ijms17020211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions.
Collapse
Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, Barcelona 08034, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, Barcelona 08034, Spain.
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, Milan 20133, Italy.
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, Barcelona 08028, Spain.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, Barcelona 08034, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, Barcelona 08034, Spain.
| |
Collapse
|
95
|
Chen P, Wu P, Chen J, Yang P, Zhang X, Zheng C, Hou X. Label-Free and Separation-Free Atomic Fluorescence Spectrometry-Based Bioassay: Sensitive Determination of Single-Strand DNA, Protein, and Double-Strand DNA. Anal Chem 2016; 88:2065-71. [DOI: 10.1021/acs.analchem.5b03307] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | | | | | | | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, China
| | | | | |
Collapse
|
96
|
Kaushik M, Kaushik S, Roy K, Singh A, Mahendru S, Kumar M, Chaudhary S, Ahmed S, Kukreti S. A bouquet of DNA structures: Emerging diversity. Biochem Biophys Rep 2016; 5:388-395. [PMID: 28955846 PMCID: PMC5600441 DOI: 10.1016/j.bbrep.2016.01.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/22/2016] [Indexed: 11/29/2022] Open
Abstract
Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications. DNA can adopt diverse range of structures other than classical Watson–Crick duplex. Discussion of alternate structures like hairpin, cruciform, triplex, quadruplex etc. This review gives some insights for the biological relevance of DNA structures.
Collapse
Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre, University of Delhi, Delhi, India.,Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mohan Kumar
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Saami Ahmed
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| |
Collapse
|
97
|
Zhao HQ, Yang SP, Ding NN, Qin L, Qiu GH, Chen JX, Zhang WH, Chen WH, Hor TSA. A zwitterionic 1D/2D polymer co-crystal and its polymorphic sub-components: a highly selective sensing platform for HIV ds-DNA sequences. Dalton Trans 2016; 45:5092-100. [DOI: 10.1039/c5dt04410c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (2, 1D chain), [Cu(dcbb)2]n (3, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n (4) have been prepared from the reaction of [Na(dcbb)(H2O)]n (1) with Cu(NO3)2·3H2O at different temperatures.
Collapse
Affiliation(s)
- Hai-Qing Zhao
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Shui-Ping Yang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ni-Ni Ding
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Liang Qin
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Gui-Hua Qiu
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - T. S. Andy Hor
- Institute of Materials Research and Engineering (IMRE)
- A*STAR
- Singapore
- Department of Chemistry
- National University of Singapore
| |
Collapse
|
98
|
Abdallah HO, Ohayon YP, Chandrasekaran AR, Sha R, Fox KR, Brown T, Rusling DA, Mao C, Seeman NC. Stabilisation of self-assembled DNA crystals by triplex-directed photo-cross-linking. Chem Commun (Camb) 2016; 52:8014-7. [DOI: 10.1039/c6cc03695c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cross-linked crystals: triplex-forming oligonucleotides can direct cross-linking reactions within or between tiles of a DNA crystal, improving their thermal stability.
Collapse
Affiliation(s)
| | | | | | - Ruojie Sha
- Department of Chemistry
- New York University
- New York
- USA
| | - Keith R. Fox
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - David A. Rusling
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | | |
Collapse
|
99
|
Ito Y, Masaki Y, Kanamori T, Ohkubo A, Seio K, Sekine M. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA. Bioorg Med Chem Lett 2016; 26:194-6. [PMID: 26602276 DOI: 10.1016/j.bmcl.2015.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/28/2022]
Abstract
5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities.
Collapse
Affiliation(s)
- Yu Ito
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259, Nagatsuta, Yokohama 226-8501, Japan.
| |
Collapse
|
100
|
Bahal R, Gupta A, Glazer PM. Precise Genome Modification Using Triplex Forming Oligonucleotides and Peptide Nucleic Acids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|