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Wang X, Wang Y, He Y, Liu L, Wang X, Jiang S, Yang N, Shi N, Li Y. A versatile technique for indiscriminate detection of unlabeled biomolecules via double-enhanced Raman scattering. Int J Biol Macromol 2023; 228:615-623. [PMID: 36581033 DOI: 10.1016/j.ijbiomac.2022.12.241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Surface-enhanced Raman scattering is a rapid, highly sensitive and non-destructive technique, whereas, it was still limited to designing different types of enhancing substrates or using probe molecules to only identify single biomolecules. Especially, some special biomolecules have weak Raman signals in solid state, so it is a huge challenge to obtain their enhanced Raman signals in liquid. To solve the problem, a double-enhanced Raman scattering (DERS) detection platform was developed in this study based on silver nanoparticles that were prepared by using an appropriate amount of sodium borohydride and guided by calcium ions to form good "hot spots". This enabled one to successfully obtain fingerprints of various types of biomolecules under the identical experimental conditions. The addition of sodium borohydride as reducing agent could protect silver nanoparticles from oxidation, and biomolecules were adsorbed on the exposed silver surface and demonstrated their initially enhanced Raman signals. Furthermore, the "hot spots" formed by silver nanoparticles without silver oxide coating could further enhance the Raman signal of biomolecules, making the enhancement factor up to 10 [8]. To sum up, the possibility of fast identification of different species of biomolecules via DERS has wide application prospects in the fields of biomarker detection and medical diagnosis.
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Affiliation(s)
- Xiaotong Wang
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China; Department of Pharmaceutical Analysis and Analytical Chemistry, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China
| | - Yunpeng Wang
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China; Department of Inorganic Chemistry and Physical Chemistry, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China
| | - Yingying He
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China
| | - Ling Liu
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China; Department of Pharmaceutical Analysis and Analytical Chemistry, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China
| | - Xiaoqing Wang
- School of Chemistry and Chemical Engineering, Guizhou University, Guizhou 550000, PR China
| | - Shen Jiang
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China
| | - Ni Yang
- School of Chemistry and Chemical Engineering, Guizhou University, Guizhou 550000, PR China
| | - Na Shi
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Jilin 130000, PR China
| | - Yang Li
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China; Department of Pharmaceutical Analysis and Analytical Chemistry, College of Pharmacy, Harbin Medical University, Heilongjiang 150081, PR China.
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2
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Li Y, Wang Y, Tian J, Huang JA. Detection of Cell-Derived Exosomes Via Surface-Enhanced Raman Scattering Using Aggregated Silver Nanoparticles. Methods Mol Biol 2023; 2668:15-22. [PMID: 37140786 DOI: 10.1007/978-1-0716-3203-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Exosomes are small extracellular vesicles that contain RNA, lipids, and proteins and can act as cellular messengers, carrying information to cells and tissues in the body. Thus, sensitive, label-free, and multiplexed analysis of exosomes may help in early diagnosis of important diseases. Here, we describe the process of pretreatment of cell-derived exosomes, preparation of surface-enhanced Raman scattering (SERS) substrates, and label-free SERS detection of exosomes using sodium borohydride aggregators. This method can enable the observation of SERS signals of exosomes that are clear and stable and have a good signal-to-noise ratio.
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Affiliation(s)
- Yang Li
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunpeng Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinwei Tian
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, The Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jian-An Huang
- Faculty of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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3
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Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
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Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
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4
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Chen L, Chen W, Liu G, Li J, Lu C, Li J, Tan W, Yang H. Nucleic acid-based molecular computation heads towards cellular applications. Chem Soc Rev 2021; 50:12551-12575. [PMID: 34604889 DOI: 10.1039/d0cs01508c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids, with the advantages of programmability and biocompatibility, have been widely used to design different kinds of novel biocomputing devices. Recently, nucleic acid-based molecular computing has shown promise in making the leap from the test tube to the cell. Such molecular computing can perform logic analysis within the confines of the cellular milieu with programmable modulation of biological functions at the molecular level. In this review, we summarize the development of nucleic acid-based biocomputing devices that are rationally designed and chemically synthesized, highlighting the ability of nucleic acid-based molecular computing to achieve cellular applications in sensing, imaging, biomedicine, and bioengineering. Then we discuss the future challenges and opportunities for cellular and in vivo applications. We expect this review to inspire innovative work on constructing nucleic acid-based biocomputing to achieve the goal of precisely rewiring, even reconstructing cellular signal networks in a prescribed way.
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Affiliation(s)
- Lanlan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Wanzhen Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Guo Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Jingying Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China. .,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China.
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5
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Li C, Luo S, Wang J, Shen Z, Wu ZS. Nuclease-resistant signaling nanostructures made entirely of DNA oligonucleotides. NANOSCALE 2021; 13:7034-7051. [PMID: 33889882 DOI: 10.1039/d1nr00197c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleic acid probes have the advantages of excellent biocompatibility, biodegradability, versatile functionalities and remarkable programmability. However, the low biostability of nucleic acid probes under complex physiological conditions limits their in vivo application. Despite impressive progress in the development of inorganic material-mediated biostable nucleic acid nanostructures, uncertain systemic toxicity of composite nanocarriers has hindered their application in living organisms. In the field of biomedicine, as a promising alternative capable of avoiding potential cytotoxicity, biologically stable nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in recent years, offering an exciting in vivo tool for cancer diagnosis and clinical treatment. In this review, we summarize the recent advances in the development of nuclease-resistant DNA nanostructures with different geometrical shapes, such as tetrahedron, octahedron, DNA triangular prism (DTP), DNA nanotubes and DNA origami, introduce innovative assembly strategies, and discuss unique structural advantages and especially biological applications in cellular imaging and targeted drug delivery in an organism. Finally, we conclude with the challenges in the clinical development of DNA nanostructures and present an outlook of the future of this rapidly expanding field.
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Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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6
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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7
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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8
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Školáková P, Renčiuk D, Palacký J, Krafčík D, Dvořáková Z, Kejnovská I, Bednářová K, Vorlíčková M. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic Acids Res 2019; 47:2177-2189. [PMID: 30715498 PMCID: PMC6412112 DOI: 10.1093/nar/gkz046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Krafčík
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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Cao Y, Kuang Y, Yang L, Ding P, Pei R. Construction of One- and Two-Dimensional Nanostructures by the Sequential Assembly of Quadruplex DNA Scaffolds. Biomacromolecules 2019; 20:2207-2217. [DOI: 10.1021/acs.biomac.9b00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ye Kuang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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10
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Yourston LE, Lushnikov AY, Shevchenko OA, Afonin KA, Krasnoslobodtsev AV. First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E613. [PMID: 31013933 PMCID: PMC6523636 DOI: 10.3390/nano9040613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022]
Abstract
Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence-an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence-twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single "basic" templating element, (dC)12, emit in "red". The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in "green". A new population of "blue" emitting clusters forms only when ssDNA templating sequence is placed on the 5' end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure-a first step towards a larger assembly.
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Affiliation(s)
- Liam E Yourston
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
| | - Alexander Y Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Oleg A Shevchenko
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Alexey V Krasnoslobodtsev
- Department of Physics, University of Nebraska Omaha, Omaha, NE 68182, USA.
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE 68198, USA.
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11
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Li Y, Han X, Yan Y, Cao Y, Xiang X, Wang S, Zhao B, Guo X. Label-Free Detection of Tetramolecular i-Motifs by Surface-Enhanced Raman Spectroscopy. Anal Chem 2018; 90:2996-3000. [DOI: 10.1021/acs.analchem.7b04277] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yang Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yuting Yan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yanwei Cao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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12
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Cao Y, Gao S, Yan Y, Bruist MF, Wang B, Guo X. Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs. Nucleic Acids Res 2016; 45:26-38. [PMID: 27899568 PMCID: PMC5224476 DOI: 10.1093/nar/gkw1049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TGiAC5) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG4AC7) and d(TGBrGGBrGAC7) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG4AC7) forms supramolecules under acidic conditions in the presence of K+ that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TGBrGGBrGAC7) forms long linear quadruplex wires under acidic conditions in the presence of Na+ that consist of both antiparallel G4s and i-motifs.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Shang Gao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yuting Yan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Michael F Bruist
- Department of Chemistry & Biochemistry, University of the Sciences, 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
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13
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Keane PM, Baptista FR, Gurung SP, Devereux SJ, Sazanovich IV, Towrie M, Brazier JA, Cardin CJ, Kelly JM, Quinn SJ. Long-Lived Excited-State Dynamics of i-Motif Structures Probed by Time-Resolved Infrared Spectroscopy. Chemphyschem 2016; 17:1281-7. [PMID: 26879336 DOI: 10.1002/cphc.201501183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 01/22/2023]
Abstract
UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ∼300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.
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Affiliation(s)
- Páraic M Keane
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK.
| | | | - Sarah P Gurung
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
- Diamond Light Source, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Stephen J Devereux
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - John A Brazier
- Department of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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14
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König SLB, Evans AC, Huppert JL. Seven essential questions on G-quadruplexes. Biomol Concepts 2015; 1:197-213. [PMID: 25961997 DOI: 10.1515/bmc.2010.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.
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15
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Zhang D, Huang T, Lukeman PS, Paukstelis PJ. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad. Nucleic Acids Res 2014; 42:13422-9. [PMID: 25389267 PMCID: PMC4245957 DOI: 10.1093/nar/gku1122] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.
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Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - Terry Huang
- Chemistry and Biochemistry Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Philip S. Lukeman
- Chemistry Department, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA,To whom correspondence should be addressed. Tel: 301.405.9933; Fax: 301.314.0386;
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16
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Singh RP, Blossey R, Cleri F. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation. Biophys J 2014; 105:2820-31. [PMID: 24359754 DOI: 10.1016/j.bpj.2013.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022] Open
Abstract
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C(+) stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.
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Affiliation(s)
- Raghvendra Pratap Singh
- Institut d'Electronique Microelectronique et Nanotechnologie (IEMN UMR Cnrs 8520), University of Lille I, Villeneuve d'Ascq, France; Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France
| | - Ralf Blossey
- Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France
| | - Fabrizio Cleri
- Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France.
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17
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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18
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Carneiro KMM, Avakyan N, Sleiman HF. Long-range assembly of DNA into nanofibers and highly ordered networks. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:266-85. [DOI: 10.1002/wnan.1218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Bhatia D, Chakraborty S, Mehtab S, Krishnan Y. A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol Biol 2013; 991:65-80. [PMID: 23546660 DOI: 10.1007/978-1-62703-336-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
DNA self-assembly has yielded various polyhedra based on platonic solids. DNA polyhedra can act as nanocapsules by entrapping various molecular entities from solution and could possibly find use in targeted delivery within living systems. A key requirement for encapsulation is that the polyhedron should have maximal encapsulation volume while maintaining minimum pore size. It is well known that platonic solids possess maximal encapsulation volumes. We therefore constructed an icosahedron from DNA using a modular self-assembly strategy. We describe a method to determine the functionality of DNA polyhedra as nanocapsules by encapsulating different cargo such as gold nanoparticles and functional biomolecules like FITC dextran from solution within DNA icosahedra.
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Affiliation(s)
- Dhiraj Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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20
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Mei H, Budow S, Seela F. Construction and assembly of chimeric DNA: oligonucleotide hybrid molecules composed of parallel or antiparallel duplexes and tetrameric i-motifs. Biomacromolecules 2012; 13:4196-204. [PMID: 23121010 DOI: 10.1021/bm301471d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chimeric DNA containing parallel (ps) and antiparallel (aps) duplex elements as well as poly-dC tracts were designed and synthesized. Oligonucleotide duplexes with ps chain orientation containing reverse Watson-Crick dA-dT base pairs and short d(C)2 tails are stabilized under slightly acidic conditions by hemiprotonated dCH+-dC base pairs ("clamp" effect). Corresponding molecules with aps orientation containing Watson-Crick dA-dT base pairs do not show this phenomenon. Chimeric DNA with ps duplex elements and long d(C)5 tails at one or at both ends assemble to tetrameric i-motif structures. Molecules with two terminal d(C)5 tails form multimeric assemblies which have the potential to form nanoscopic scaffolds. A preorganization of the ps duplex chains stabilizes the i-motif assemblies up to almost neutral conditions as evidenced by thermal melting and gel electrophoresis. Although, ps DNA is generally less stable than aps DNA, the aps duplexes contribute less to the stability of the i-motif than ps DNA.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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21
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Abstract
The physicochemical properties of small molecules as well as macromolecules are modulated by solution pH, and DNA is no exception. Special sequences of DNA can adopt unusual conformations e.g., triplex, i-motif and A-motif, depending on solution pH. The specific range of pH for these unusual structures is dictated by the pKa of protonation of the relevant nucleobase involved in the resultant non-canonical base pairing that is required to stabilise the structure. The biological significance of these pH-dependent structures is not yet clear. However, these non-B-DNA structures have been used to design different devices to direct chemical reactions, generate mechanical force, sense pH, etc. The performance of these devices can be monitored by a photonic signal. They are autonomous and their ‘waste free’ operation cycles makes them highly processive. Applications of these devices help to increase understanding of the structural polymorphism of the motifs themselves. The design of these devices has continuously evolved to improve their performance efficiency in different contexts. In some examples, these devices have been shown to perform inside complex living systems with similar efficiencies, to report on the chemical environment there. The robust performance of these devices opens up exciting possibilities for pH-sensitive DNA devices in the study of various pH-regulated biological events.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
| | - Yamuna Krishnan*
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
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22
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Escaja N, Viladoms J, Garavís M, Villasante A, Pedroso E, González C. A minimal i-motif stabilized by minor groove G:T:G:T tetrads. Nucleic Acids Res 2012; 40:11737-47. [PMID: 23042679 PMCID: PMC3526289 DOI: 10.1093/nar/gks911] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d<pTCGTTTCGTT>. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.
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Affiliation(s)
- Núria Escaja
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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23
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Yang Y, Sun Y, Yang Y, Xing Y, Zhang T, Wang Z, Yang Z, Liu D. Influence of Tetra(ethylene glycol) (EG4) Substitution at the Loop Region on the Intramolecular DNA i-Motif. Macromolecules 2012. [DOI: 10.1021/ma300230q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhe Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yawei Sun
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yang Yang
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yongzheng Xing
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Tao Zhang
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Zeming Wang
- Department of Chemistry, University of Science and Technology of China, Hefei
230026, China
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
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24
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Guittet E, Renciuk D, Leroy JL. Junctions between i-motif tetramers in supramolecular structures. Nucleic Acids Res 2012; 40:5162-70. [PMID: 22362739 PMCID: PMC3367196 DOI: 10.1093/nar/gks161] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.
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Affiliation(s)
- Eric Guittet
- Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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25
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Yang Y, Zhou C, Zhang T, Cheng E, Yang Z, Liu D. DNA pillars constructed from an i-motif stem and duplex branches. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:552-556. [PMID: 22287104 DOI: 10.1002/smll.201102061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/11/2011] [Indexed: 05/31/2023]
Abstract
At an acidic pH, cytosine-rich DNA strands can form i-motif tetramers. Pillar-like DNA structures are self-assembled with such i-motifs as the central stems. The central stem has some overhanging structures that can enable hybridization with complementary units by Watson-Crick pairing and, thus, multiple i-motifs can join to form the pillar.
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Affiliation(s)
- Yang Yang
- National Center for Nanoscience and Technology, Beijing 100190, China
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26
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Bhatia D, Sharma S, Krishnan Y. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol 2011; 22:475-84. [PMID: 21652202 DOI: 10.1016/j.copbio.2011.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/10/2011] [Accepted: 05/15/2011] [Indexed: 02/05/2023]
Abstract
Structural DNA nanotechnology seeks to create architectures of highly precise dimensions using the physical property that short lengths of DNA behave as rigid rods and the chemical property of Watson-Crick base-pairing that acts as a specific molecular glue with which such rigid rods may be joined. Thus DNA has been used as a molecular scale construction material to make molecular devices that can be broadly classified under two categories (i) rigid scaffolds and (ii) switchable architectures. This review details the growing impact of such synthetic nucleic acid based molecular devices in biology and biotechnology. Notably, a significant trend is emerging that integrates morphology-rich nucleic acid motifs and alternative molecular glues into DNA and RNA architectures to achieve biological functionality.
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Affiliation(s)
- Dhiraj Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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27
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Bhatia D, Surana S, Chakraborty S, Koushika SP, Krishnan Y. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nat Commun 2011; 2:339. [PMID: 21654639 DOI: 10.1038/ncomms1337] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 05/05/2011] [Indexed: 11/09/2022] Open
Abstract
The encapsulation of molecular cargo within well-defined supramolecular architectures is highly challenging. Synthetic hosts are desirable because of their well-defined nature and addressability. Encapsulation of biomacromolecules within synthetic hosts is especially challenging because of the former's large size, sensitive nature, retention of functionality post-encapsulation and demonstration of control over the cargo. Here we encapsulate a fluorescent biopolymer that functions as a pH reporter within synthetic, DNA-based icosahedral host without molecular recognition between host and cargo. Only those cells bearing receptors for the DNA casing of the host-cargo complex engulf it. We show that the encapsulated cargo is therefore uptaken cell specifically in Caenorhabditis elegans. Retention of functionality of the encapsulated cargo is quantitatively demonstrated by spatially mapping pH changes associated with endosomal maturation within the coelomocytes of C. elegans. This is the first demonstration of functionality and emergent behaviour of a synthetic host-cargo complex in vivo.
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Affiliation(s)
- Dhiraj Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bellary Road, Bangalore 560065, India
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28
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Zikich D, Liu K, Sagiv L, Porath D, Kotlyar A. I-motif nanospheres: unusual self-assembly of long cytosine strands. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1029-34. [PMID: 21381197 DOI: 10.1002/smll.201002213] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 01/14/2011] [Indexed: 05/25/2023]
Abstract
The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i-motifs or i-tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C-strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i-motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)-poly(dC) molecules in similar conditions.
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Affiliation(s)
- Dragoslav Zikich
- Department of Biochemistry George S. Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv 69978, Israel
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29
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Ghosh S, Majumder P, Pradhan SK, Dasgupta D. Mechanism of interaction of small transcription inhibitors with DNA in the context of chromatin and telomere. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:795-809. [PMID: 20638489 DOI: 10.1016/j.bbagrm.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/23/2010] [Accepted: 06/30/2010] [Indexed: 01/13/2023]
Abstract
Small molecules from natural and synthetic sources have long been employed as human drugs. The transcription inhibitory potential of one class of these molecules has paved their use as anticancer drugs. The principal mode of action of these molecules is via reversible interaction with genomic DNA, double and multiple stranded. In this article we have revisited the mechanism of the interaction in the context of chromatin and telomere. The established modes of association of these molecules with double helical DNA provide a preliminary mechanism of their transcription inhibitory potential, but the scenario assumes a different dimension when the genomic DNA is associated with proteins in the transcription apparatus of both prokaryotic and eukaryotic organisms. We have discussed this altered scenario as a prelude to understand the chemical biology of their action in the cell. For the telomeric quadruplex DNA, we have reviewed the mechanism of their association with the quadruplex and resultant cellular consequence.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhan Nagar, Kolkata Pin, 700064, India
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30
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Wang C, Huang Z, Lin Y, Ren J, Qu X. Artificial DNA nano-spring powered by protons. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:2792-2798. [PMID: 20422657 DOI: 10.1002/adma.201000445] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Chunyan Wang
- Chinese Academy of Sciences, Changchun, People's Republic of China
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31
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Laisné A, Pompon D, Leroy JL. [C7GC4]4 association into supra molecular i-motif structures. Nucleic Acids Res 2010; 38:3817-26. [PMID: 20185569 PMCID: PMC2887966 DOI: 10.1093/nar/gkq102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The self-associative properties of cytidine-rich oligonucleotides into symmetrical i-motif tetramers give to these oligonucleotides the capacity of forming supramolecular structures (sms) that have potential applications in the nanotechnology domain. In order to facilitate sms formation, oligonucleotides containing two cytidine stretches of unequal length (CnXCm) separated by a non-cytidine spacer were synthesized. They were designed to associate into a tetramer including an i-motif core built by intercalation of the C·C+ pairs of the longer C stretch with the two dangling non-intercalated strands of the shorter C stretch at each end. Gel filtration chromatography shows that the non-intercalated C-rich ends give to this structure the capacity of forming extremely stable sms. Using C7GC4 as a model, we find that the sms formation rate varies as the oligonucleotide concentration and increases at high temperature. Competitively with the tetramer involved in sms elongation, CnXCm oligonucleotides form i-motif dimers that compete with sms elongation. The dimer stability is strongly reduced when the pH is moved away from the cytidine pK. This results in an equilibrium shift towards the tetramer and in the acceleration of the sms formation rate. The chromatograms of the sms formed by C7GC4 indicate a broad distribution. In a 1.5 mM solution incubated at 37°C, the equilibrium distribution is centered on a molecular weight corresponding to the assembly of nine tetramers and the upper limit corresponds to 80 tetramers. The lifetime of this structure is about 4 days at 40°C, pH 4.6.
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Affiliation(s)
- Aude Laisné
- Laboratoire d'Ingénerie des Proteines Membranaires, Centre de Génétique Moléculaire, CNRS FRE3144, Unité associé à l'Université Pierre et Marie Curie, Gif-sur-Yvette, 91190, France
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Ke Y, Sharma J, Liu M, Jahn K, Liu Y, Yan H. Scaffolded DNA origami of a DNA tetrahedron molecular container. NANO LETTERS 2009; 9:2445-7. [PMID: 19419184 DOI: 10.1021/nl901165f] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a strategy of scaffolded DNA origami to design and construct 3D molecular cages of tetrahedron geometry with inside volume closed by triangular faces. Each edge of the triangular face is approximately 54 nm in dimension. The estimated total external volume and the internal cavity of the triangular pyramid are about 1.8 x 10(-23) and 1.5 x 10(-23) m(3), respectively. Correct formation of the tetrahedron DNA cage was verified by gel electrophoresis, atomic force microscopy, transmission electron microscopy, and dynamic light scattering techniques.
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Affiliation(s)
- Yonggang Ke
- Department of Chemistry and Biochemistry and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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Bhatia D, Mehtab S, Krishnan R, Indi S, Basu A, Krishnan Y. Icosahedral DNA Nanocapsules by Modular Assembly. Angew Chem Int Ed Engl 2009; 48:4134-7. [DOI: 10.1002/anie.200806000] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bhatia D, Mehtab S, Krishnan R, Indi S, Basu A, Krishnan Y. Icosahedral DNA Nanocapsules by Modular Assembly. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806000] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The i-motif is a four-stranded structure formed by two intercalated parallel duplexes containing hemiprotonated C•C+ pairs. In order to describe the sequence of reactions by which four C-rich strands associate, we measured the formation and dissociation rates of three [TCn]4 tetramers (n = 3, 4 and 5), their dissociation constant and the reaction order for tetramer formation by NMR. We find that TCn association results in the formation of several tetramers differing by the number of intercalated C•C+ pairs. The formation rates of the fully and partially intercalated species are comparable but their lifetimes increase strongly with the number of intercalated C•C+ pairs, and for this reason the single tetramer detected at equilibrium is that with optimal intercalation. The tetramer half formation times vary as the power −2 of the oligonucleotide concentration indicating that the reaction order for i-motif formation is 3. This observation is inconsistent with a model supposing association of two preformed duplex and suggests that quadruplex formation proceeds via sequential strand association into duplex and triplex intermediate species and that triplex formation is rate limiting.
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Affiliation(s)
- Jean-Louis Leroy
- Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette 91190, France.
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Chakraborty S, Sharma S, Maiti PK, Krishnan Y. The poly dA helix: a new structural motif for high performance DNA-based molecular switches. Nucleic Acids Res 2009; 37:2810-7. [PMID: 19279188 PMCID: PMC2685084 DOI: 10.1093/nar/gkp133] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report a pH-dependent conformational transition in short, defined homopolymeric deoxyadenosines (dA15) from a single helical structure with stacked nucleobases at neutral pH to a double-helical, parallel-stranded duplex held together by AH+-H+A base pairs at acidic pH. Using native PAGE, 2D NMR, circular dichroism (CD) and fluorescence spectroscopy, we have characterized the two different pH dependent forms of dA15. The pH-triggered transition between the two defined helical forms of dA15 is characterized by CD and fluorescence. The kinetics of this conformational switch is found to occur on a millisecond time scale. This robust, highly reversible, pH-induced transition between the two well-defined structured states of dA15 represents a new molecular building block for the construction of quick-response, pH-switchable architectures in structural DNA nanotechnology.
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Zhang C, Ko SH, Su M, Leng Y, Ribbe AE, Jiang W, Mao C. Symmetry Controls the Face Geometry of DNA Polyhedra. J Am Chem Soc 2009; 131:1413-5. [PMID: 19173666 DOI: 10.1021/ja809666h] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuan Zhang
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Seung Hyeon Ko
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Min Su
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Yujun Leng
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Alexander E. Ribbe
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Wen Jiang
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Chengde Mao
- Department of Chemistry, Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
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Chakraborty S, Modi S, Krishnan Y. The RNA2-PNA2 hybrid i-motif-a novel RNA-based building block. Chem Commun (Camb) 2008:70-2. [PMID: 18401893 DOI: 10.1039/b713525d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the formation of a hybrid RNA2-PNA2 i-motif comprised of two RNA and two PNA strands based on the sequence specific self assembly of RNA, with potential as a building block for structural RNA nanotechnology.
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Affiliation(s)
- Saikat Chakraborty
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore, 560065, India
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Patwa AN, Gupta S, Gonnade RG, Kumar VA, Bhadbhade MM, Ganesh KN. Ferrocene-Linked Thymine/Uracil Conjugates: Base Pairing Directed Self-Assembly and Supramolecular Packing. J Org Chem 2008; 73:1508-15. [DOI: 10.1021/jo7023416] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amit N. Patwa
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
| | - Susmita Gupta
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
| | - Rajesh G. Gonnade
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
| | - Vaijayanti A. Kumar
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
| | - Mohan M. Bhadbhade
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
| | - Krishna N. Ganesh
- Division of Organic Synthesis and Center for Materials Characterization, National Chemical Laboratory, Pune 411008, India and Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune 411008, India
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Khan N, Aviñó A, Tauler R, González C, Eritja R, Gargallo R. Solution equilibria of the i-motif-forming region upstream of the B-cell lymphoma-2 P1 promoter. Biochimie 2007; 89:1562-72. [PMID: 17850948 DOI: 10.1016/j.biochi.2007.07.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 07/30/2007] [Indexed: 11/19/2022]
Abstract
The 5'-end of the P1 promoter of the B-cell lymphoma-2 (bcl-2) gene contains a highly guaninecytosine-rich region, which has a role in the regulation of bcl-2 transcription. Whereas the guanine-rich region has been the focus of recent studies, little attention has been paid to the cytosine-rich strand. Here we examine the structural transitions of the cytosine-rich sequence by means of acid-base, mole-ratio and melting experiments monitored by molecular absorption, circular dichroism, and NMR spectroscopies. Two intramolecular i-motif structures have been detected in the pH range 2-7, with maximal formation at pH 4 and 6, respectively. At pH 7.6 the majority species has been associated with a hairpin involving Watson-Crick base pairs. Upon addition of the quadruplex-interacting ligand TmPyP4, bcl-2c structures at pH 6.1 and 7.6 yield identical interaction species with stoichiometries 1:2 (DNA:ligand) and logarithms of formation constant 12.4+/-0.2 and 11.7+/-0.1, respectively. The initial i-motif structure at pH 6.1 is lost upon interaction with TmPyP4.
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Affiliation(s)
- Nasiruddin Khan
- Department of Analytical Chemistry, University of Barcelona, Diagonal 647, E-08028 Barcelona, Spain
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