1
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Mattath MN, Zhang H, Ghosh D, Govindaraju T, Shi S. Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection. NANOSCALE 2023; 15:17386-17397. [PMID: 37847391 DOI: 10.1039/d3nr04167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.
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Affiliation(s)
- Mohamed Nabeel Mattath
- School of Chemical Science and Engineering, Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, PR China.
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Haibin Zhang
- Endoscopy Center, Department of Gastroenterology, Shanghai East Hospital, Tongji University, School of Medicine, Shanghai, 200092, PR China
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India.
| | - Shuo Shi
- School of Chemical Science and Engineering, Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, 1239 Siping Rd, Shanghai, 200092, PR China.
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2
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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3
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Liang Y, Miao S, Mao J, Devari S, Gonzalez M, Bong D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry 2022; 28:e202103616. [PMID: 34693570 PMCID: PMC8758549 DOI: 10.1002/chem.202103616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/12/2023]
Abstract
We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi-rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100-1000× fluorescence enhancement over background. Binding is strongly context-dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine-rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi-rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Jie Mao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Maricarmen Gonzalez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210
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4
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Das S, Yau M, Noble J, De Pascalis L, Finn MG. Transport of Molecular Cargo by Interaction with Virus‐Like Particle RNA. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Soumen Das
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Mei‐Kwan Yau
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Jeffery Noble
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Lucrezia De Pascalis
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - M. G. Finn
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
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5
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Das S, Yau MK, Noble J, De Pascalis L, Finn MG. Transport of Molecular Cargo by Interaction with Virus-Like Particle RNA. Angew Chem Int Ed Engl 2022; 61:e202111687. [PMID: 34717043 PMCID: PMC9280655 DOI: 10.1002/anie.202111687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 01/12/2023]
Abstract
Virus-like particles (VLPs) derived from Leviviridae virions contain substantial amounts of cellular and plasmid-derived RNA. This encapsidated polynucleotide serves as a reservoir for the efficient binding of the intercalating dye thiazole orange (TO). Polyethylene glycol (PEG) molecules and oligopeptides of varying length, end-functionalized with TO, were loaded into VLPs up to approximately 50 % of the mass of the capsid protein (hundreds to thousands of cargo molecules per particle, depending on size). The kinetics of TO-PEG binding included a significant entropic cost for the reptation of long chains through the capsid pores. Cargo molecules were released over periods of 20-120 hours following simple reversible first-order kinetics in most cases. These observations define a simple general method for the noncovalent packaging, and subsequent release, of functional molecules inside nucleoprotein nanocages in a manner independent of modifications to the capsid protein.
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Affiliation(s)
- Soumen Das
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Mei-Kwan Yau
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Jeffery Noble
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Lucrezia De Pascalis
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - M G Finn
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
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6
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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7
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Ang YS, Bando T, Sugiyama H, Yung LYL. Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide. Chembiochem 2020; 21:2912-2915. [PMID: 32458592 DOI: 10.1002/cbic.202000245] [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: 04/21/2020] [Revised: 05/20/2020] [Indexed: 11/12/2022]
Abstract
We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py-Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py-Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py-Im polyamide as a molecular tool to modulate the formation of DNA assemblies.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo,-ku, Kyoto, 606-8501, Japan
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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8
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Lee JH, Cho HY, Choi HK, Lee JY, Choi JW. Application of Gold Nanoparticle to Plasmonic Biosensors. Int J Mol Sci 2018; 19:E2021. [PMID: 29997363 PMCID: PMC6073481 DOI: 10.3390/ijms19072021] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 02/06/2023] Open
Abstract
Gold nanoparticles (GNPs) have been widely utilized to develop various biosensors for molecular diagnosis, as they can be easily functionalized and exhibit unique optical properties explained by plasmonic effects. These unique optical properties of GNPs allow the expression of an intense color under light that can be tuned by altering their size, shape, composition, and coupling with other plasmonic nanoparticles. Additionally, they can also enhance other optical signals, such as fluorescence and Raman scattering, making them suitable for biosensor development. In this review, we provide a detailed discussion of the currently developed biosensors based on the aforementioned unique optical features of GNPs. Mainly, we focus on four different plasmonic biosensing methods, including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), fluorescence enhancement, and quenching caused by plasmon and colorimetry changes based on the coupling of GNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of novel GNP-based biosensors in the future.
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Affiliation(s)
- Jin-Ho Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea.
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Hyeon-Yeol Cho
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea.
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Hye Kyu Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea.
| | - Ji-Young Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea.
| | - Jeong-Woo Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Korea.
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9
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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10
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Ma H, Li Z, Xue N, Cheng Z, Miao X. A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA. Mikrochim Acta 2018; 185:93. [DOI: 10.1007/s00604-017-2633-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022]
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11
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Pramanik S, Chatterjee S, Suresh Kumar G, Sujatha Devi P. Egg-shell derived carbon dots for base pair selective DNA binding and recognition. Phys Chem Chem Phys 2018; 20:20476-20488. [DOI: 10.1039/c8cp02872a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here, we have used food waste derived chicken egg shell membrane as a cost effective carbon source for the synthesis of heteroatom doped fluorescent carbon dots. We are able to apply these synthesized carbon dots as a new fluorescent probe for label free base pair selective and sequence specific double stranded DNA binding.
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Affiliation(s)
- Srikrishna Pramanik
- Sensor and Actuator Division
- CSIR-Central Glass and Ceramic Research Institute
- Kolkata 700 032
- India
| | - Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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12
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Synthesis of pyrrole-imidazole polyamide oligomers based on a copper-catalyzed cross-coupling strategy. Bioorg Med Chem Lett 2017; 27:2197-2200. [PMID: 28389153 DOI: 10.1016/j.bmcl.2017.03.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are useful tools for chemical biology and medicinal chemistry studies due to their unique binding properties to the minor groove of DNA. We developed a novel method of synthesizing Py-Im polyamide oligomers based on a Cu-catalyzed cross-coupling strategy. All four patterns of dimer fragments could be synthesized using a Cu-catalyzed Ullmann-type cross-coupling with easily prepared monomer units. Moreover, we demonstrated that pyrrole dimer, trimer, and tetramer building blocks for Py-Im polyamide synthesis were accessible by combining site selective iodination of the pyrrole/pyrrole coupling adduct.
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13
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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14
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Lai HP, Gao RC, Huang CL, Chen IC, Tan KT. Fluorescence switchable probes based on a molecular rotor for selective detection of proteins and small molecules. Chem Commun (Camb) 2016; 51:16197-200. [PMID: 26396997 DOI: 10.1039/c5cc06714f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this communication, we report a general strategy to create fluorescence switchable probes, where a small molecule ligand is conjugated to a fluorescent molecular rotor, for the selective detection of proteins through a non-enzymatic process. In the presence of target proteins, bond rotation of the molecular rotor is restricted, thereby triggering the emission of strong fluorescence.
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Affiliation(s)
- Hsiu-Ping Lai
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - Ruo-Cing Gao
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - Chi-Ling Huang
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - I-Chia Chen
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China
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15
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Han YW, Sugiyama H, Harada Y. The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation. Biomater Sci 2016; 4:391-9. [DOI: 10.1039/c5bm00214a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation of protein–DNA complex dynamics.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Department of Chemistry
| | - Yoshie Harada
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Biostudies
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16
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Alexander SC, Busby KN, Cole CM, Zhou CY, Devaraj NK. Site-Specific Covalent Labeling of RNA by Enzymatic Transglycosylation. J Am Chem Soc 2015; 137:12756-9. [DOI: 10.1021/jacs.5b07286] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Seth C. Alexander
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kayla N. Busby
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christian M. Cole
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Cun Yu Zhou
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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17
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Nozeret K, Bonan M, Yarmoluk SM, Novopashina DS, Boutorine AS. Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA. Bioorg Med Chem 2015; 23:5932-45. [PMID: 26190459 DOI: 10.1016/j.bmc.2015.06.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]
Abstract
Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications.
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Affiliation(s)
- Karine Nozeret
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
| | - Marc Bonan
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France; Université Paris René Descartes, 12 Rue de l'École de Médecine, 75006 Paris, France.
| | - Serguiy M Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, ul. Zabolotnogo, 150, P.O. 88, 03187 Kiev, Ukraine.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Lavrentyev prosp., 8, 630090 Novosibirsk, Russia.
| | - Alexandre S Boutorine
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France.
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18
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Liu Q, Wang J, Boyd BJ. Peptide-based biosensors. Talanta 2015; 136:114-27. [PMID: 25702993 DOI: 10.1016/j.talanta.2014.12.020] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/26/2014] [Accepted: 12/18/2014] [Indexed: 12/24/2022]
Abstract
Peptides have been used as components in biological analysis and fabrication of novel biosensors for a number of reasons, including mature synthesis protocols, diverse structures and as highly selective substrates for enzymes. Bio-conjugation strategies can provide an efficient way to convert interaction information between peptides and analytes into a measurable signal, which can be used for fabrication of novel peptide-based biosensors. Many sensitive fluorophores can respond rapidly to environmental changes and stimuli manifest as a change in spectral characteristics, hence environmentally-sensitive fluorophores have been widely used as signal markers to conjugate to peptides to construct peptide-based molecular sensors. Additionally, nanoparticles, fluorescent polymers, graphene and near infrared dyes are also used as peptide-conjugated signal markers. On the other hand, peptides may play a generalist role in peptide-based biosensors. Peptides have been utilized as bio-recognition elements to bind various analytes including proteins, nucleic acid, bacteria, metal ions, enzymes and antibodies in biosensors. The selectivity of peptides as an enzymatic substrate has thus been utilized to construct enzyme sensors or enzyme-activity sensors. In addition, progress on immobilization and microarray techniques of peptides has facilitated the progress and commercial application of chip-based peptide biosensors in clinical diagnosis.
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Affiliation(s)
- Qingtao Liu
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia
| | - Jinfeng Wang
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong 3217, VIC, Australia
| | - Ben J Boyd
- Drug Delivery Disposition and Dynamics-Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville 3052, VIC, Australia.
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19
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Jia H, Lv Y, Wang S, Sun D, Wang L. Synthesis, crystal structures, and spectral properties of double N-alkylated dimethine cyanine dyes and their interactions with biomolecules and living cells. RSC Adv 2015. [DOI: 10.1039/c4ra10741a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of new doubleN-alkylated dimethine cyanine dyes were synthesized, and their crystal structures and spectral properties, as well as their interaction with biomolecules and living cells, were investigated.
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Affiliation(s)
- Hongliang Jia
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry
- Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710069
| | - Ying Lv
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry
- Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710069
| | - Shu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry
- Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710069
| | - Dan Sun
- Institute of Photonics & Photon-Technology
- Northwest University
- Xi'an 710069
- P. R. China
| | - Lanying Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry
- Ministry of Education
- College of Chemistry and Materials Science
- Northwest University
- Xi'an 710069
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20
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Fang L, Yao G, Pan Z, Wu C, Wang HS, Burley GA, Su W. Fully Automated Synthesis of DNA-Binding Py-Im Polyamides Using a Triphosgene Coupling Strategy. Org Lett 2014; 17:158-61. [DOI: 10.1021/ol503388a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lijing Fang
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Guiyang Yao
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Zhengyin Pan
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Chunlei Wu
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Heng-Shan Wang
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Wu Su
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
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21
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Fluorescence-labeled bis-benzamidines as fluorogenic DNA minor-groove binders: photophysics and binding dynamics. Chemistry 2014; 21:1609-19. [PMID: 25418429 DOI: 10.1002/chem.201404926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 01/19/2023]
Abstract
In recent decades there has been great interest in the design of highly sensitive sequence-specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis-benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double-stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.
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Affiliation(s)
- Jorge Bordello
- Department of Physical Chemistry, Faculty of Science, Campus Lugo, University of Santiago de Compostela, 27002 Lugo (Spain), Fax: (+34) 982824001
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22
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Minoshima M, Matsumoto T, Kikuchi K. Development of a Fluorogenic Probe Based on a DNA Staining Dye for Continuous Monitoring of the Histone Deacetylase Reaction. Anal Chem 2014; 86:7925-30. [DOI: 10.1021/ac501881s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Masafumi Minoshima
- Graduate School of Engineering, ‡Institute for Academic
Initiatives, and §Immunology Frontier
Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tetsuaki Matsumoto
- Graduate School of Engineering, ‡Institute for Academic
Initiatives, and §Immunology Frontier
Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, ‡Institute for Academic
Initiatives, and §Immunology Frontier
Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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23
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Sato Y, Kudo M, Toriyabe Y, Kuchitsu S, Wang CX, Nishizawa S, Teramae N. Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids. Chem Commun (Camb) 2014; 50:515-7. [DOI: 10.1039/c3cc47717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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24
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Tanaka M, Shigi N, Sumaoka J, Komiyama M. Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage. RSC Adv 2014. [DOI: 10.1039/c4ra13780a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugates of thiazole orange (TO) with a pseudo-complementary peptide nucleic acid (pcPNA) functioned as (i) fluorescent detector of specific DNA and (ii) site-selective photodamage inducer through generation of 1O2.
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Affiliation(s)
- Makiko Tanaka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
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25
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Han YW, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y. Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome. Biomater Sci 2014; 2:297-307. [DOI: 10.1039/c3bm60202h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Yamamoto M, Bando T, Morinaga H, Kawamoto Y, Hashiya K, Sugiyama H. Sequence-Specific DNA Recognition by Cyclic Pyrrole-Imidazole Cysteine-Derived Polyamide Dimers. Chemistry 2013; 20:752-9. [DOI: 10.1002/chem.201302482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/21/2013] [Indexed: 11/12/2022]
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27
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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28
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Pazos E, Vázquez ME. Advances in lanthanide-based luminescent peptide probes for monitoring the activity of kinase and phosphatase. Biotechnol J 2013; 9:241-52. [DOI: 10.1002/biot.201300203] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 08/27/2013] [Accepted: 09/25/2013] [Indexed: 01/16/2023]
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29
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Doluca O, Hale TK, Edwards PJB, González C, Filichev VV. Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA. Chempluschem 2013; 79:58-66. [PMID: 31986766 DOI: 10.1002/cplu.201300310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/29/2013] [Indexed: 12/19/2022]
Abstract
In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (ΦF ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (ΦF =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.
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Affiliation(s)
- Osman Doluca
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682.,International Burch University, Francuske Revolucije, 71210 Sarajevo (Bosnia and Herzegovina)
| | - Tracy K Hale
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Patrick J B Edwards
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Carlos González
- Instituto de Química Física Rocasalano, CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Vyacheslav V Filichev
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
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30
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Zhang N, Chu X, Fathalla M, Jayawickramarajah J. Photonic DNA-chromophore nanowire networks: harnessing multiple supramolecular assembly modes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10796-806. [PMID: 23895408 PMCID: PMC3826913 DOI: 10.1021/la402214p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photonic DNA nanostructures are typically prepared by the assembly of multiple sequences of long DNA strands that are conjugated covalently to various dye molecules. Herein we introduce a noncovalent method for the construction of porphyrin-containing DNA nanowires and their networks that uses the programmed assembly of a single, very short, oligodeoxyribonucleotide sequence. Specifically, our strategy exploits a number of supramolecular binding modalities (including DNA base-pairing, metal-ion coordination, and β-cyclodextrin-adamantane derived host-guest interactions) for simultaneous nanowire assembly and porphyrin incorporation. Furthermore, we also show that the resultant DNA-porphyrin assembly can be further functionalized with a complementary "off-the-shelf" DNA binding dye resulting in photonic structures with broadband absorption and energy transfer capabilities.
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Affiliation(s)
- Nan Zhang
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana, 70118. Fax: (+1) 504-865-5596 Tel: (+1) 504-862-3580;
| | - Xiaozhu Chu
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana, 70118. Fax: (+1) 504-865-5596 Tel: (+1) 504-862-3580;
| | - Maher Fathalla
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana, 70118. Fax: (+1) 504-865-5596 Tel: (+1) 504-862-3580;
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Janarthanan Jayawickramarajah
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana, 70118. Fax: (+1) 504-865-5596 Tel: (+1) 504-862-3580;
- Corresponding author: Janarthanan Jayawickramarajah, Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana, 70118. Fax: (+1) 504-865-5596 Tel: (+1) 504-862-3580;
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31
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Saha A, Pandian GN, Sato S, Taniguchi J, Hashiya K, Bando T, Sugiyama H. Synthesis and biological evaluation of a targeted DNA-binding transcriptional activator with HDAC8 inhibitory activity. Bioorg Med Chem 2013; 21:4201-9. [PMID: 23719282 DOI: 10.1016/j.bmc.2013.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/02/2013] [Accepted: 05/03/2013] [Indexed: 11/30/2022]
Abstract
Development of multifunctional transcriptional activators is of increasing importance as they could trigger complicated gene networks. Recently, we developed a differential gene activating multifunctional small molecule SAHA-PIP (Sδ) by conjugating a histone deacetylase (HDAC) inhibitor, SAHA, to a selective DNA-binding pyrrole-imidazole polyamide (PIP). Epigenetic activity of Sδ was attributed to the active metal-binding (-NHOH) domain of SAHA. We synthesized a derivative of Sδ, called Jδ to evaluate the role of surface recognition domain (-phenyl) of SAHA in Sδ-mediated transcriptional activation. In vitro studies revealed that Jδ displayed potent inhibitory activity against HDAC8. Jδ retained the pluripotency gene-inducing ability of Sδ when used alone and in combination with Sδ; a notable increase in the pluripotency gene expression was observed. Interestingly, Jδ significantly induced the expression of HDAC8-controlled Otx2 and Lhx1. Our results suggest that the epigenetic activity of our multifunctional molecule could be altered to improve its efficiency as a transcriptional activator for intricate gene network(s).
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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32
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Blackledge MS, Melander C. Programmable DNA-binding small molecules. Bioorg Med Chem 2013; 21:6101-14. [PMID: 23665141 DOI: 10.1016/j.bmc.2013.04.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression is responsible for a myriad of human diseases from infectious diseases to cancer. Precise regulation of these genes via specific interactions with the DNA double helix could pave the way for novel therapeutics. Pyrrole-imidazole polyamides are small molecules capable of binding to pre-determined DNA sequences up to 16 base pairs with affinity and specificity comparable to natural transcription factors. In the three decades since their development, great strides have been made relating to synthetic accessibility and improved sequence specificity and binding affinity. This perspective presents a brief history of early seminal developments in the field and highlights recent reports of the utility of polyamides as both genetic modulators and molecular probes.
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Affiliation(s)
- Meghan S Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8024, United States
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33
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Satam V, Patil P, Babu B, Gregory M, Bowerman M, Savagian M, Lee M, Tzou S, Olson K, Liu Y, Ramos J, Wilson WD, Bingham JP, Kiakos K, Hartley JA, Lee M. Hx-amides: DNA sequence recognition by the fluorescent Hx (p-anisylbenzimidazole)•pyrrole and Hx•imidazole pairings. Bioorg Med Chem Lett 2013; 23:1699-702. [PMID: 23395654 DOI: 10.1016/j.bmcl.2013.01.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/06/2013] [Accepted: 01/16/2013] [Indexed: 01/01/2023]
Abstract
Hx-amides are fluorescent hybrids of imidazole (I)- and pyrrole (P)-containing polyamides and Hoechst 33258, and they bind in the minor groove of specific DNA sequences. Synthesis and DNA binding studies of HxII (5) complete our studies on the first set of Hx-amides: Hx-I/P-I/P. HxPP (2), HxIP (3) and HxPI (4) were reported earlier. Results from DNase I footprinting, biosensor-SPR, CD and ΔTM studies showed that Hx-amides interacted with DNA via the anti-parallel and stacked, side-by-side motif. Hx was found to mimic the DNA recognition properties of two consecutive pyrrole units (PP) in polyamides. Accordingly, the stacked Hx/PP pairing binds preferentially to two consecutive AT base pairs, A/T-A/T; Hx/IP prefers C-A/T; Hx/PI prefers A/T-C; and Hx/II prefers C-C. The results also showed that Hx-amides bound their cognate sequence at a higher affinity than their formamido-triamide counterparts.
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Affiliation(s)
- Vijay Satam
- Division of Natural & Applied Sciences and Department of Chemistry, Hope College, Holland, MI 49423, USA
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Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn. Bioorg Med Chem 2012; 21:852-5. [PMID: 23313608 DOI: 10.1016/j.bmc.2012.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/14/2012] [Accepted: 12/15/2012] [Indexed: 12/24/2022]
Abstract
Fluorophores that are conjugated with N-methylpyrrole-N-methylimidazole (Py-Im) polyamides postulates versatile applications in biological and physicochemical studies. Here, we show the design and synthesis of new types of pyrene-conjugated hairpin Py-Im polyamides (1-5). We evaluated the steady state fluorescence of the synthesized conjugates (1-5) in the presence and absence of oligodeoxynucleotides 5'-CGTATGGACTCGG-3' (ODN 1) and 5'-CCGAGTCCATACG-3' (ODN 2) and observed a distinct increase in emission at 386nm with conjugates 4 and 5. Notably, conjugate 5 that contains a β-alanine linker had a stronger binding affinity (K(D)=1.73×10(-8)M) than that of conjugate 4 (K(D)=1.74×10(-6)M). Our data suggests that Py-Im polyamides containing pyrene fluorophore with a β-alanine linker at the γ-turn NH(2) position can be developed as the competent fluorescent DNA-binding probes.
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35
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Evenson WE, Boden LM, Muzikar KA, O'Leary DJ. 1H and 13C NMR assignments for the cyanine dyes SYBR Safe and thiazole orange. J Org Chem 2012; 77:10967-71. [PMID: 23137048 DOI: 10.1021/jo3021659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analysis of (1)H and (13)C NMR and mass spectral data for the fluorescent nucleic acid stain SYBR Safe indicates that it contains a cyanine-based cationic core structure identical to thiazole orange. The difference between these two compounds is the type of N-substitution on the quinolinium ring system (SYBR Safe, n-Pr; thiazole orange, Me). The (1)H and (13)C NMR resonances for both compounds were assigned on the basis of one- and two-dimensional (COSY, ROESY, HSQC, and HMBC) experiments. The preferred conformation of these compounds was computed by ab initio methods and found to be consistent with the NMR data.
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Affiliation(s)
- William E Evenson
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711, USA
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36
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Vaijayanthi T, Bando T, Pandian GN, Sugiyama H. Progress and prospects of pyrrole-imidazole polyamide-fluorophore conjugates as sequence-selective DNA probes. Chembiochem 2012; 13:2170-85. [PMID: 23023993 DOI: 10.1002/cbic.201200451] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 12/24/2022]
Abstract
Recently, the versatility of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamide conjugates, which have been developed from the DNA-binding antibiotics distamycin A and netropsin, has been shown. These synthetic small molecules can permeate cells to bind with duplex DNA in a sequence-specific manner, and hence can influence gene expression in vivo. Accordingly, several reports demonstrating the sequence specificity and biological activity of Py-Im polyamides have accumulated. However, the benefits of Py-Im polyamides, in particular those conjugated with fluorophores, has been overlooked. Moreover, clear directions for the employment of these attractive artificial small molecules have not yet been shown. Here, we present a detailed overview of the current and prospective applications of Py-Im polyamide-fluorophore conjugates, including sequence-specific recognition with fluorescence emission properties, and their potential roles in biological imaging.
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Affiliation(s)
- Thangavel Vaijayanthi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa oiwakecho, Kyoto 606-8502, Japan
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Yasarawan N, Thipyapong K, Ruangpornvisuti V. Structures and conformations of acridinium mono- and polymethine cyanine dyes and their UV–Vis absorption spectra in protic solvents: A PCM/TD-DFT study. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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38
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Morinaga H, Bando T, Takagaki T, Yamamoto M, Hashiya K, Sugiyama H. Cysteine Cyclic Pyrrole–Imidazole Polyamide for Sequence-Specific Recognition in the DNA Minor Groove. J Am Chem Soc 2011; 133:18924-30. [DOI: 10.1021/ja207440p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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39
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Pazos E, Mosquera J, Vázquez ME, Mascareñas JL. DNA Recognition by Synthetic Constructs. Chembiochem 2011; 12:1958-73. [DOI: 10.1002/cbic.201100247] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Indexed: 12/29/2022]
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40
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Chavda S, Liu Y, Babu B, Davis R, Sielaff A, Ruprich J, Westrate L, Tronrud C, Ferguson A, Franks A, Tzou S, Adkins C, Rice T, Mackay H, Kluza J, Tahir SA, Lin S, Kiakos K, Bruce CD, Wilson WD, Hartley JA, Lee M. Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides. Biochemistry 2011; 50:3127-36. [PMID: 21388229 DOI: 10.1021/bi102028a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5'-AAATTT-3', 5'-ATCGAT-3', and 5'-ACATGT-3', respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Hx-containing polyamides gave binding constants in the 10(6) M(-1) range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formamido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Hx moiety behaved similarly to two consecutive pyrroles (PP found in 5-7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8-10. The biophysical characterization of polyamides 2-7 on their binding to the abovementioned DNA sequences was determined using thermal melts (ΔT(M)), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.
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Affiliation(s)
- Sameer Chavda
- Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, Michigan 49423, United States
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Abstract
Sequence-specific DNA modification is of significance for applications in bio- and nano-technology, medical diagnostics and fundamental life sciences research. Preferentially, labelling should be performed covalently, which avoids doubts about label dissociation from the DNA under various conditions. Several methods to label native DNA have been developed in the last two decades. Triple-helix-forming oligodeoxynucleotides and hairpin polyamides that bind DNA sequences specifically in the major and minor groove respectively were used as targeting devices for subsequent covalent labelling. In addition, enzyme-directed labelling approaches utilizing nicking endonucleases in combination with DNA polymerases or DNA methyltransferases have been employed. This review summarizes various techniques useful for functionalization of long native DNA.
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Su W, Schuster M, Bagshaw CR, Rant U, Burley GA. Site-specific assembly of DNA-based photonic wires by using programmable polyamides. Angew Chem Int Ed Engl 2011; 50:2712-5. [PMID: 21387472 PMCID: PMC3210824 DOI: 10.1002/anie.201006735] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/13/2010] [Indexed: 11/26/2022]
Affiliation(s)
- Wu Su
- Department of Chemistry, University of LeicesterUniversity Road, Leicester, LE1 7RH (UK), Fax: (+44) 116-252-3789
| | - Markus Schuster
- Walter Schottky Institute, Technical University of MunichAm Coulombwall 3, 85748 Garching (Germany)
| | - Clive R Bagshaw
- Department of BiochemistryUniversity of Leicester Lancaster Road, Leicester LE1 9HN (UK)
| | - Ulrich Rant
- Walter Schottky Institute, Technical University of MunichAm Coulombwall 3, 85748 Garching (Germany)
| | - Glenn A Burley
- Department of Chemistry, University of LeicesterUniversity Road, Leicester, LE1 7RH (UK), Fax: (+44) 116-252-3789
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Su W, Schuster M, Bagshaw CR, Rant U, Burley GA. Site‐Specific Assembly of DNA‐Based Photonic Wires by Using Programmable Polyamides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006735] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wu Su
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH (UK), Fax: (+44) 116‐252‐3789 http://www.burleylabs.co.uk
| | - Markus Schuster
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 3, 85748 Garching (Germany)
| | - Clive R. Bagshaw
- Department of Biochemistry, University of Leicester Lancaster Road, Leicester LE1 9HN (UK)
| | - Ulrich Rant
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 3, 85748 Garching (Germany)
| | - Glenn A. Burley
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH (UK), Fax: (+44) 116‐252‐3789 http://www.burleylabs.co.uk
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Ruiz-Carretero A, Janssen PGA, Kaeser A, Schenning APHJ. DNA-templated assembly of dyes and extended π-conjugated systems. Chem Commun (Camb) 2011; 47:4340-7. [DOI: 10.1039/c0cc05155a] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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45
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Li H, Franzini RM, Bruner C, Kool ET. Templated chemistry for sequence-specific fluorogenic detection of duplex DNA. Chembiochem 2010; 11:2132-7. [PMID: 20859985 PMCID: PMC4418650 DOI: 10.1002/cbic.201000329] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Indexed: 12/25/2022]
Abstract
We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple-helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine group that is designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of about 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably; this demonstrated high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and could allow detection of double-stranded DNA, at least for homopurine-homopyrimidine target sites, under native and nondenaturing conditions.
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Affiliation(s)
| | | | | | - Eric T. Kool
- Prof. Dr. E. T. Kool, H. Li, R.M. Franzini, C. Bruner, Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA), Fax: (+1)650-725-0259,
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46
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Porter JR, Lockwood SH, Segal DJ, Ghosh I. Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER). Methods Mol Biol 2010; 649:365-382. [PMID: 20680847 DOI: 10.1007/978-1-60761-753-2_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Virtually all methods for reading the sequence of bases in DNA rely on the ability to denature double-stranded DNA into single strands and then use Watson-Crick base-pairing rules to hybridize the strands with high specificity to another DNA primer or probe. However, nature frequently uses an alternative method, reading the sequence information directly from double-stranded DNA using sequence-specific DNA-binding proteins. Here we describe methods for the construction and testing of sequence probes based on engineered zinc finger DNA-binding proteins. Background is reduced using split-reporter molecules, and signal is amplified using enzymatic reporters. The resulting sequence-enabled reassembly (SEER) probes can be configured to detect DNA sequence (genetic) or DNA methylation (epigenetic) information.
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Affiliation(s)
- Jason R Porter
- Department of Chemistry, University of Arizona, Tucson, AZ, USA
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47
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Vázquez O, Sánchez MI, Mascareñas JL, Vázquez ME. dsDNA-triggered energy transfer and lanthanide sensitization processes. Luminescent probing of specific A/T sequences. Chem Commun (Camb) 2010; 46:5518-20. [DOI: 10.1039/b927305k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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48
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Vázquez O, Sánchez MI, Martínez-Costas J, Vázquez ME, Mascareñas JL. Bis-4-aminobenzamidines: Versatile, Fluorogenic A/T-Selective dsDNA Binders. Org Lett 2009; 12:216-9. [DOI: 10.1021/ol902501j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Olalla Vázquez
- Departamento de Química Orgánica and Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mateo I. Sánchez
- Departamento de Química Orgánica and Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José Martínez-Costas
- Departamento de Química Orgánica and Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Departamento de Química Orgánica and Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L. Mascareñas
- Departamento de Química Orgánica and Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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49
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Zhang XH, Wang LY, Zhai GH, Wen ZY, Zhang ZX. The absorption, emission spectra as well as ground and excited states calculations of some dimethine cyanine dyes. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Garanger E, Hilderbrand SA, Blois JT, Sosnovik DE, Weissleder R, Josephson L. A DNA-binding Gd chelate for the detection of cell death by MRI. Chem Commun (Camb) 2009:4444-6. [PMID: 19597620 DOI: 10.1039/b907375b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GadoTO, a MR contrast agent for the detection of cell death, consists of a nucleic acid-binding fluorophore attached to a gadolinium chelate.
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Affiliation(s)
- Elisabeth Garanger
- Center for Molecular Imaging Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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