1
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Gras M, Adler P, Smietana M. A Catalytic Approach for the Synthesis of Peptide-Oligonucleotides Conjugates in Aqueous Solution or On-Column. Chemistry 2024; 30:e202401069. [PMID: 38709711 DOI: 10.1002/chem.202401069] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene-targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post-synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA-Encoded Libraries.
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Affiliation(s)
- Marion Gras
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Pauline Adler
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Michael Smietana
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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2
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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3
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Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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4
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Xu M, Zhou B, Ding Y, Du S, Su M, Liu H. Programmable Oligonucleotide-Peptide Complexes: Synthesis and Applications. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-1265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Hering A, Braga Emidio N, Muttenthaler M. Expanding the versatility and scope of the oxime ligation: rapid bioconjugation to disulfide-rich peptides. Chem Commun (Camb) 2022; 58:9100-9103. [PMID: 35880482 PMCID: PMC9367247 DOI: 10.1039/d2cc03752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The oxime ligation is a valuable bioorthogonal conjugation reaction but with limited compatibility with disulfide-rich peptides/proteins and time-sensitive applications. Here we overcome these limitations by introducing a strategy that supports regiospecific control, oxidative folding, production of stable aminooxy-precursors for on-demand modification, and complete ligation within 5 min. Regiospecific incorporation of a protected aminooxy group into disulfide-rich peptides compatible with oxidative folding. This strategy supports the production of aminooxy precursors for long-term storage and on-demand modifications.![]()
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Affiliation(s)
- Anke Hering
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia. .,Institute of Biological Chemistry, University of Vienna, Währingerstraße 38, Vienna, 1090, Austria.
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6
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Giraud T, Hoschtettler P, Pickaert G, Averlant-Petit MC, Stefan L. Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives. NANOSCALE 2022; 14:4908-4921. [PMID: 35319034 DOI: 10.1039/d1nr06131c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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7
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Masaki Y, Maruyama A, Yoshida K, Tomori T, Kishimura T, Seio K. Oligodeoxynucleotides Modified with 2'- O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions. Bioconjug Chem 2022; 33:272-278. [PMID: 35129971 DOI: 10.1021/acs.bioconjchem.1c00575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We used native chemical ligation (NCL) to synthesize a 2'-O-{N-[N-(S-tert-butylthiocysteinyl)aminobutyl]carbamoylethyl} (CysBCE) ribothymidine-derived oligonucleotide to expand the variety of peptide conjugation sites, allowing the incorporation of peptides at the 2'-hydroxy group when the oligonucleotide forms a duplex with the complementary strand. The NCL reaction with a peptide thioester and the modified oligonucleotide proceeded smoothly even when the CysBCE modification was in the middle of the oligonucleotide sequence. In addition, we incorporated two CysBCEs into an oligonucleotide to conjugate two peptides to one oligonucleotide. The results indicated that the tandem NCL reactions proceeded efficiently when the oligonucleotide hybridized to the complementary strand to avoid intramolecular disulfide formation between the two CysBCE groups. This method could be useful for peptide conjugation on the 2'-position.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
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8
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Hadianamrei R, Zhao X. Current state of the art in peptide-based gene delivery. J Control Release 2022; 343:600-619. [PMID: 35157938 DOI: 10.1016/j.jconrel.2022.02.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
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9
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Huang Y, Cohen TA, Sperry BM, Larson H, Nguyen HA, Homer MK, Dou FY, Jacoby LM, Cossairt BM, Gamelin DR, Luscombe CK. Organic building blocks at inorganic nanomaterial interfaces. MATERIALS HORIZONS 2022; 9:61-87. [PMID: 34851347 DOI: 10.1039/d1mh01294k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This tutorial review presents our perspective on designing organic molecules for the functionalization of inorganic nanomaterial surfaces, through the model of an "anchor-functionality" paradigm. This "anchor-functionality" paradigm is a streamlined design strategy developed from a comprehensive range of materials (e.g., lead halide perovskites, II-VI semiconductors, III-V semiconductors, metal oxides, diamonds, carbon dots, silicon, etc.) and applications (e.g., light-emitting diodes, photovoltaics, lasers, photonic cavities, photocatalysis, fluorescence imaging, photo dynamic therapy, drug delivery, etc.). The structure of this organic interface modifier comprises two key components: anchor groups binding to inorganic surfaces and functional groups that optimize their performance in specific applications. To help readers better understand and utilize this approach, the roles of different anchor groups and different functional groups are discussed and explained through their interactions with inorganic materials and external environments.
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Affiliation(s)
- Yunping Huang
- Department of Materials Science & Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Theodore A Cohen
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Breena M Sperry
- Department of Materials Science & Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Helen Larson
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hao A Nguyen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Micaela K Homer
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Florence Y Dou
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Laura M Jacoby
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Brandi M Cossairt
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Daniel R Gamelin
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Christine K Luscombe
- Department of Materials Science & Engineering, University of Washington, Seattle, WA 98195, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98195, USA
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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10
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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11
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Tan DJY, Cheong VV, Lim KW, Phan AT. A modular approach to enzymatic ligation of peptides and proteins with oligonucleotides. Chem Commun (Camb) 2021; 57:5507-5510. [PMID: 34036975 DOI: 10.1039/d1cc01348c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Joining peptides and oligonucleotides offers potential benefits, but current methods remain laborious. Here we present a novel approach towards enzymatic ligation of the two modalities through the development of tag phosphoramidites as adaptors that can be readily incorporated onto oligonucleotides. This simple and highly efficient approach paves the way towards streamlined development and production of peptide/protein-oligonucleotide conjugates.
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Affiliation(s)
- Derrick Jing Yang Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
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12
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Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
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13
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Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study. Molecules 2021; 26:molecules26041144. [PMID: 33672783 PMCID: PMC7924657 DOI: 10.3390/molecules26041144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/29/2022] Open
Abstract
The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.
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14
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Kiesman WF, McPherson AK, Diorazio LJ, Van den Bergh L, Smith PD, Northall JM, Fettes A, Wang T, Mehlmann M, Raza S, Held G. Perspectives on the Designation of Oligonucleotide Starting Materials. Nucleic Acid Ther 2021; 31:93-113. [PMID: 33534646 PMCID: PMC7997719 DOI: 10.1089/nat.2020.0909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The designation of starting materials (SMs) for pharmaceuticals has been a topic of great interest and debate since the first ICH quality guidance was published. The increase in the number and variety of commercialized oligonucleotides (antisense oligonucleotides—ASOs, small interfering RNAs—siRNAs, etc.) in recent years has reignited dialogue on this topic because of the unique complexity of the monomeric nucleotides and other contributory materials used to manufacture oligonucleotides. The SM working group in the European Pharma Oligonucleotide Consortium (EPOC) was formed to help establish simple, risk-based criteria to guide the justification of oligonucleotide SMs. This article provides a description of the common types of SMs, classes of SM impurities, and control strategies that will be helpful to maintain manufacturing consistency.
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Affiliation(s)
- William F Kiesman
- Antisense Oligonucleotide Development and Manufacturing, Biogen, Inc., Cambridge, Massachusetts, USA
| | - Andrew K McPherson
- Process Organic Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Louis J Diorazio
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | | | - Peter D Smith
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, United Kingdom
| | - John M Northall
- Chemical Development, Product Development and Supply, GlaxoSmithKline, Stevenage, United Kingdom
| | - Alec Fettes
- Pharmaceutical Division, Small Molecule Technical Development, Department of Process Chemistry and Catalysis, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Tiejun Wang
- Global Regulatory Affairs, CMC & Devices, Sanofi, Bridgewater, New Jersey, USA
| | - Martin Mehlmann
- External Technical Oversight Analytics, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Syed Raza
- Amidite Manufacturing and Process Development, Thermo Fisher Scientific, Milwaukee, Wisconsin, USA
| | - Gary Held
- Amidite Quality Control and Analytical Development, Thermo Fisher Scientific, Milwaukee, Wisconsin, USA
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15
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RNA-Peptide Conjugation through an Efficient Covalent Bond Formation. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10248920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many methods for modification of an oligonucleotide with a peptide have been developed to apply for the therapeutic and diagnostic applications or for the assembly of nanostructure. We have developed a method for the construction of receptor-based fluorescent sensors and catalysts using the ribonucleopeptide (RNP) as a scaffold. Formation of a covalent linkage between the RNA and the peptide subunit of RNP improved its stability, thereby expanding the application of functional RNPs. A representative method was applied for the formation of Schiff base or dihydroxy-morpholino linkage between a dialdehyde group at the 3′-end of sugar-oxidized RNA and a hydrazide group introduced at the C-terminal of a peptide subunit through a flexible peptide linker. In this report, we investigated effects of the solution pH and contribution of the RNA and peptide subunits to the conjugation reaction by using RNA and peptide mutants. The reaction yield reached 90% at a wide range of solution pH with reaction within 3 h. The efficient reaction was mainly supported by the electrostatic interaction between the RNA subunit and the cationic peptide subunit of the RNP scaffold. Formation of the RNP complex was verified to efficiently promote the reaction for construction of the RNA-peptide conjugate.
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16
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Diala I, Shiohama Y, Fujita T, Kotake Y, Demonacos C, Krstic-Demonacos M, Leva GD, Fujii M. Telomerase inhibition, telomere attrition and proliferation arrest of cancer cells induced by phosphorothioate ASO-NLS conjugates targeting hTERC and siRNAs targeting hTERT. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:407-425. [PMID: 32310030 DOI: 10.1080/15257770.2020.1713357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Telomerase activity has been regarded as a critical step in cellular immortalization and carcinogenesis and because of this, regulation of telomerase represents an attractive target for anti-tumor specific therapeutics. Recently, one avenue of cancer research focuses on antisense strategy to target the oncogenes or cancer driver genes, in a sequence specific fashion to down-regulate the expression of the target gene. The protein catalytic subunit, human telomerase reverse transcriptase (hTERT) and the template RNA component (hTERC) are essential for telomerase function, thus theoretically, inhibition of telomerase activity can be achieved by interfering with either the gene expression of hTERT or the hTERC of the telomerase enzymatic complex. The present study showed that phosphorothioate antisense oligonucleotide (sASO)-nuclear localization signal (NLS) peptide conjugates targeting hTERC could inhibit telomerase activity very efficiently at 5 μM concentration but less efficiently at 1 μM concentration. On the other hand, siRNA targeting hTERT mRNA could strongly suppress hTERT expression at 200 nM concentration. It was also revealed that siRNA targeting hTERT could induce telomere attrition and then irreversible arrest of proliferation of cancer cells.
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Affiliation(s)
- Irmina Diala
- Department of Biological & Environmental Chemistry, Faculty of Humanity Oriented Science and Engineering, Kindai University, Iizuka, Japan
| | - Yasuo Shiohama
- Department of Biological & Environmental Chemistry, Faculty of Humanity Oriented Science and Engineering, Kindai University, Iizuka, Japan
| | - Takashi Fujita
- Department of Biological & Environmental Chemistry, Faculty of Humanity Oriented Science and Engineering, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, Faculty of Humanity Oriented Science and Engineering, Kindai University, Iizuka, Japan
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health Sciences, University of Manchester, Manchester, UK
| | - Marija Krstic-Demonacos
- College of Science & Technology, School of Environment & Life Sciences, University of Salford, Salford, UK
| | - Gianpiero Di Leva
- College of Science & Technology, School of Environment & Life Sciences, University of Salford, Salford, UK
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, Faculty of Humanity Oriented Science and Engineering, Kindai University, Iizuka, Japan
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17
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Jiang Z, Thayumanavan S. Non-cationic Material Design for Nucleic Acid Delivery. ADVANCED THERAPEUTICS 2020; 3:1900206. [PMID: 34164572 PMCID: PMC8218910 DOI: 10.1002/adtp.201900206] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 12/16/2022]
Abstract
Nucleic acid delivery provides effective options to control intracellular gene expression and protein production. Efficient delivery of nucleic acid typically requires delivery vehicles to facilitate the entry of nucleic acid into cells. Among non-viral delivery vehicles, cationic materials are favored because of their high loading capacity of nucleic acids and prominent cellular uptake efficiency through electrostatic interaction. However, cationic moieties at high dosage tend to induce severe cytotoxicity due to the interference on cell membrane integrity. In contrast, non-cationic materials present alternative delivery approaches with less safety concerns than cationic materials. In this Progress Report, principles of non-cationic material design for nucleic acid delivery are discussed. Examples of such non-cationic platforms are highlighted, including complexation or conjugation with nucleic acids and self-assembled nucleic acid structures.
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Affiliation(s)
- Ziwen Jiang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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18
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Aviñó A, Jorge AF, Huertas CS, Cova TFGG, Pais A, Lechuga LM, Eritja R, Fabrega C. Aptamer-peptide conjugates as a new strategy to modulate human α-thrombin binding affinity. Biochim Biophys Acta Gen Subj 2019; 1863:1619-1630. [PMID: 31265898 DOI: 10.1016/j.bbagen.2019.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/23/2022]
Abstract
Aptamers are single-stranded RNA or DNA molecules that specifically recognize their targets and have proven valuable for functionalizing sensitive biosensors. α-thrombin is a trypsin-like serine proteinase which plays a crucial role in haemostasis and thrombosis. An abnormal activity or overexpression of this protein is associated with a variety of diseases. A great deal of attention was devoted to the construction of high-throughput biosensors for accurately detect thrombin for the early diagnosis and treatment of related diseases. Herein, we propose a new approach to modulate the interaction between α-thrombin and the aptamer TBA15. To this end, TBA15 was chemically conjugated to two peptide sequences (TBA-G3FIE-Ac and TBA-G3EIF-Ac) corresponding to a short fragment of the acidic region of the human factor V, which is known to interact directly with exosite I. Surface Plasmon Resonance (SPR) results showed enhanced analytical performances of thrombin with TBA-G3EIF-Ac than with TBA wild-type, reaching a limit of detection as low as 44.9 pM. Electrophoresis mobility shift assay (EMSA) corroborated the SPR results. Molecular dynamics (MD) simulations support experimental evidences and provided further insight into thrombin/TBA-peptide interaction. Our findings demonstrate that the combination of TBA15 with key interacting peptides offers good opportunities to produce sensitive devices for thrombin detection and potential candidates to block thrombin activity.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Andreia F Jorge
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - César S Huertas
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Tânia F G G Cova
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Alberto Pais
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Laura M Lechuga
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Carme Fabrega
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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19
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Stephanopoulos N. Peptide-Oligonucleotide Hybrid Molecules for Bioactive Nanomaterials. Bioconjug Chem 2019; 30:1915-1922. [PMID: 31082220 DOI: 10.1021/acs.bioconjchem.9b00259] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptides and oligonucleotides are two of the most interesting molecular platforms for making bioactive materials. Peptides provide bioactivity that can mimic that of proteins, whereas oligonucleotides like DNA can be used as scaffolds to immobilize other molecules with nanoscale precision. In this Topical Review, we discuss covalent conjugates of peptides and DNA for creating bioactive materials that can interface with cells. In particular, we focus on two areas. The first is multivalent presentation of peptides on a DNA scaffold, both linear assemblies and more complex nanostructures. The second is the reversible tuning of the extracellular environment-like ligand presentation, stiffness, and hierarchical morphology-in peptide-DNA biomaterials. These examples highlight the potential for creating highly potent materials with benefits not possible with either molecule alone, and we outline a number of future directions and applications for peptide-DNA conjugates.
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20
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MacCulloch T, Buchberger A, Stephanopoulos N. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials. Org Biomol Chem 2019; 17:1668-1682. [PMID: 30483688 DOI: 10.1039/c8ob02436g] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent constructs that link a molecule like DNA to a synthetic peptide sequences. These materials merge the programmable self-assembly of oligonucleotides with the bioactivity and chemical diversity of polypeptides. Recent years have seen the widespread use of POCs in a range of fields, driven the by relative advantages of each molecular type. In this review, we will present an overview of the synthesis and application of POCs, with an emphasis on emerging areas where these molecules will have a unique impact. We first discuss two main strategies for synthesizing POCs from synthetic monomers such as phosphoramidites and functionalized amino acids. We then describe four key fields of research in POCs: (1) biomaterials for interfacing with, and controlling the behavior of cells; (2) hybrid self-assembling systems that balance peptide and oligonucleotide intermolecular forces; (3) template-enhanced coupling of POCs into larger molecules; and (4) display of peptides on self-assembled oligonucleotide scaffolds. We also highlight several promising areas for future applications in each of these four directions, and anticipate ever increasing uses of POCs in interdisciplinary research.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe AZ, USA.
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21
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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22
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Zhou X, Pathak P, Jayawickramarajah J. Design, synthesis, and applications of DNA-macrocyclic host conjugates. Chem Commun (Camb) 2018; 54:11668-11680. [PMID: 30255866 DOI: 10.1039/c8cc06716c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With this Feature Article we review, for the first time, the development of DNA-host conjugates-a nascent yet rapidly growing research focus within the ambit of DNA supramolecular chemistry. Synthetic hosts (such as cyclodextrins, cucurbiturils, and calixarenes) are well-suited to be partnered with DNA, since DNA assembly and host-guest binding both thrive in aqueous media, are largely orthogonal, and exhibit controllable and input-responsive properties. The covalent braiding of these two supramolecular synthons thus leads to advanced self-assemblies and nanostructures with exciting function that range from drug delivery agents to input-triggered switches. The latter class of DNA-host conjugates have been demonstrated to precisely control protein activity, and have also been used as modulable catalysts and versatile biosensors.
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Affiliation(s)
- X Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, USA.
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23
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Shoji T, Fukutomi H, Okada Y, Chiba K. Artificial bioconjugates with naturally occurring linkages: the use of phosphodiester. Beilstein J Org Chem 2018; 14:1946-1955. [PMID: 30112100 PMCID: PMC6071721 DOI: 10.3762/bjoc.14.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/06/2018] [Indexed: 12/22/2022] Open
Abstract
Artificial orthogonal bond formations such as the alkyne–azide cycloaddition have enabled selective bioconjugations under mild conditions, yet naturally occurring linkages between native functional groups would be more straightforward to elaborate bioconjugates. Herein, we describe the use of a phosphodiester bond as a versatile option to access various bioconjugates. An opposite activation strategy, involving 5’-phosphitylation of the supported oligonucleotides, has allowed several biomolecules that possess an unactivated alcohol to be directly conjugated. It should be noted that there is no need to pre-install artificial functional groups and undesired and unpredictable perturbations possibly caused by bioconjugation can be minimized.
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Affiliation(s)
- Takao Shoji
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Hiroki Fukutomi
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Okada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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24
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Chotera A, Sadihov H, Cohen-Luria R, Monnard PA, Ashkenasy G. Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras. Chemistry 2018; 24:10128-10135. [PMID: 29732630 DOI: 10.1002/chem.201800500] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Indexed: 01/24/2023]
Abstract
Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.
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Affiliation(s)
- Agata Chotera
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Hava Sadihov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Pierre-Alain Monnard
- Institute for Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
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25
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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26
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Wojciechowska M, Dudek M, Trylska J. Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA. Biopolymers 2018; 109:e23116. [PMID: 29570767 DOI: 10.1002/bip.23116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 01/13/2023]
Abstract
A fragment of E. coli 16S rRNA formed by nucleotides 500 to 545 is termed helix 18. Nucleotides 505-507 and 524-526 form a pseudo-knot and its distortion affects ribosome function. Helix 18 isolated from the ribosome context is thus an interesting fragment to investigate the structural properties and folding of RNA with pseudo-knots. With all-atom molecular dynamics simulations, spectroscopic and gel electrophoresis experiments, we investigated thermodynamics of helix 18, with a focus on its pseudo-knot. In solution studies at ambient conditions we observed dimerization of helix 18. We proposed that the loop, containing nucleotides forming the pseudo-knot, interacts with another monomer of helix 18. The native dimer is difficult to break but introducing mutations in the pseudo-knot indeed assured a monomeric form of helix 18. Molecular dynamics simulations at 310 K confirmed the stability of the pseudo-knot but at elevated temperatures this pseudo-knot was the first part of helix 18 to lose the hydrogen bond pattern. To further determine helix 18 stability, we analyzed the interactions of helix 18 with short oligomers complementary to a nucleotide stretch containing the pseudo-knot. The formation of higher-order structures by helix 18 impacts hybridization efficiency of peptide nucleic acid and 2'-O methyl RNA oligomers.
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Affiliation(s)
- Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
| | - Marta Dudek
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland.,School of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.,First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, Warsaw, 02-091, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
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27
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Merg AD, Thaner RV, Mokashi-Punekar S, Nguyen ST, Rosi NL. Triblock peptide-oligonucleotide chimeras (POCs): programmable biomolecules for the assembly of morphologically tunable and responsive hybrid materials. Chem Commun (Camb) 2018; 53:12221-12224. [PMID: 29082986 DOI: 10.1039/c7cc07708d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Triblock peptide-oligonucleotide chimeras (POCs) consisting of peptides and oligonucleotides interlinked by an organic core are presented and their assembly behaviour is investigated. Several factors influence POC assembly, resulting in the formation of either vesicles or fibres. Design rules are introduced and used to predict and alter POC assembly morphology.
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Affiliation(s)
- Andrea D Merg
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA.
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28
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Ejlersen M, Christensen NJ, Sørensen KK, Jensen KJ, Wengel J, Lou C. Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA. Bioconjug Chem 2018; 29:1025-1029. [PMID: 29505242 DOI: 10.1021/acs.bioconjchem.8b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.
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Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
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29
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Hayashi G, Tamai M, Okamoto A. Hybridization-sensitive Fluorescent Oligonucleotide Probe Conjugated with Cell-penetrating Peptides for Enhanced Cellular Uptake. CHEM LETT 2017. [DOI: 10.1246/cl.170813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656
| | - Makoto Tamai
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904
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30
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Pifferi C, Daskhan GC, Fiore M, Shiao TC, Roy R, Renaudet O. Aminooxylated Carbohydrates: Synthesis and Applications. Chem Rev 2017; 117:9839-9873. [PMID: 28682060 DOI: 10.1021/acs.chemrev.6b00733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.
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Affiliation(s)
- Carlo Pifferi
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Gour Chand Daskhan
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Michele Fiore
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Tze Chieh Shiao
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - René Roy
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France.,Institut Universitaire de France , 103 Boulevard Saint-Michel, 75005 Paris, France
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31
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Shinkai Y, Kashihara S, Minematsu G, Fujii H, Naemura M, Kotake Y, Morita Y, Ohnuki K, Fokina AA, Stetsenko DA, Filichev VV, Fujii M. Silencing ofBCR/ABLChimeric Gene in Human Chronic Myelogenous Leukemia Cell Line K562 by siRNA-Nuclear Export Signal Peptide Conjugates. Nucleic Acid Ther 2017; 27:168-175. [DOI: 10.1089/nat.2016.0647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Yasuhiro Shinkai
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Shinichi Kashihara
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Go Minematsu
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Hirofumi Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Madoka Naemura
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yasutaka Morita
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Koichiro Ohnuki
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Alesya A. Fokina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry A. Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Masayuki Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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32
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Kirmizialtin S, Yildiz BS, Yildiz I. A DFT-based mechanistic study on the formation of oximes. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Serdal Kirmizialtin
- Chemistry Program; New York University at Abu Dhabi; Abu Dhabi United Arab Emirates
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33
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Chelushkin PS, Leko MV, Dorosh MY, Burov SV. Oxime ligation in acetic acid: efficient synthesis of aminooxy-peptide conjugates. J Pept Sci 2016; 23:13-15. [PMID: 27699914 DOI: 10.1002/psc.2931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 11/09/2022]
Abstract
Oxime ligation is a powerful tool in various bioconjugation strategies. Nevertheless, high reaction rates and quantitative yields are typically reported for aldehyde-derived compounds. In contrary, keto groups react much slower, with quantitative yields achieved at 5 h for low-molecular weight compounds and more than 15 h for polymers or dendrimers. In this communication, we report that oxime ligation proceeds rapidly with quantitative (>95%) conversion within 1.5-2 h in pure acetic acid. The practical utility of suggested technique is illustrated by the synthesis of peptide-steroid and peptide-polymer conjugates of model aminooxy-peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Pavel S Chelushkin
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Maria V Leko
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Marina Yu Dorosh
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Sergey V Burov
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
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34
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Brun O, Agramunt J, Raich L, Rovira C, Pedroso E, Grandas A. Selective Derivatization of N-Terminal Cysteines Using Cyclopentenediones. Org Lett 2016; 18:4836-4839. [DOI: 10.1021/acs.orglett.6b02301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | | | - Carme Rovira
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
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35
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Kye M, Lim YB. Reciprocal Self-Assembly of Peptide-DNA Conjugates into a Programmable Sub-10-nm Supramolecular Deoxyribonucleoprotein. Angew Chem Int Ed Engl 2016; 55:12003-7. [DOI: 10.1002/anie.201605696] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/22/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
| | - Yong-beom Lim
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
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36
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Kye M, Lim YB. Reciprocal Self-Assembly of Peptide-DNA Conjugates into a Programmable Sub-10-nm Supramolecular Deoxyribonucleoprotein. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
| | - Yong-beom Lim
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
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37
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Pokharel D, Fueangfung S, Zhang M, Fang S. Peptide and peptide nucleic acid syntheses using a DNA/RNA synthesizer. Biopolymers 2016; 102:487-93. [PMID: 25298082 DOI: 10.1002/bip.22574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/18/2014] [Accepted: 09/27/2014] [Indexed: 11/07/2022]
Abstract
The use of an ABI 394 DNA/RNA synthesizer for peptide and peptide nucleic acid (PNA) syntheses is described. No additional physical part or software is needed for the application. A commercially available large DNA synthesis column was used, and only about half of its volume was filled with resin when the resin was fully swollen. With additional space in the top portion of the column, agitation of reaction mixture was achieved by bubbling argon from the bottom without losing solution. Removing solutions from column was achieved by flushing argon from top to bottom. Two peptide and two PNA sequences were synthesized. Good yields were obtained in all the cases. The method is easy to follow by researchers who are familiar with DNA/RNA synthesizer.
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Affiliation(s)
- Durga Pokharel
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931
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38
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Fragment-based solid-phase assembly of oligonucleotide conjugates with peptide and polyethylene glycol ligands. Eur J Med Chem 2016; 121:132-142. [PMID: 27236069 DOI: 10.1016/j.ejmech.2016.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/25/2016] [Accepted: 05/01/2016] [Indexed: 12/26/2022]
Abstract
Ligand conjugation to oligonucleotides is an attractive strategy for enhancing the therapeutic potential of antisense and siRNA agents by inferring properties such as improved cellular uptake or better pharmacokinetic properties. Disulfide linkages enable dissociation of ligands and oligonucleotides in reducing environments found in endosomal compartments after cellular uptake. Solution-phase fragment coupling procedures for producing oligonucleotide conjugates are often tedious, produce moderate yields and reaction byproducts are frequently difficult to remove. We have developed an improved method for solid-phase coupling of ligands to oligonucleotides via disulfides directly after solid-phase synthesis. A 2'-thiol introduced using a modified nucleotide building block was orthogonally deprotected on the controlled pore glass solid support with N-butylphosphine. Oligolysine peptides and a short monodisperse ethylene glycol chain were successfully coupled to the deprotected thiol. Cleavage from the resin and full removal of oligonucleotide protection groups were achieved using methanolic ammonia. After standard desalting, and without further purification, homogenous conjugates were obtained as demonstrated by HPLC, gel electrophoresis, and mass spectrometry. The attachment of both amphiphilic and cationic ligands proves the versatility of the conjugation procedure. An antisense oligonucleotide conjugate with hexalysine showed pronounced gene silencing in a cell culture tumor model in the absence of a transfection reagent and the corresponding ethylene glycol conjugate resulted in down regulation of the target gene to nearly 50% after naked application.
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39
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Duan Q, Lu K, Ma L, Zhao D. Concise Synthesis of Triazole-Linked 5'-Peptide-Oligonucleotide Conjugates by Click Chemistry. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:579-89. [PMID: 26167666 DOI: 10.1080/15257770.2015.1037455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A concise synthesis of oligonucleotide 5'-peptide-conjugates via copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition in aqueous solution is described. Synthesis of reagents was accomplished by on-column derivatization of corresponding peptides and oligonucleotides. This method is well suited for the preparation of peptide-oligonucleotide conjugates containing 1,2,3-triazole linkage between the 5'-position of an oligonucleotide and the N-terminus of a peptide.
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Affiliation(s)
- Qunpeng Duan
- a School of Material and Chemical Engineering, Henan Institute of Engineering , Zhengzhou , China
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40
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Agten SM, Dawson PE, Hackeng TM. Oxime conjugation in protein chemistry: from carbonyl incorporation to nucleophilic catalysis. J Pept Sci 2016; 22:271-9. [PMID: 27006095 DOI: 10.1002/psc.2874] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
Abstract
Use of oxime forming reactions has become a widely applied strategy for peptide and protein bioconjugation. The efficiency of the reaction and robust stability of the oxime product has led to the development of a growing list of methods to introduce the required ketone or aldehyde functionality site specifically into proteins. Early methods focused on site-specific oxidation of an N-terminal serine or threonine and more recently transamination methods have been developed to convert a broader set of N-terminal amino acids into a ketone or aldehyde. More recently, site-specific modification of protein has been attained through engineering enzymes involved in posttranslational modifications in order to accommodate aldehyde-containing substrates. Similarly, a growing list of unnatural amino acids can be introduced through development of selective amino-acyl tRNA synthetase/tRNA pairs combined with codon reassignment. In the case of glycoproteins, glycans can be selectively modified chemically or enzymatically to introduce aldehyde functional groups. Finally, the total chemical synthesis of proteins complements these biological and chemoenzymatic approaches. Once introduced, the oxime ligation of these aldehyde and ketone groups can be catalyzed by aniline or a variety of aniline derivatives to tune the activity, pH preference, stability and solubility of the catalyst. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Stijn M Agten
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Tilman M Hackeng
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
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41
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Concise postsynthetic preparation of oligonucleotide-oligopeptide conjugates through facile disulfide bond formation. Future Med Chem 2015; 7:1657-73. [PMID: 26381134 DOI: 10.4155/fmc.15.109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Despite recent advances, major hurdles still need to be cleared for widespread application of therapeutic antisense technologies. In particular, pharmacokinetic properties and efficient cellular uptake need to be improved through chemical derivatization or bioconjugation. RESULTS The 2'-O-thioethylene nucleotide building block affords easy implementation into standard oligonucleotide synthesis protocols and was used to attach oligolysine chains to phosphodiester oligonucleotides by direct reaction with S-sulfonate protected peptides. Efficient gene silencing was induced in a cell culture model after transfection reagent-free application of the conjugates. CONCLUSION A facile optimized procedure for generating oligonucleotide-peptide conjugates was established. The attachment of short basic peptides via a labile linker is sufficient to enhance membrane permeability of oligonucleotides and result in successful gene silencing.
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Affiliation(s)
- Yuhe R. Yang
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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43
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Serva S, Lagunavičius A. Direct conjugation of peptides and 5-hydroxymethylcytosine in DNA. Bioconjug Chem 2015; 26:1008-12. [PMID: 25982286 DOI: 10.1021/acs.bioconjchem.5b00165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent discovery of functional 5-hydroxymethylcytosine in vertebrate genomes prompted for elaboration of methods to localize this modification at the nucleotide resolution level. Among several covalent modification-based approaches, atypical activity of cytosine-5 DNA methyltransferases to couple small molecules to 5-hydroxymethylcytosine stands out for acceptance of broad range of ligands. We went further to explore the possibility for methyltransferase-maintained coupling of compounds possessing autonomous functions. Functionalization of DNA was achieved by direct conjugation of chemically synthesized peptides of regular structure. Sequence, residue, and position-specific coupling of DNA containing 5-hydroxymethylcytosine and different peptides has been demonstrated, with the nature of the resulting conjugates confirmed by protease treatment and mass spectrometry. Coupling products were compatible with affinity-driven separation from the unmodified DNA. This approach highlights an emerging avenue toward the enzymatic, sequence-specific DNA functionalization, enabling a single step merge of the DNA and peptide moieties into a bifunctional entity.
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Affiliation(s)
- Saulius Serva
- †Thermo Fisher Scientific Baltics, Graičiu̅no 8, Vilnius LT-02241, Lithuania.,‡Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Vilnius University, MK Čiurlionio 21/27, LT-03101 Vilnius, Lithuania
| | - Arūnas Lagunavičius
- †Thermo Fisher Scientific Baltics, Graičiu̅no 8, Vilnius LT-02241, Lithuania
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44
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Strazewski P. Omne Vivum Ex Vivo … Omne? How to Feed an Inanimate Evolvable Chemical System so as to Let it Self-evolve into Increased Complexity and Life-like Behaviour. Isr J Chem 2015. [DOI: 10.1002/ijch.201400175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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45
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Micksch T, Herrmann E, Scharnweber D, Schwenzer B. A modular peptide-based immobilization system for ZrO2, TiZr and TiO2 surfaces. Acta Biomater 2015; 12:290-297. [PMID: 25449919 DOI: 10.1016/j.actbio.2014.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/14/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
Abstract
The present study describes a novel versatile immobilization system for the modification of implant materials with biologically active molecules (BAMs), e.g. antibiotics or growth factors. Specific adsorbing peptides are used as anchor molecules to immobilize oligodesoxynucleotides (ODNs) on the implant surface (anchor strand, AS). The BAM is conjugated to a complementary ODN strand (CS) which is able to hybridize to the AS on the implant surface to immobilize the BAM. The ODN double strand allows for a controlled release of the BAM adjustable by the ODN sequence and length. The immobilization system was developed and proven on three typical implant materials, namely ZrO2, TiZr and Ti, respectively. The parathyroid hormone (PTH) fragment 1-34 was conjugated to the CS and immobilized on these different implant materials. To investigate the biological activity of the immobilized PTH, alkaline phosphatase was quantified after incubation of the osteoblast precursor cells C2C12 on the modified samples. The results demonstrate the successful immobilization of biologically active PTH (1-34) and the high potential of the established surfaces to achieve an increased osseointegration of variable implants, especially for patients with risk factors.
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46
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Fu Y, Li B, Jiang YB, Dunphy DR, Tsai A, Tam SY, Fan H, Zhang H, Rogers D, Rempe S, Atanassov P, Cecchi JL, Brinker CJ. Atomic layer deposition of L-alanine polypeptide. J Am Chem Soc 2014; 136:15821-4. [PMID: 25355683 DOI: 10.1021/ja5043403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
L-Alanine polypeptide thin films were synthesized via atomic layer deposition (ALD). Instead of using an amino acid monomer as the precursor, an L-alanine amino acid derivatized with a protecting group was used to prevent self-polymerization, increase the vapor pressure, and allow linear cycle-by-cycle growth emblematic of ALD. The successful deposition of a conformal polypeptide film has been confirmed by FTIR, TEM, and Mass Spectrometry, and the ALD process has been extended to polyvaline.
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Affiliation(s)
- Yaqin Fu
- Department of Chemical and Biological Engineering and Center for Micro-engineered Materials, University of New Mexico , Albuquerque, New Mexico 87131, United States
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47
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Chu CC, Wong OY, Silverman SK. A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. Chembiochem 2014; 15:1905-10. [PMID: 25056930 DOI: 10.1002/cbic.201402255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/11/2023]
Abstract
We report DNA catalysts (deoxyribozymes) that join tyrosine-containing peptides to RNA and DNA in one step and without requiring protecting groups on either the peptide or the nucleic acid. Our previous efforts towards this goal required tethering the peptide to a DNA anchor oligonucleotide. Here, we established direct in vitro selection for deoxyribozymes that use untethered, free peptide substrates. This approach enables imposition of selection pressure via reduced peptide concentration and leads to preparatively useful lower apparent Km values of ∼100 μM peptide. Use of phosphorimidazolide (Imp) rather than triphosphate as the electrophile enables reactivity of either terminus (5' or 3') of both RNA and DNA. Our findings establish a generalizable means of joining unprotected peptide to nucleic acid in one step by using DNA catalysts identified by in vitro selection.
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Affiliation(s)
- Chih-Chi Chu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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48
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Zhou Z, Xiang Y, Tong A, Lu Y. Simple and efficient method to purify DNA-protein conjugates and its sensing applications. Anal Chem 2014; 86:3869-75. [PMID: 24605905 PMCID: PMC4004194 DOI: 10.1021/ac4040554] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/08/2014] [Indexed: 11/28/2022]
Abstract
DNA-protein conjugates are very useful in analytical chemistry for target recognition and signal amplification. While a number of methods for conjugating DNA with proteins are known, methods for purification of DNA-protein conjugates from reaction mixture containing unreacted proteins are much less investigated. In this work, a simple and efficient approach to purify DNA-invertase conjugates from reaction mixture via a biotin displacement strategy to release desthiobiotinylated DNA-invertase conjugates from streptavidin-coated magnetic beads was developed. The conjugates purified by this approach were utilized for quantitative detection of cocaine and DNA using a personal glucose meter through structure-switching DNA aptamer sensors and competitive DNA hybridization assays, respectively. In both cases, the purified DNA-invertase conjugates showed better performance compared to the same assays using unpurified conjugates. The approach demonstrated here can be further expanded to other DNA and proteins to generate purified DNA-protein conjugates for analytical and other applications.
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Affiliation(s)
- Zhaojuan Zhou
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yu Xiang
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Aijun Tong
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Yi Lu
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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49
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Tang X, Han J, Zhu Z, Lu X, Chen H, Cai Y. Facile synthesis, sequence-tuned thermoresponsive behaviours and reaction-induced reorganization of water-soluble keto-polymers. Polym Chem 2014. [DOI: 10.1039/c4py00146j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water-soluble keto-polymers: facile synthesis in methanol on irradiation with visible light at 25 °C, sequence-tuned thermoresponsive behaviours and reaction-induced reorganization.
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Affiliation(s)
- Xianghua Tang
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
| | - Jie Han
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
| | - Zhengguang Zhu
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
| | - Xinhua Lu
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
| | - Hong Chen
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
| | - Yuanli Cai
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123, China
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50
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Abramova TV, Morozova OB, Silnikov VN, Yurkovskaya AV. Synthesis of nucleotide-amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach. Beilstein J Org Chem 2013; 9:2898-909. [PMID: 24367455 PMCID: PMC3869286 DOI: 10.3762/bjoc.9.326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/15/2013] [Indexed: 11/23/2022] Open
Abstract
Conjugates of 2’-deoxyguanosine, L-tryptophan and benzophenone designed to study pathways of fast radical reactions by the photo Chemically Induced Dynamic Nuclear Polarization (photo-CIDNP) method were obtained by the phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates.
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Affiliation(s)
- Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia ; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Olga B Morozova
- Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia ; International Tomography Center, SB RAS, Institutskaya 3a, Novosibirsk 630090, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Alexandra V Yurkovskaya
- Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia ; International Tomography Center, SB RAS, Institutskaya 3a, Novosibirsk 630090, Russia
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