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Agrawal S. Considerations for Creating the Next Generation of RNA Therapeutics: Oligonucleotide Chemistry and Innate Immune Responses to Nucleic Acids. Nucleic Acid Ther 2024; 34:37-51. [PMID: 38578231 DOI: 10.1089/nat.2024.29009.sud] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
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2
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Green MR, Sambrook J. Preparation of Labeled DNA, RNA, and Oligonucleotide Probes. Cold Spring Harb Protoc 2022; 2022:2022/1/pdb.top100578. [PMID: 34983861 DOI: 10.1101/pdb.top100578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Labeled nucleic acids and oligonucleotides are typically generated by enzymatic methods such as end-labeling, random priming, nick translation, in vitro transcription, and variations of the polymerase chain reaction (PCR). Some of these methods place the label in specific locations within the nucleic acid (e.g., at the 5' or 3' terminus); others generate molecules that are labeled internally at multiple sites. Some methods yield labeled single-stranded products, whereas others generate double-stranded nucleic acids. Finally, some generate probes of defined length, whereas others yield a heterogeneous population of labeled molecules. Options available for generating and detecting labeled nucleic acids, as well as advice on designing oligonucleotides for use as probes, is included here.
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Housh K, Gates KS. Synthesis of DNA Duplexes Containing Site-Specific Interstrand Cross-Links via Sequential Reductive Amination Reactions Involving Diamine Linkers and Abasic Sites on Complementary Oligodeoxynucleotides. Chem Res Toxicol 2021; 34:2384-2391. [PMID: 34694787 PMCID: PMC8650211 DOI: 10.1021/acs.chemrestox.1c00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interstrand DNA cross-links are important in biology, medicinal chemistry, and materials science. Accordingly, methods for the targeted installation of interstrand cross-links in DNA duplexes may be useful in diverse fields. Here, a simple procedure is reported for the preparation of DNA duplexes containing site-specific, chemically defined interstrand cross-links. The approach involves sequential reductive amination reactions between diamine linkers and two abasic (apurinic/apyrimidinic, AP) sites on complementary oligodeoxynucleotides. Use of the symmetrical triamine, tris(2-aminoethyl)amine, in this reaction sequence enabled the preparation of a cross-linked DNA duplex bearing a derivatizable aminoethyl group.
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Affiliation(s)
- Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
- University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States
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4
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Agrawal S. The Evolution of Antisense Oligonucleotide Chemistry-A Personal Journey. Biomedicines 2021; 9:503. [PMID: 34063675 PMCID: PMC8147625 DOI: 10.3390/biomedicines9050503] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 01/03/2023] Open
Abstract
Over the last four decades, tremendous progress has been made in use of synthetic oligonucleotides as therapeutics. This has been possible largely by introducing chemical modifications to provide drug like properties to oligonucleotides. In this article I have summarized twists and turns on use of chemical modifications and their road to success and highlight areas of future directions.
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Affiliation(s)
- Sudhir Agrawal
- ARNAY Sciences LLC, Shrewsbury, MA 01545, USA; or
- Department of Medicine, University of Massachusetts Medical School, 55 N Lake Ave, Worcester, MA 01655, USA
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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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6
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Yanachkov I, Zavizion B, Metelev V, Stevens LJ, Tabatadze Y, Yanachkova M, Wright G, Krichevsky AM, Tabatadze DR. Self-neutralizing oligonucleotides with enhanced cellular uptake. Org Biomol Chem 2018; 15:1363-1380. [PMID: 28074950 DOI: 10.1039/c6ob02576e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is tremendous potential for oligonucleotide (ON) therapeutics, but low cellular penetration due to their polyanionic nature is a major obstacle. We addressed this problem by developing a new approach for ON charge neutralization in which multiple branched charge-neutralizing sleeves (BCNSs) are attached to the internucleoside phosphates of ON by phosphotriester bonds. The BCNSs are terminated with positively charged amino groups, and are optimized to form ion pairs with the neighboring phosphate groups. The new modified ONs can be prepared by standard automated phosphoramidite chemistry in good yield and purity. They possess good solubility and hybridization properties, are not involved in non-standard intramolecular aggregation, have low cytotoxicity, adequate chemical stability, improved serum stability, and above all, display significantly enhanced cellular uptake. Thus, the new ON derivatives exhibit properties that make them promising candidates for the development of novel therapeutics or research tools for modulation of the expression of target genes.
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Affiliation(s)
- Ivan Yanachkov
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Boris Zavizion
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | - Valeri Metelev
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and Department of Chemistry, Moscow State University, Leninskye gory1/40, Moscow 119991, Russian Federation
| | - Laura J Stevens
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | | | - Milka Yanachkova
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - George Wright
- GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, USA
| | - David R Tabatadze
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
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Kojima N, Komatsu Y. Synthesis and application of highly reactive amino linkers for functional oligonucleotides. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.48.1-23. [PMID: 22395967 DOI: 10.1002/0471142700.nc0448s48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oligonucleotides are functionalized by conjugation with a variety of molecules, and aliphatic amino linkers have been frequently used as a tether for their modifications. This unit describes the syntheses and applications of novel amino linkers having a carbamate structure. Two major chemical properties of the primary amine are induced by the neighboring effect of the carbamate group, which are found to be optimum in an aminoethyl carbamate structure. First, the hydrophobic monomethoxytrityl group can be rapidly removed from the aminoethyl carbamate under very mild acidic conditions, while the deprotection is not completed in standard aliphatic amines even under high acid concentration. This significant feature enables the convenient purification of amino-modified oligonucleotides by using the hydrophobic interaction of the monomethoxytrityl group with a reverse-phase resin. Second, the introduction of the carbamate linkage reduces the pK(a) value of the neighboring primary amine, resulting in an increase in the conjugation yields with various functional molecules, such as those having active esters. The novel amino linkers that have an aminoethyl carbamate linkage indicate potent activity and are applicable for the preparation of various functional oligonucleotides.
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Affiliation(s)
- Naoshi Kojima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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Aaronson JG, Klein LJ, Momose AA, O’Brien AM, Shaw AW, Tucker TJ, Yuan Y, Tellers DM. Rapid HATU-Mediated Solution Phase siRNA Conjugation. Bioconjug Chem 2011; 22:1723-8. [PMID: 21744777 DOI: 10.1021/bc2001227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey G. Aaronson
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Lee J. Klein
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Aaron A. Momose
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Ann M. O’Brien
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Anthony W. Shaw
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Thomas J. Tucker
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yu Yuan
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - David M. Tellers
- Department of Medicinal Chemistry and ‡Department of Pharmaceutical Analytical Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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Petra DGI, de Boer RF, Koomen GJ, Meeuwenoord NJ, Kuyl-Yeheskiely E, van der Marel GA, van Boom JH. Synthesis and properties of a fluorescent nucleotide derivative. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19961150117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Putta MR, Zhu FG, Wang D, Bhagat L, Dai M, Kandimalla ER, Agrawal S. Peptide conjugation at the 5'-end of oligodeoxynucleotides abrogates toll-like receptor 9-mediated immune stimulatory activity. Bioconjug Chem 2010; 21:39-45. [PMID: 20020767 DOI: 10.1021/bc900425s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Bacterial and synthetic DNA containing unmethylated CpG motifs act as ligands of Toll-like receptor 9 (TLR9). Our earlier studies showed that 5'-accessibility of synthetic oligodeoxynucleotides containing CpG motif (ODN) is required for TLR9-mediated immune stimulatory activity. Blocking the 5'-end of ODN through conjugation to a variety of moieties reduces immune stimulatory activity (Bioconjugate Chem. 2002, 13, 966-974). In the present study, we conjugated a model peptide, a 28-amino-acid-long beta-amyloid peptide, to either the 5'- or the 3'-end of an ODN via C3 and C6 alkyl linkers. We compared the immune stimulatory activity of the resulting conjugates with that of a parent ODN without conjugation in TLR9-transfected cells, mouse spleen cell cultures, and in vivo in mice. ODN with the peptide conjugated at the 3'-end via C3 and C6 linkers had immune stimulatory activity similar to that of the parent ODN in both in vitro and in vivo in mice. On the contrary, conjugation of peptide at the 5'-end of the ODN significantly abrogated immune stimulatory activity. In conclusion, the results presented here demonstrate that peptide/protein conjugation to ODN is optimal at the 3'-end with either C3 or C6 linker and conjugation at the 5'-end leads to significant loss of TLR9-mediated immune stimulation.
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11
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Pfleiderer W, Maier T. Nucleotides Part: LXXVII. New Types of Fluorescence Labeling of 2’-Deoxyguanosine. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Karayel E, Bürckstümmer T, Bilban M, Dürnberger G, Weitzer S, Martinez J, Superti-Furga G. The TLR-independent DNA recognition pathway in murine macrophages: Ligand features and molecular signature. Eur J Immunol 2009; 39:1929-36. [PMID: 19551900 DOI: 10.1002/eji.200939344] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recognition of foreign DNA by cytosolic innate immune receptors triggers the production of IFN-beta. However, it is unclear whether different types of DNA ligands are recognized by similar receptors and whether the resulting response is distinct from the endosomal TLR response. To address these questions, we compared the two most commonly used types of DNA ligands (IFN-stimulatory DNA (ISD) and poly(dAdT)) and assessed the minimal structural requirements for stimulatory capacity in RAW264.7 cells. Gene expression signatures and competition experiments suggest that ISD and poly(dAdT) are qualitatively indistinguishable and differ from the CpG-containing oligonucleotides triggering the TLR9 pathway. Structure - activity relationship analyses revealed that a minimal length of two helical turns is sufficient for ISD-mediated IFN-beta induction, while phosphorylation at the 5'-end is dispensable. Altogether, our data suggest that, in murine macrophages, only one major cytosolic DNA recognition pathway is operational.
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Affiliation(s)
- Evren Karayel
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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14
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Jin W, Lin X, Lv S, Zhang Y, Jin Q, Mu Y. A DNA sensor based on surface plasmon resonance for apoptosis-associated genes detection. Biosens Bioelectron 2009; 24:1266-9. [DOI: 10.1016/j.bios.2008.07.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 07/01/2008] [Accepted: 07/16/2008] [Indexed: 11/25/2022]
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15
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Fang S, Bergstrom DE. Reversible biotinylation of the 5'-terminus of oligodeoxyribonucleotides and its application in affinity purification. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.20. [PMID: 18428910 DOI: 10.1002/0471142700.nc0420s14] [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: 11/07/2022]
Abstract
The preparation of two reversible biotinylation phosphoramidites and their application in labeling and affinity purification of synthetic oligodeoxyribonucleotides will be described. In both cases, the biotin is linked to the 5'-terminus of DNA through a diisopropyl silyl acetal functionality. This linkage is completely stable under certain postsynthetic cleavage/deprotection conditions, but can be readily broken by fluoride ions, releasing unmodified 5'-OH and 5'-phosphate DNA, respectively. To demonstrate the use of these reversible biotinylation methods, crude DNA was incubated with NeutrAvidin-coated microspheres, full-length biotinylated DNA was efficiently attached to the solid phase, and nonbiotinylated failure sequences and other impurities were readily removed by washing with buffer. Cleavage of the silyl acetal linkage afforded high-quality, full-length, unmodified 5'-OH and 5'-phosphate DNA, respectively, depending on which of the two phosphoramidites was used. It is anticipated that this method will find applications in areas that require efficient isolation of DNA from a complex mixture.
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Affiliation(s)
- Shiyue Fang
- Purdue University, West Lafayette, Indiana, USA
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16
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Thuong NT, Asseline U. Modification of the 5' terminus of oligonucleotides for attachment of reporter and conjugate groups. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.2. [PMID: 18428849 DOI: 10.1002/0471142700.nc0402s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reporter and conjugate groups can be added directly to the 5' terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5' modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step-by-step protocols for attachment of conjugate groups are given elsewhere in the series.
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Affiliation(s)
- N T Thuong
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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Tabatadze D, Zamecnik P, Yanachkov I, Wright G, Pierson K, Zhang S, Bogdanov A, Metelev V. A novel thymidine phosphoramidite synthon for incorporation of internucleoside phosphate linkers during automated oligodeoxynucleotide synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:157-72. [PMID: 18205070 DOI: 10.1080/15257770701795938] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A novel thymidine phosphoramidite synthon was synthesized and successfully used for incorporation of primary amino groups, attached through a triethylene glycol linker to the internucleoside phosphates, at desired locations during automated oligodeoxynucleotide synthesis. The synthesized amino-linker bearing oligonucleotides are stable under deprotection conditions and exhibit Watson-Crick base-pairing properties. Covalent labeling of oligonucleotides with carbocyanine near-infrared fluorochromes resulted in 2.5 times higher labeling yields when compared with oligonucleotides containing base-attached aminolinkers. We anticipate that the developed synthetic approach will be useful for nucleotide sequence-specific attachment of single or multiple ligands or reporter molecules.
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Affiliation(s)
- David Tabatadze
- Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
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Heyde M, Claeyssens M, Schacht EH. Interaction between Proteins and Polyphosphazene Derivatives Having a Galactose Moiety. Biomacromolecules 2008; 9:672-7. [DOI: 10.1021/bm7010278] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mieke Heyde
- Polymer Chemistry & Biomaterials Research Group, Ghent University, Krijgslaan 281, S4-bis, 9000 Ghent, Belgium, and Department of Biochemistry, Physiology and Microbiology, Gent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Marc Claeyssens
- Polymer Chemistry & Biomaterials Research Group, Ghent University, Krijgslaan 281, S4-bis, 9000 Ghent, Belgium, and Department of Biochemistry, Physiology and Microbiology, Gent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Etienne H. Schacht
- Polymer Chemistry & Biomaterials Research Group, Ghent University, Krijgslaan 281, S4-bis, 9000 Ghent, Belgium, and Department of Biochemistry, Physiology and Microbiology, Gent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Construction of oligonucleotide microarrays (biochip) using heterobifunctional reagents. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2007. [PMID: 17984518 DOI: 10.1007/978-1-59745-303-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
A number of hetero- and homobifunctional reagents have been reported to immobilize biomolecules on a variety of supports. However, efforts are on to search for a method, which is relatively simple, involving minimum of steps, cost effective, easy to reproduce, and that produces stable oligonucleotide arrays. Two new reagents, viz., [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], and [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide] have been designed considering the above points. These reagents contain different functional groups at their two ends. In [N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine], one end (triethoxysilyl) is capable of binding to the virgin glass surface and the other one consists of trifluoroethanesulfonate (tresyl) function specific toward aminoalkyl and mercaptoalkyl functionalities, which are easy to introduce at the 3'- or 5'-end of oligonucleotides. Likewise, in [N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide], one end consists of photoactivatable moiety (anthraquinone) capable of reacting to a C-H containing surface and the tresyl function at the other end reacts specifically with aminoalkyl and mercaptoalkyl functionalities in modified oligonucleotides. These reagents have successfully been utilized to construct a number of oligonucleotide arrays and subsequently used for the detection of mismatches.
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Komatsu Y, Kojima N, Sugino M, Mikami A, Nonaka K, Fujinawa Y, Sugimoto T, Sato K, Matsubara K, Ohtsuka E. Novel amino linkers enabling efficient labeling and convenient purification of amino-modified oligonucleotides. Bioorg Med Chem 2007; 16:941-9. [PMID: 17950606 DOI: 10.1016/j.bmc.2007.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 10/01/2007] [Accepted: 10/04/2007] [Indexed: 11/17/2022]
Abstract
We developed new amino linker reagents for an oligonucleotide (ONT) terminus. These reagents consist of an aminoethyl carbamate main linkage and a side-chain residue, which was a naphthylmethoxymethyl, methoxymethyl, or methyl group or a hydrogen atom. The primary amine was protected with a monomethoxytrityl (MMT) group. The chemical properties of ONTs containing these amino-modifications were investigated. The MMT group of these amino-modifications could be quite rapidly removed from the amine under very mild acidic conditions, which are not strong enough for the deprotection of a conventional aliphatic amine. This significant feature enabled the amino-modified ONTs to be conveniently purified with a reverse phase column. Furthermore, the amino-modifications efficiently reacted to active esters, as compared with other amino-modifications. We also found that the pK(a) values of the amino-modifications were lower than that of the aliphatic amine. All of the experimental results showed that these chemical properties are closely related to their structures. We report here the chemical properties and the availability of the new amino linker reagents.
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Affiliation(s)
- Yasuo Komatsu
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science & Technology (AIST Hokkaido), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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22
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Uehara H, Kunitomi Y, Ikai A, Osada T. mRNA detection of individual cells with the single cell nanoprobe method compared with in situ hybridization. J Nanobiotechnology 2007; 5:7. [PMID: 17925043 PMCID: PMC2148050 DOI: 10.1186/1477-3155-5-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 10/10/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The localization of specific mRNA generates cell polarity by controlling the translation sites of specific proteins. Although most of these events depend on differences in gene expression, no method is available to examine time dependent gene expression of individual living cells. In situ hybridization (ISH) is a powerful and useful method for detecting the localization of mRNAs, but it does not allow a time dependent analysis of mRNA expression in single living cells because the cells have to be fixed for mRNA detection. To overcome these issues, the extraction of biomolecules such as mRNAs, proteins, and lipids from living cells should be performed without severe damage to the cells. In previous studies, we have reported a single cell nanoprobe (SCN) method to examine gene expression of individual living cells using atomic force microscopy (AFM) without killing the cells. RESULTS In order to evaluate the SCN method, we compared the SCN method with in situ hybridization (ISH). First, we examined spatial beta-actin mRNA expression in single living cells with the SCN method, and then the same cells were subjected to ISH for beta-actin mRNA. In the SCN method, quantity of beta-actin mRNA were analysed by quantitative PCR, and in ISH we used intensity of ISH as a parameter of concentration of beta-actin mRNA. We showed that intensity of ISH is higher; quantity of beta-actin mRNA detected by the SCN method increased more. CONCLUSION In this study, we compare the SCN method with the ISH. We examined beta-actin mRNA expression in single cells using both methods. We picked up beta-actin mRNA from several loci of a single living cell using an AFM nanoprobe, and identical cells were subjected to ISH. The results showed a good correlation between the SCN method and ISH. The SCN method is suitable and reliable to examine mRNAs at medium or higher expression level.
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Affiliation(s)
- Hironori Uehara
- Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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23
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Smith EE, McClean JN, Cooke LA, Duprey JL, McCourt M, Fabani MM, Tucker JH, Vyle JS. A novel structural class of photoswitchable oligonucleotide. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cocuzza AJ, Zagursky RJ. A Simple Preparation of 5′-Biotinylated Oligonucleotides and Their use as Primers in Dideoxy-Sequencing of DNA. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Anthony J. Cocuzza
- a Central Research and Development Department, E. I. Du Pont de Nemours and Company , Wilmington , DE , 19880-0328
| | - Robert J. Zagursky
- a Central Research and Development Department, E. I. Du Pont de Nemours and Company , Wilmington , DE , 19880-0328
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25
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Teoule R, Bazins H, Fouqué B, Roget A, Sauvaigo S. Nucleic Acids Probes in Diagnostic. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Robert Teoule
- a Département de Recherche Fondamentale, Laboratoires de Chimie , BP 85X, 38041 , Grenoble , FRANCE
| | - Hervé Bazins
- b CIS bio international, Laboratoire des Sondes Moléculaires Centre d'Etudes Nucléaires , BP 85X, 38041 , Grenoble , FRANCE
| | - Brigitte Fouqué
- b CIS bio international, Laboratoire des Sondes Moléculaires Centre d'Etudes Nucléaires , BP 85X, 38041 , Grenoble , FRANCE
| | - André Roget
- b CIS bio international, Laboratoire des Sondes Moléculaires Centre d'Etudes Nucléaires , BP 85X, 38041 , Grenoble , FRANCE
| | - Sylvie Sauvaigo
- b CIS bio international, Laboratoire des Sondes Moléculaires Centre d'Etudes Nucléaires , BP 85X, 38041 , Grenoble , FRANCE
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26
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Seliger H, Fröhlich A, Montenarh M, Ortigao JFR, Rösch H. Oligonucleotide Analogues with Terminal 3′-3′- and 5′-5′-Internucleotidic Linkages as Antisense Inhibitors of Viral Gene Expression. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- H. Seliger
- a Univ. Ulm, Sektion Polymere , Albert-Einstein-Allee 11, D-7900 , Ulm , Fed. Rep. of Germany
| | - A. Fröhlich
- a Univ. Ulm, Sektion Polymere , Albert-Einstein-Allee 11, D-7900 , Ulm , Fed. Rep. of Germany
| | - M. Montenarh
- b Abteilung Biochemie , Albert-Einstein-Allee 11, D-7900 , Ulm , Fed. Rep. of Germany
| | - J. F. Ramalho Ortigao
- a Univ. Ulm, Sektion Polymere , Albert-Einstein-Allee 11, D-7900 , Ulm , Fed. Rep. of Germany
| | - H. Rösch
- a Univ. Ulm, Sektion Polymere , Albert-Einstein-Allee 11, D-7900 , Ulm , Fed. Rep. of Germany
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27
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Vos MJD, Cravador A, Lenders JP, Houard S, Bollen A. Solid Phase Non Isotopic Labelling of Oligodeoxynucleotides Using 5′- Protected Aminoalkyl Phosphoramidites: Application to the Specific Detection of Human Papilloma Virus Dna. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319008045137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Kojima N, Sugino M, Mikami A, Nonaka K, Fujinawa Y, Muto I, Matsubara K, Ohtsuka E, Komatsu Y. Enhanced reactivity of amino-modified oligonucleotides by insertion of aromatic residue. Bioorg Med Chem Lett 2006; 16:5118-21. [PMID: 16876408 DOI: 10.1016/j.bmcl.2006.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 06/28/2006] [Accepted: 07/11/2006] [Indexed: 11/18/2022]
Abstract
We developed novel amino-modifying reagents, of which an amino group was connected with an aromatic residue by aliphatic linker. It was proved that the insertion of the aromatic residue could increase the reactivity of the amino group on oligonucleotides in comparison with conventional amino-modification.
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Affiliation(s)
- Naoshi Kojima
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, AIST, 2-17-2-1 Tsukisamu-Higashi, Sapporo 062-8517, Japan
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29
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Timchenko MA, Rybalkina EY, Lomakin AY, Evlakov KI, Serdyuk IN, Ivanovskaya MG. Modified DNA fragments specifically and irreversibly bind transcription factor NF-kappaB in lysates of human tumor cells. BIOCHEMISTRY (MOSCOW) 2006; 71:454-60. [PMID: 16615867 DOI: 10.1134/s0006297906040158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Covalent binding of a synthetic DNA fragment with eukaryotic transcription factor NF-kappaB has been studied in lysates of human colon carcinoma HCT-116 cells. For binding we used 32P-labeled 17/19 bp nucleotide DNA duplex containing an NF-kappaB recognition site (kappaB-site) in which one of internucleotide phosphate groups was replaced by a chemically active trisubstituted pyrophosphate group. Using gel electrophoresis under denaturing conditions (Laemmli electrophoresis) followed by immunoblotting revealed selective irreversible binding of 32P-labeled DNA duplex with NF-kappaB in lysates of tumor cells in the presence of other cell components. Experiment on delivery of this DNA duplex containing rhodamine at 3 -end of the modified chain in an intact cell revealed that rhodamine-labeled DNA penetrated through the plasma membrane of tumor cells without any additional delivery systems. Using fluorescent microscopy, we found that the rhodamine-labeled DNA is initially localized in the cytoplasm. Confocal laser scanning microscopy revealed that subsequent treatment of the cells with TNF-alpha promoted partial translocation of the DNA reagent into the nucleus.
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Affiliation(s)
- M A Timchenko
- Belozersky Institute of Physico-Chemical Biology and Faculty of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia.
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30
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Miduturu CV, Silverman SK. Synthesis and Application of a 5‘-Aldehyde Phosphoramidite for Covalent Attachment of DNA to Biomolecules. J Org Chem 2006; 71:5774-7. [PMID: 16839163 DOI: 10.1021/jo060723m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We recently reported the use of covalently attached DNA as a structural constraint for rational control of macromolecular conformation. Reductive amination was employed to attach each strand of the duplex DNA constraint to RNA, utilizing an aldehyde tethered to the 5'-terminus of the DNA. Here we describe the synthesis of a thymidine phosphoramidite that has the 5'-tethered aldehyde masked as a 1,2-diol. We also describe optimized reductive amination conditions for linking 5'-aldehyde-DNA with 2'-amino-2'-deoxy-RNA. These procedures should be generally applicable for attaching DNA to biomolecules.
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Affiliation(s)
- Chandrasekhar V Miduturu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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31
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Guiot E, Carayon K, Delelis O, Simon F, Tauc P, Zubin E, Gottikh M, Mouscadet JF, Brochon JC, Deprez E. Relationship between the oligomeric status of HIV-1 integrase on DNA and enzymatic activity. J Biol Chem 2006; 281:22707-19. [PMID: 16774912 DOI: 10.1074/jbc.m602198200] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The 3'-processing of the extremities of viral DNA is the first of two reactions catalyzed by HIV-1 integrase (IN). High order IN multimers (tetramers) are required for complete integration, but it remains unclear which oligomer is responsible for the 3'-processing reaction. Moreover, IN tends to aggregate, and it is unknown whether the polymerization or aggregation of this enzyme on DNA is detrimental or beneficial for activity. We have developed a fluorescence assay based on anisotropy for monitoring release of the terminal dinucleotide product in real-time. Because the initial anisotropy value obtained after DNA binding and before catalysis depends on the fractional saturation of DNA sites and the size of IN.DNA complexes, this approach can be used to study the relationship between activity and binding/multimerization parameters in the same assay. By increasing the IN:DNA ratio, we found that the anisotropy increased but the 3'-processing activity displayed a characteristic bell-shaped behavior. The anisotropy values obtained in the first phase were predictive of subsequent activity and accounted for the number of complexes. Interestingly, activity peaked and then decreased in the second phase, whereas anisotropy continued to increase. Time-resolved fluorescence anisotropy studies showed that the most competent form for catalysis corresponds to a dimer bound to one viral DNA end, whereas higher order complexes such as aggregates predominate during the second phase when activity drops off. We conclude that a single IN dimer at each extremity of viral DNA molecules is required for 3'-processing, with a dimer of dimers responsible for the subsequent full integration.
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Affiliation(s)
- Elvire Guiot
- Laboratoire de Biotechnologie et Pharmacologie Genetique Appliquee, CNRS, UMR8113, Ecole Normale Supérieure de Cachan, 61 av du Président Wilson, 94235 Cachan, France
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32
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Mahajan S, Patnaik S, Kumar P, Gandhi RP, Gupta KC. A new synthetic protocol for labeled oligonucleotides, using a chemically cleavable universal linker. Bioorg Med Chem 2006; 14:4302-9. [PMID: 16495059 DOI: 10.1016/j.bmc.2006.01.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 01/21/2006] [Accepted: 01/23/2006] [Indexed: 10/25/2022]
Abstract
A two-step general method for labeling of synthetic oligonucleotides is described. The protocol employs a cleavable universal linker, 5'-O-(4,4'-dimethoxytrityl)-3'-O-benzoyl-2'-O-(2-cyanoethyl-N,N-diisopropyl)-uridine phosphoramidite, to effect coupling to polymer-bound oligonucleotide chains. Sequentially, coupling with commercially available phosphoramidite reagent of an appropriate label (Biotin, HEX etc.) in an automated DNA synthesizer is carried out. The labeled oligomers, obtained after cleavage and deprotection reactions, are analyzed on RP-HPLC. A distinctive feature of this protocol is the recovery of free oligomers from their labeled analogs under mild conditions. The oligomers obtained are comparable to the corresponding standard oligonucleotides (HPLC).
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Affiliation(s)
- Shweta Mahajan
- Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India
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33
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Valeeva Y, Dorodnykh T, Alexandrova N, Zubin E, Kachalova A, Volkov E, Gottikh M, Melik-Nubarov N. Block copolymers of Pluronics and poly-(2-dimethylamino+ethyl methacrylate) for delivery of oligonucleotides into tumor cells. J Drug Deliv Sci Technol 2006. [DOI: 10.1016/s1773-2247(06)50046-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Engels J, Uhlmann E. Gene synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 37:73-127. [PMID: 3140610 DOI: 10.1007/bfb0009178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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35
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Bannwarth W, Schmidt D, Stallard RL, Hornung C, Knorr R, Müller F. Bathophenanthroline-ruthenium(II) complexes as non-radioactive labels for oligonucleotides which can be measured by time-resolved fluorescence techniques. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19880710826] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Morocho AM, Karamyshev VN, Polushin NN. Stability, vigor, and inherent versatility of novel amino linker and spacer phosphoramidites. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1407-9. [PMID: 14565430 DOI: 10.1081/ncn-120022997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Novel amino linker and spacer phosphoramidites were synthesized from methoxyoxalamido (MOX) percursors possessing a secondary hydroxyl, which when phosphitylated endowed stability to the corresponding phosphoramidites. The synthetic strategy is robust, and the chemistry is reactive towards a variety of primary aliphatic diamines and amino alcohols to produce distinctly unique phosphoramidites. The selection of building blocks determines the length and physico-chemical properties of the phosphoramidite tethering arms, and the synthesis can be specifically tailored to suit individual requirement.
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Affiliation(s)
- A M Morocho
- Fidelity Systems, Inc., Gaithersburg, Maryland 20879, USA
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37
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Femino AM, Fogarty K, Lifshitz LM, Carrington W, Singer RH. Visualization of single molecules of mRNA in situ. Methods Enzymol 2003; 361:245-304. [PMID: 12624916 DOI: 10.1016/s0076-6879(03)61015-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea M Femino
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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38
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Augood SJ, McGowan EM, Finsen BR, Heppelmann B, Emson PC. Non-radioactive in situ hybridization using alkaline phosphatase-labelled oligonucleotides. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2003; 47:173-201. [PMID: 12198799 DOI: 10.1016/s0074-7742(02)47060-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Affiliation(s)
- S J Augood
- Massachusetts General Hospital, Charlestown, MA 02129, USA
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39
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Fang S, Bergstrom DE. Fluoride-cleavable biotinylation phosphoramidite for 5'-end-labeling and affinity purification of synthetic oligonucleotides. Nucleic Acids Res 2003; 31:708-15. [PMID: 12527780 PMCID: PMC140496 DOI: 10.1093/nar/gkg130] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Revised: 11/01/2002] [Accepted: 11/01/2002] [Indexed: 11/13/2022] Open
Abstract
A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be completely stable under certain post-synthetic DNA cleavage/deprotection conditions [0.05 M K(2)CO(3) in MeOH, room temperature, 24 h and MeNH(2) (approximately 40%)/NH(4)OH (approximately 29%), 1:1 v/v, 65 degrees C, 30 min] while it can be readily broken by fluoride ion, releasing unmodified DNA. To demonstrate the use of this DNA biotinylation method, we applied this method in affinity purification of synthetic DNA. As revealed by HPLC analysis, biotinylated full-length DNA can be efficiently attached to NeutrAvidin coated microspheres, and failure sequences can be readily removed. Subsequent treatment of the microspheres with pyridine/HF released high quality full-length unmodified DNA in good yield.
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Affiliation(s)
- Shiyue Fang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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40
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van Gijlswijk RPM, Talman EG, Peekel I, Bloem J, van Velzen MA, Heetebrij RJ, Tanke HJ. Use of Horseradish Peroxidase- and Fluorescein-modified Cisplatin Derivatives for Simultaneous Labeling of Nucleic Acids and Proteins. Clin Chem 2002. [DOI: 10.1093/clinchem/48.8.1352] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background: Microarray platforms will change immunochemical and nucleic acid-based analysis of cell homogenates and body fluids compared with classic analyses. Microarrays use labeled target and immobilized probes, rather than fixed targets and labeled probes. We describe a method for simultaneous labeling of nucleic acids and proteins.
Methods: Horseradish peroxidase- and fluorescein-modified cisplatin derivatives were used for labeling of nucleic acids and proteins. These reagents, called the Universal Linkage System (ULS), bind to sulfur- and nitrogen-donor ligands present in amino acids and nucleotides. For automated screening of proteins and nucleic acids on microarrays, it is advantageous to label these biomolecules without pre- or postpurification procedures. The labeling of antibodies and nucleic acids in whole serum was therefore pursued.
Results: Immunoglobulins in nonpurified serum were labeled efficiently enough to be used for immunochemistry. To investigate whether protein-adapted labeling allowed nucleic acid labeling as well, 1 μg of plasmid DNA was added to 1 μL of serum. DNA and serum proteins were simultaneously labeled, and this labeled DNA could be used as a probe for direct fluorescence in situ hybridization.
Conclusion: ULS provides a direct labeling tool for the (simultaneous) modification of proteins and nucleic acids even in unpurified samples.
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Affiliation(s)
- Rob PM van Gijlswijk
- Kreatech Biotechnology, Vlierweg 20, 1032 LG Amsterdam, The Netherlands
- Laboratory for Cytochemistry and Cytometry, Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
| | - Eduard G Talman
- Kreatech Biotechnology, Vlierweg 20, 1032 LG Amsterdam, The Netherlands
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Inge Peekel
- Kreatech Biotechnology, Vlierweg 20, 1032 LG Amsterdam, The Netherlands
| | - Judith Bloem
- Kreatech Biotechnology, Vlierweg 20, 1032 LG Amsterdam, The Netherlands
| | | | - Rob J Heetebrij
- Kreatech Biotechnology, Vlierweg 20, 1032 LG Amsterdam, The Netherlands
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Hans J Tanke
- Laboratory for Cytochemistry and Cytometry, Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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41
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Kiyama H, Emson PC, Ruth J. Distribution of Tyrosine Hydroxylase mRNA in the Rat Central Nervous System Visualized by Alkaline Phosphatase in situ Hybridization Histochemistry. Eur J Neurosci 2002; 2:512-524. [PMID: 12106021 DOI: 10.1111/j.1460-9568.1990.tb00442.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The expression of tyrosine hydroxylase mRNA in the rat brain was examined using a novel alkaline phosphatase labelled antisense oligodeoxynucleotide probe. The alkaline phosphatase labelled probe revealed the presence of tyrosine hydroxylase mRNA in all the major cell groups and cell bodies previously described as containing catecholamine fluorescence or known to contain tyrosine hydroxylase immunoreactivity. Using standardized development protocols qualitative comparisons between the amount of mRNA signal in different adrenergic, noradrenergic or dopaminergic cell groups could be made. These studies showed that of the three known catecholaminergic cell types the level of tyrosine hydroxylase mRNA signal was high in the noradrenergic and dopaminergic cells, but much lower in the adrenergic cell groups. The sensitivity of this nonradioactive method of in situ hybridization is excellent and has considerable potential for studies of coexistence or coexpression of two mRNA signals for the localization of mRNA signals at the electron-microscope level.
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Affiliation(s)
- H. Kiyama
- MRC Group, AFRC Institute of Animal Physiology & Genetics Research, Babraham, Cambridge CB2 4AT, UK
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42
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An Optical Biosensor for Monitoring Antigen Recognition Based on Surface Plasmon Resonance Using Avidin-Biotin System. SENSORS 2001. [DOI: 10.3390/s10300091] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Hill KW, Taunton-Rigby J, Carter JD, Kropp E, Vagle K, Pieken W, McGee DP, Husar GM, Leuck M, Anziano DJ, Sebesta DP. Diels--Alder bioconjugation of diene-modified oligonucleotides. J Org Chem 2001; 66:5352-8. [PMID: 11485455 DOI: 10.1021/jo0100190] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an effort to offer complementary technology for covalent biomolecule modification (bioconjugation), we have developed a method that exploits the aqueous acceleration of Diels--Alder reactions for this purpose. Three different diene phosphoramidite reagents have been synthesized that enable diene modification of synthetic oligonucleotides prepared by the phosphoramidite method. Clean and efficient Diels--Alder cycloaddition of these diene oligonucleotides with maleimide dieneophiles was carried out, and the labeled oligonucleotide bioconjugates were characterized by HPLC and electrospray mass spectrometry. Dieneophile stoichiometry, temperature, and pH are all parameters that were shown to influence the efficiency of the process.
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Affiliation(s)
- K W Hill
- NeXstar Pharmaceuticals, 2860 Wilderness Place, Boulder, Colorado 80301, USA.
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44
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Sasaki M, Hayashi J, Fujii M, Koizumi K, Fujita H, Kobayashi M, Kawakubo Y, Ito A. Neutral liposome-mediated delivery process of fluorescein-modified oligonucleotides in cultured human keratinocytes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2001; 60:120-8. [PMID: 11470568 DOI: 10.1016/s1011-1344(01)00135-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a model of the intracellular delivery process in which fluorescein-labeled natural oligonucleotides (F-DNA) are transferred into the nuclei of cultured human keratinocytes. By encapsulation in neutral multilamellar lecithin liposomes, the F-DNA appeared to be protected against intracellular interactions with cellular materials and nuclease attacks in the cytoplasm during the process. The intracellular behavior of F-DNA and fluorescent phospholipid-labeled liposomes was observed by means of fluorescence analysis. Results showed that: F-DNA encapsulated in neutral multilamellar liposomes reached the cellular nuclei more efficiently than either free F-DNA, or F-DNA in unilamellar liposomes; the liposomal membranes appeared to be left in the cytoplasm. The reaction of F-DNA with complementary DNA was suggested by a rapid quenching of the fluorescence in the nucleus. In addition, the fluorescence decrease was evidently suppressed in the cytoplasm, indicating a protective effect of the neutral multilamellar liposomes against the interaction of F-DNA with cytoplasmic materials. The application of these findings to 'photo'-antisense studies has been discussed, where suppression of a gene expression is attempted by using oligonucleotide-attached fluorescein with the aid of a photo-induced covalent binding property.
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Affiliation(s)
- M Sasaki
- Research Institute of Science and Technology, Tokai University, 1117 Kitakaname, Hiratsuka, 259-1292, Kanagawa, Japan.
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45
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Husar GM, Anziano DJ, Leuck M, Sebesta DP. Covalent modification and surface immobilization of nucleic acids via the Diels-Alder bioconjugation method. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:559-66. [PMID: 11563073 DOI: 10.1081/ncn-100002332] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The importance of chemically modified and surface immobilized nucleic acids has inspired the development of a wide variety of complementary techniques for covalent oligonucleotide preparation and immobilization. We are developing technology based on the use of a Diels-Alder reaction for accomplishing the covalent modification of oligonucleotides. Reported herein is preliminary progress toward the establishment of robust reagents for introducing the reactive functionality, as well as studies employing the BIACORE system to demonstrate surface immobilization by the method.
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Affiliation(s)
- G M Husar
- Proligo, LLC, 2995 Wilderness Place, Suite 207, Boulder, Colorado 80301, USA
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46
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Ermolinsky BS, Mikhailov SN. Periodate oxidation in chemistry of nucleic acids: Dialdehyde derivatives of nucleosides, nucleotides, and oligonucleotides (Review). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02758613] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Politz JC, Singer RH. In situ reverse transcription for detection of hybridization between oligonucleotides and their intracellular targets. Methods 1999; 18:281-5. [PMID: 10454986 DOI: 10.1006/meth.1999.0785] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
It is often important to know that a phenotypic change caused by antisense treatment has occurred because the antisense molecule has specifically hybridized to its intracellular target, rather than by some nonspecific, indirect route. We describe here a method that can be used to detect hybridization of an antisense oligodeoxynucleotide to its intracellular target RNA and, furthermore, to identify the sites at which hybrids are located in situ. Oligodeoxynucleotides are first taken up by the live cell and then cells are fixed and subjected to an in situ reverse transcription reaction. The reverse transcription assay exploits the fact that only oligonucleotides that are hybridized to RNA will act as primers for reverse transcriptase and allow incorporation of labeled nucleotide into cDNA; unhybridized oligonucleotides will not prime reverse transcription. We illustrate this approach by comparing the levels of oligo(dT) hybridized to poly(A) RNA in cells that have taken up the oligo(dT) with and without cationic lipid in the medium.
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Affiliation(s)
- J C Politz
- Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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48
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Yamana K, Mitsui T, Nakano H. Synthesis and properties of oligonucleotide duplexes containing donor and acceptor fluorophores at 2′-positions. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00484-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Simonsson T, Sjöback R. DNA tetraplex formation studied with fluorescence resonance energy transfer. J Biol Chem 1999; 274:17379-83. [PMID: 10358100 DOI: 10.1074/jbc.274.24.17379] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It is emerging that DNA tetraplexes are pivotal for many major cellular processes, and techniques that assess their structure and nature to the point are under development. Here we show how the structural conversion of largely unstructured single-stranded DNA molecules into compact intrastrand DNA tetraplexes can be monitored by fluorescence resonance energy transfer. We recently reported that intrastrand tetraplex formation takes place in a nuclease hypersensitive element upstream of the human c-myc proto-oncogene. Despite the highly repetitive guanine-rich sequence of the hypersensitive element, fluorescence resonance energy transfer measurements indicate that only one well defined tetraplex structure forms therein. The proposed structure, which is specifically stabilized by potassium ions in vitro, has a core of three stacked guanine tetrads that is capped by two intrastrand A-T base pairs.
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Affiliation(s)
- T Simonsson
- Department of Biochemistry, Lundberg Institute, Chalmers University of Technology, Box 462, SE 405 30 Göteborg, Sweden.
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Sjöback R, Nygren J, Kubista M. Characterization of fluorescein-oligonucleotide conjugates and measurement of local electrostatic potential. Biopolymers 1998; 46:445-53. [PMID: 9838871 DOI: 10.1002/(sici)1097-0282(199812)46:7<445::aid-bip2>3.0.co;2-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The properties of fluorescein are substantially altered upon conjugation to nucleic acids, affecting not only the molar absorptivities and fluorescence quantum yields but also the protolytic equilibrium constant and fluorescence lifetimes. Around neutral pH, the fluorescein moiety is present as both mono- and dianion, and the pKa relating them is increased from 6.43 for free fluorescein to about 6.90 for fluorescein attached to both single- and double-stranded oligonucleotides of at least 12 bases/base pairs. This difference reflects the local electrostatic potential around the nucleic acid, which is calculated to -28 mV. The molar absorptivities and spectral responses of the conjugated fluorescein protolytic species are also determined, from which the concentrations of fluorescein-oligonucleotide conjugates can be calculated by assuming: epsilon 494 = 62000/[1 + 10-(pH-6.90)] + 12000/[1 + 10(pH-6.90)] (M-1 cm-1). The fluorescence quantum yield of the conjugates depends, in a complex way, on temperature, environment and oligonucleotide length, sequence and conformation, and must be determined for each experimental situation.
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Affiliation(s)
- R Sjöback
- Department of Biochemistry and Biophysics, Chalmers University of Technology, Göteborg, Sweden
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