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Delvaux NA, Mathew B, Rice KG. Fluorescent labeling of plasmid DNA for gene delivery: Implications of dye hydrophobicity on labeling efficiencies and nanoparticle size. Anal Biochem 2022; 644:113895. [PMID: 32783899 PMCID: PMC7870724 DOI: 10.1016/j.ab.2020.113895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022]
Abstract
Covalent fluorescent labels are important tools for monitoring the in vitro and in vivo localization of plasmid DNA nanoparticles, but must meet several criteria including high DNA labeling efficiencies and minimal impact on nanoparticle size. We developed a novel fluorescent labeling strategy utilizing an aryl azide photolabel conjugated to a short cationic peptide to label plasmid DNA with Cyanine 5 and sulfo-Cyanine 5. Using a simple camera flash apparatus, photolabel-peptide-dyes can be conjugated to DNA in minutes with preservation of DNA structure and minimal dye photobleaching. The addition of two anionic sulfonates to the Cyanine 5 core greatly improved labeling efficiencies from ~13 to ~53% and mitigated PEGylated polyacridine peptide-DNA nanoparticle size increases over a range of labeling densities. Comparison of our sulfo-Cyanine 5 peptide label to the Mirus Bio Label IT-Cy5 kit revealed that while both did not affect nanoparticle sizes appreciably, labeling efficiencies with our conjugate were higher, possibly due to the higher positive charge density on the peptide linker. The results from this work provide important considerations for choosing fluorophore tags to track DNA nanoparticles.
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Affiliation(s)
- Nathan A Delvaux
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 52242, Iowa City, IA, USA
| | - Basil Mathew
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 52242, Iowa City, IA, USA
| | - Kevin G Rice
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 52242, Iowa City, IA, USA.
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Leyva E, Platz MS, Loredo-Carrillo SE, Aguilar J. Fluoro Aryl Azides: Synthesis, Reactions and Applications. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200608132505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The complex photochemistry of aryl azides has fascinated scientists
for several decades. Spectroscopists have investigated the intermediates formed by
different analytical techniques. Theoretical chemists have explained the intrinsic interplay of
intermediates under different experimental conditions.
Objective & Method:
A complete understanding of the photochemistry of a given fluoro
aryl azide is a basic requisite for its use in chemistry. In this review, we will discuss the
synthesis of several fluoro substituted aryl azides and the reactions and intermediates generated
upon photolysis and thermolysis of these azides and some examples of their applications
in photoaffinity labeling and organic synthesis.
Conclusion:
In spite of the extensive research on the photochemistry of fluoro aryl azides, there are some areas
that remain to be investigated. The application of this reaction in the synthesis of novel heterocyclic compounds
has not been fully studied. Since fluorophenyl azides are known to undergo C-H and N-H insertion reactions,
they could be used to prepare new fluorinated molecules or in the biochemical process known as photoaffinity
labeling.
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Affiliation(s)
- Elisa Leyva
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
| | - Matthew S. Platz
- Department of Chemistry, University of Hawaii, Hilo, 200 West Kawili St. Hilo, HI 96720, United States
| | - Silvia E. Loredo-Carrillo
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
| | - Johana Aguilar
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Manuel Nava No. 6, San Luis Potosí, S.L.P., 78210, Mexico
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Leyva E, Leyva S, Moctezuma E, González-Balderas RM, de Loera D. Microwave-assisted synthesis of substituted fluorophenyl mono- and diazides by SNAr. A fast methodology to prepare photoaffinity labeling and crosslinking reagents. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gritsan NP. Study of photochemical transformations of organic azides by matrix isolation techniques and quantum chemistry. RUSSIAN CHEMICAL REVIEWS 2008. [DOI: 10.1070/rc2007v076n12abeh003702] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pandurangi RS, Karra SR, Kuntz RR, Volkert WA. Recent Trends in the Evaluation of Photochemical Insertion Characteristics of Heterobifunctional Perfluoroaryl Azide Chelating Agents: Biochemical Implications in Nuclear Medicine. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1997.tb08547.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gritsan NP, Platz MS. Kinetics, Spectroscopy, and Computational Chemistry of Arylnitrenes. Chem Rev 2006; 106:3844-67. [PMID: 16967923 DOI: 10.1021/cr040055+] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N P Gritsan
- Institute of Chemical Kinetics and Combustion and Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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Redman JE, Ghadiri MR. Synthesis of photoactive p-azidotetrafluorophenylalanine containing peptide by solid-phase Fmoc methodology. Org Lett 2002; 4:4467-9. [PMID: 12465914 DOI: 10.1021/ol026998f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] N-Fmoc-L-p-azidotetrafluorophenylalanine was prepared from achiral starting materials using an acetamidomalonate synthesis and enzymatic resolution. A photoactive peptide containing this fluorinated residue could be assembled using solid-phase Fmoc chemistry.
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Affiliation(s)
- James E Redman
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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Lin W, Li K, Doughty MB. Characterization of a binding site for template competitive inhibitors of HIV-1 reverse transcriptase using photolabeling derivatives. Bioorg Med Chem 2002; 10:4131-41. [PMID: 12413867 DOI: 10.1016/s0968-0896(02)00259-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Analogues of a novel class of template-competitive reverse transcriptase inhibitors (Li, K.; Lin, W.; Chong, K. H.; Moore, B. M.; Doughty, M. B. Bioorg. Med. Chem. 2002, 10, 507) were analyzed as photoprobes of HIV-1 reverse transcriptase (RT) heterodimer. The two photoprobes, 2-(4-azidophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 2 and the tetrafluoro analogue 2-(4-azido-2,3,5,6-tetrafluorophenacyl)thio-1,N(6)-etheno-2'-deoxyadenosine 5'-triphosphate 3, photodecomposed at 3500 A with half-lives of 4.0 and 2.5 min, respectively. Analysis of the photoproducts of 2m demonstrated that the etheno group is stable but the azido decomposes primarily to the 2-(S-[3H-diazepinon-4-yl]thio)-1,N(6)-etheno-dAMP. Photolysis of both 2 and 3 with RT resulted in a time-dependent loss of activity, with maximum inactivation of 83 and 60%, respectively. Both 2 and 3 showed concentration-dependent photoinactivation of RT in the concentration range from 0 to 100 microM, with EC(50)s of 20 and 25 microM and maximum inactivation of 80 and 60%, respectively. Both the time and concentration dependent photoinactivation were strongly protected by template-primer, but only poorly inhibited by even high concentrations of TTP. Radiolabeled analogues [beta,gamma-(32)P]-2 and [beta,gamma-(32)P]-3 photoincorporated into the p66 subunit, an incorporation also protected by template primer. Identification of the site of incorporation was problematic for both photoprobes, but evidence presented is consistent with labeling sites for the phenacyl side chains of both 2 and 3 in the template grip. Nevertheless, the photoinactivation and incorporation data are consistent with our earlier conclusions from the kinetic data that these inhibitors are specific for the free form of RT in competition with template/primer, and thus represent a novel class of inhibitors.
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Affiliation(s)
- Weiying Lin
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, KS 66045, USA
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Gritsan NP, Gudmundsdóttir AD, Tigelaar D, Zhu Z, Karney WL, Hadad CM, Platz MS. A laser flash photolysis and quantum chemical study of the fluorinated derivatives of singlet phenylnitrene. J Am Chem Soc 2001; 123:1951-62. [PMID: 11456816 DOI: 10.1021/ja9944305] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laser flash photolysis (LFP, Nd:YAG laser, 35 ps, 266 nm, 10 mJ or KrF excimer laser, 10 ns, 249 nm, 50 mJ) of 2-fluoro, 4-fluoro, 3,5-difluoro, 2,6-difluoro, and 2,3,4,5,6-pentafluorophenyl azides produces the corresponding singlet nitrenes. The singlet nitrenes were detected by transient absorption spectroscopy, and their spectra are characterized by sharp absorption bands with maxima in the range of 300-365 nm. The kinetics of their decay were analyzed as a function of temperature to yield observed decay rate constants, k(OBS). The observed rate constant in inert solvents is the sum of k(R) + k(ISC) where k(R) is the absolute rate constant of rearrangement of singlet nitrene to an azirine and k(ISC) is the absolute rate constant of nitrene intersystem crossing (ISC). Values of k(R) and k(ISC) were deduced after assuming that k(ISC) is independent of temperature. Barriers to cyclization of 4-fluoro-, 3,5-difluoro-, 2-fluoro-, 2,6-difluoro-, and 2,3,4,5,6-pentafluorophenylnitrene in inert solvents are 5.3 +/- 0.3, 5.5 +/- 0.3, 6.7 +/- 0.3, 8.0 +/- 1.5, and 8.8 +/- 0.4 kcal/mol, respectively. The barrier to cyclization of parent singlet phenylnitrene is 5.6 +/- 0.3 kcal/mol. All of these values are in good quantitative agreement with CASPT2 calculations of the relative barrier heights for the conversion of fluoro-substituted singlet aryl nitrenes to benzazirines (Karney, W. L. and Borden, W. T. J. Am. Chem. Soc. 1997, 119, 3347). A single ortho-fluorine substituent exerts a small but significant bystander effect on remote cyclization that is not steric in origin. The influence of two ortho-fluorine substituents on the cyclization is pronounced. In the case of the singlet 2-fluorophenylnitrene system, evidence is presented that the benzazirine is an intermediate and that the corresponding singlet nitrene and benzazirine interconvert. Ab initio calculations at different levels of theory on a series of benzazirines, their isomeric ketenimines, and the transition states converting the benzazirines to ketenimines were performed. The computational results are in good qualitative and quantitative agreement with the experimental findings.
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Affiliation(s)
- N P Gritsan
- Institute of Chemical Kinetics and Combustion and Novosibirsk State University, 630090 Novosibirsk, Russia
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Grisant NP, Platz MS. Kinetics and spectroscopy of substituted phenylnitrenes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2001. [DOI: 10.1016/s0065-3160(01)36006-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Michalak J, Zhai HB, Platz MS. The Photochemistry of Various Para-Substituted Tetrafluorophenyl Azides in Acidic Media and the Formation of Nitrenium Ions. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961100n] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacek Michalak
- Department of Chemistry, The Ohio State University, 120 W. 18th Avenue, Columbus, Ohio 43210
| | - Hong Bin Zhai
- Department of Chemistry, The Ohio State University, 120 W. 18th Avenue, Columbus, Ohio 43210
| | - Matthew S. Platz
- Department of Chemistry, The Ohio State University, 120 W. 18th Avenue, Columbus, Ohio 43210
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Pandurangl RS, Karra SR, Kuntz RR, Volkert WA. Preservation of immunoreactivity in the photolabeling of the B72.3 human antibody. Photochem Photobiol 1996; 64:100-5. [PMID: 8787004 DOI: 10.1111/j.1751-1097.1996.tb02427.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A versatile photochemical method of labeling human antibodies is described. Labeling is achieved by photolyzing 4-azido-2,3,5,6-tetrafluoro-14C-methylbenzoate and the B72.3 human antibody in a buffer at physiological pH. The photochemically produced nitrene presumably inserts into bonds in the hydrophobic part of the antibody resulting in > 75% attachment of the photoprobe. An immunoassay of B72.3 with mucin (B72.3 antigen) reveals > 97% retention of immunoreactivity and suggests that photochemical labeling is a viable alternative for the conjugation of biomolecules.
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Affiliation(s)
- R S Pandurangl
- Department of Chemistry, University of Missouri, Columbia 65211, USA
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Cai SX, Keana JFW. Design and synthesis of trifunctional perfluorophenyl azide-based photoactivatable reagents. SYNTHETIC COMMUN 1996. [DOI: 10.1080/00397919608086757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kotzyba-Hibert F, Kapfer I, Goeldner M. Neue Entwicklungen bei der Photoaffinitätsmarkierung. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951071204] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pandurangi RS, Katti KV, Barnes CL, Volkert WA, Kuntz RR. High yields of nitrene insertion into unactivated C–H bonds. First example of X-ray crystallographic and19F NMR analysis of the photochemically produced C–H inserted adduct. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/c39940001841] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dwyer L, Crocker P, Watt D, Vanaman T. The effects of calcium site occupancy and reagent length on reactivity of calmodulin lysyl residues with heterobifunctional aryl azides. Mapping interaction domains with specific calmodulin photoprobe derivatives. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41716-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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