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Kanamori T, Kaneko S, Hamamoto K, Yuasa H. Mapping the diffusion pattern of 1O 2 along DNA duplex by guanine photooxidation with an appended biphenyl photosensitizer. Sci Rep 2023; 13:288. [PMID: 36690669 PMCID: PMC9871026 DOI: 10.1038/s41598-023-27526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
To realize nucleic acid-targeting photodynamic therapy, a photosensitizer should be attached at the optimal position on a complementary oligonucleotide, where a guanine photooxidation is maximized. Here we show the photooxidation of 22 DNA duplexes with varied lengths between a 1O2-generating biphenyl photosensitizer attached at a midchain thymine in a strand and the single guanine reactant in the other strand. The best photooxidation efficiencies are achieved at 9, 10, and 21 base intervals, which coincides with the pitch of 10.5 base pairs per turn in a DNA duplex. The low efficiencies for near and far guanines are due to quenching of the biphenyl by guanine and dilution of 1O2 by diffusion, respectively. The 1O2-diffusion mapping along DNA duplex provides clues to the development of efficient and selective photosensitizer agents for nucleic acid-targeting photodynamic therapy, as well as an experimental demonstration of diffusion of a particle along cylindrical surface in molecular level.
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Affiliation(s)
- Takashi Kanamori
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan.
| | - Shota Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan
| | - Koji Hamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan
| | - Hideya Yuasa
- School of Life Science and Technology, Tokyo Institute of Technology, J2-10 4259, Nagatsuta, Midoriku, Yokohama, 226-8501, Japan.
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2
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Chibly AM, Aure MH, Patel VN, Hoffman MP. Salivary Gland Function, Development and Regeneration. Physiol Rev 2022; 102:1495-1552. [PMID: 35343828 DOI: 10.1152/physrev.00015.2021] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Salivary glands produce and secrete saliva, which is essential for maintaining oral health and overall health. Understanding both the unique structure and physiological function of salivary glands, as well as how they are affected by disease and injury will direct the development of therapy to repair and regenerate them. Significant recent advances, particularly in the OMICS field, increase our understanding of how salivary glands develop at the cellular, molecular and genetic levels; the signaling pathways involved, the dynamics of progenitor cell lineages in development, homeostasis and regeneration and the role of the extracellular matrix microenvironment. These provide a template for cell and gene therapies as well as bioengineering approaches to repair or regenerate salivary function.
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Affiliation(s)
- Alejandro Martinez Chibly
- Matrix and Morphogenesis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Marit H Aure
- Matrix and Morphogenesis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Vaishali N Patel
- Matrix and Morphogenesis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Matthew Philip Hoffman
- Matrix and Morphogenesis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
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3
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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4
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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5
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Ahoulou EO, Drinkard KK, Basnet K, St. Lorenz A, Taratula O, Henary M, Grant KB. DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes. Molecules 2020; 25:molecules25122926. [PMID: 32630496 PMCID: PMC7355653 DOI: 10.3390/molecules25122926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.
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Affiliation(s)
- Effibe O. Ahoulou
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kaitlyn K. Drinkard
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kanchan Basnet
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Anna St. Lorenz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Maged Henary
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
| | - Kathryn B. Grant
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
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6
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Tikhomirova AA, Tcyrulnikov NA, Wilson RM. Aerobic Oxidation of in Situ Generated Cyanine Dyes Leading to DNA Damage. Org Lett 2019; 21:1449-1452. [PMID: 30763104 DOI: 10.1021/acs.orglett.9b00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA damage induced by noncatalytic aerobic oxidation of pyridinocyanine dyes is described. The dyes are generated in situ during spontaneous oxidations of tetrakis- and bis( N-methylpyridin-4-ium)alkane salts. The mechanism of aerobic oxidation of the latter compound is proposed, and a rare direct catalyst-free transition from saturated alkane to a gem-diol is demonstrated. Thermal DNA oxidation by cyanine dyes has potential in ROS-based cancer treatment and biomedical research.
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Affiliation(s)
- Anastasiia A Tikhomirova
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Nikolai A Tcyrulnikov
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - R Marshall Wilson
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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7
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Yuen LH, Franzini RM. Stability of Oligonucleotide-Small Molecule Conjugates to DNA-Deprotection Conditions. Bioconjug Chem 2017; 28:1076-1083. [PMID: 28233987 DOI: 10.1021/acs.bioconjchem.7b00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oligonucleotide conjugates of small molecules are widely used in chemical biology and have found increasing interest in the context of DNA-encoded chemical libraries for drug discovery. Attachment of molecules to DNA bound to the solid support is an attractive small-molecule conjugation method that permits the use of organic solvents, rigorous reaction conditions, and simple workup. However, the conjugated structures must be resistant to the harsh DNA deprotection/cleavage conditions and the stabilities of building blocks under various deprotection conditions are mostly unexplored. In the present study, we analyzed the stability of 131 structurally diverse fragments that contain amides and amide-like elements during DNA deprotection protocols. Structural features susceptible to decomposition in DNA deprotection conditions were identified and a protocol that enabled the synthesis of DNA conjugates with labile fragments on solid support was identified.
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Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
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9
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Shemesh Y, Yavin E. PNA-Rose Bengal Conjugates as Efficient DNA Photomodulators. Bioconjug Chem 2015; 26:1916-22. [PMID: 26263421 DOI: 10.1021/acs.bioconjchem.5b00406] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Selective photoinduced modulation of DNA may provide a powerful therapeutic tool allowing spatial and temporal control of the photochemical reaction. We have explored the photoreactivity of peptide nucleic acid (PNA) conjugates that were conjugated to a highly potent photosensitizer, Rose Bengal (RB). In addition, a short PEGylated peptide (K-PEG8-K) was conjugated to the C-terminus of the PNA to improve its water solubility. A short irradiation (visible light) of PNA conjugates with a synthetic DNA resulted in highly efficient photomodulation of the DNA as evidenced by polyacrylamide gel electrophoresis (PAGE). In addition, a PNA-RB conjugate replacing K-PEG8-K with four l-glutamic acids (E4) was found to be photoinactive. Irradiation of active PNA-RB conjugates with synthetic DNA in D20 augments the photoactivity; supporting the involvement of singlet oxygen. PAGE, HPLC, and MALDI-TOF analyses indicate that PNA-DNA photo-cross-linking is a significant pathway in the observed photoreactivity. Selective photo-cross-linking of such PNA-RB conjugates may be a novel approach to selective photodynamic therapy (sPDT) as such molecules would be sequence-specific, cell-permeable, and photoactivated in the visible region.
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Affiliation(s)
- Yossi Shemesh
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
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10
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11
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Tanaka M, Shigi N, Sumaoka J, Komiyama M. Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage. RSC Adv 2014. [DOI: 10.1039/c4ra13780a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugates of thiazole orange (TO) with a pseudo-complementary peptide nucleic acid (pcPNA) functioned as (i) fluorescent detector of specific DNA and (ii) site-selective photodamage inducer through generation of 1O2.
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Affiliation(s)
- Makiko Tanaka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
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12
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Oxidative cleavage of DNA by pentamethine carbocyanine dyes irradiated with long-wavelength visible light. Bioorg Med Chem Lett 2013; 24:214-9. [PMID: 24332091 DOI: 10.1016/j.bmcl.2013.11.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/26/2022]
Abstract
Here we report the synthesis of seven symmetrical carbocyanine dyes in which two nitrogen-substituted benz[e]indolium rings are joined by a pentamethine bridge that is meso-substituted with chlorine or bromine versus hydrogen. The heteroatom of benz[e]indolium is modified with a phenylpropyl, methyl, or cationic quaternary ammonium group. In reactions containing micro molar concentrations of halogenated dye, irradiation at 575, 588, 623, or 700nm produces good photocleavage of plasmid DNA. UV-visible spectra show that the carbocyanines are in their H-aggregated and monomeric forms. Scavenger experiments point to the involvement of singlet oxygen and hydroxyl radicals in DNA photocleavage.
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13
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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14
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Eick A, Riechert-Krause F, Weisz K. Binding and NMR structural studies on indoloquinoline-oligonucleotide conjugates targeting duplex DNA. Bioconjug Chem 2012; 23:1127-37. [PMID: 22571630 DOI: 10.1021/bc200582u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An 11-phenyl-indolo[3,2-b]quinoline (PIQ) was tethered through an aminoalkyl linker to the 5'-end of four pyrimidine oligonucleotides with T/C scrambled sequences at their two 5'-terminal positions. Binding to different double-helical DNA targets formed parallel triple helices with a PIQ-mediated stabilization that strongly depends on pH and the terminal base triad at the 5'-triplex-duplex junction. The most effective stabilization was observed with a TAT triplet at the 5'-junction under low pH conditions, pointing to a protonated ligand with a high triplex binding affinity and unfavorable charge repulsions in the case of a terminal C(+)GC triplet at the junction. The latter preference of the PIQ ligand for TAT over CGC is alleviated yet still preserved at higher pH. Intercalation of PIQ at the 5'-triplex-duplex junction as suggested by the triplex melting experiments was confirmed by homonuclear and heteronuclear NMR structural studies on a specifically isotope-labeled triplex. The NMR analysis revealed two coexisting species that only differ by a 180° rotation of the indoloquinoline within the intercalation pocket. NOE-derived molecular models indicate extensive stacking interactions of the indoloquinoline moiety with the TAT base triplet and CG base pair at the junction and a phenyl substituent that is positioned in the major groove and oriented almost perpendicular to the plane of the indoloquinoline.
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Affiliation(s)
- Andrea Eick
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Kolevzon N, Yavin E. Site-Specific DNA Photocleavage and Photomodulation by Oligonucleotide Conjugates. Oligonucleotides 2010; 20:263-75. [DOI: 10.1089/oli.2010.0247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Netanel Kolevzon
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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