1
|
Amin SM, Islam T, Price NE, Wallace A, Guo X, Gomina A, Heidari M, Johnson KM, Lewis CD, Yang Z, Gates KS. Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA. ACS OMEGA 2022; 7:36888-36901. [PMID: 36278095 PMCID: PMC9583646 DOI: 10.1021/acsomega.2c05736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.
Collapse
Affiliation(s)
- Saosan
Binth Md. Amin
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Amanda Wallace
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Xu Guo
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Anuoluwapo Gomina
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Marjan Heidari
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Calvin D. Lewis
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| |
Collapse
|
2
|
Catalano MJ, Liu S, Andersen N, Yang Z, Johnson KM, Price NE, Wang Y, Gates KS. Chemical structure and properties of interstrand cross-links formed by reaction of guanine residues with abasic sites in duplex DNA. J Am Chem Soc 2015; 137:3933-45. [PMID: 25710271 DOI: 10.1021/jacs.5b00669] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A new type of interstrand cross-link resulting from the reaction of a DNA abasic site with a guanine residue on the opposing strand of the double helix was recently identified, but the chemical connectivity of the cross-link was not rigorously established. The work described here was designed to characterize the chemical structure and properties of dG-AP cross-links generated in duplex DNA. The approach involved characterization of the nucleoside cross-link "remnant" released by enzymatic digestion of DNA duplexes containing the dG-AP cross-link. We first carried out a chemical synthesis and complete spectroscopic structure determination of the putative cross-link remnant 9b composed of a 2-deoxyribose adduct attached to the exocyclic N(2)-amino group of dG. A reduced analogue of the cross-link remnant was also prepared (11b). Liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis revealed that the retention times and mass spectral properties of synthetic standards 9b and 11b matched those of the authentic cross-link remnants released by enzymatic digestion of duplexes containing the native and reduced dG-AP cross-link, respectively. These results establish the chemical connectivity of the dG-AP cross-link released from duplex DNA and provide a foundation for detection of this lesion in biological samples. The dG-AP cross-link in duplex DNA was remarkably stable, decomposing with a half-life of 22 days at pH 7 and 23 °C. The intrinsic chemical stability of the dG-AP cross-link suggests that this lesion in duplex DNA may have the power to block DNA-processing enzymes involved in transcription and replication.
Collapse
Affiliation(s)
| | - Shuo Liu
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Nisana Andersen
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | | | | | | | - Yinsheng Wang
- ‡Environmental Toxicology Graduate Program and Department of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | | |
Collapse
|
3
|
Tumir LM, Radić Stojković M, Piantanida I. Come-back of phenanthridine and phenanthridinium derivatives in the 21st century. Beilstein J Org Chem 2014; 10:2930-54. [PMID: 25550761 PMCID: PMC4273281 DOI: 10.3762/bjoc.10.312] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/21/2014] [Indexed: 12/23/2022] Open
Abstract
Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.
Collapse
Affiliation(s)
- Lidija-Marija Tumir
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| |
Collapse
|
4
|
Price N, Johnson KM, Wang J, Fekry MI, Wang Y, Gates KS. Interstrand DNA-DNA cross-link formation between adenine residues and abasic sites in duplex DNA. J Am Chem Soc 2014; 136:3483-90. [PMID: 24506784 PMCID: PMC3954461 DOI: 10.1021/ja410969x] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Indexed: 01/28/2023]
Abstract
The loss of a coding nucleobase from the structure of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating mixture of a cyclic hemiacetal and a ring-opened aldehyde. Aldehydes are electrophilic functional groups that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially reactive aldehyde as part of the internal structure of DNA. Here we report evidence that the aldehyde group of Ap sites in duplex DNA can form a covalent adduct with the N(6)-amino group of adenine residues on the opposing strand. The resulting interstrand DNA-DNA cross-link occurs at 5'-ApT/5'-AA sequences in remarkably high yields (15-70%) under physiologically relevant conditions. This naturally occurring DNA-templated reaction has the potential to generate cross-links in the genetic material of living cells.
Collapse
Affiliation(s)
- Nathan
E. Price
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Jin Wang
- Department
of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Mostafa I. Fekry
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California-Riverside, Riverside, California 92521-0403, United States
| | - Kent S. Gates
- Department of Chemistry and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| |
Collapse
|
5
|
Holzhauser C, Wagenknecht HA. DNA and RNA “Traffic Lights”: Synthetic Wavelength-Shifting Fluorescent Probes Based on Nucleic Acid Base Substitutes for Molecular Imaging. J Org Chem 2013; 78:7373-9. [DOI: 10.1021/jo4010102] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
| |
Collapse
|
6
|
Prunkl C, Pichlmaier M, Winter R, Kharlanov V, Rettig W, Wagenknecht HA. Optical, Redox, and DNA-Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA. Chemistry 2010; 16:3392-402. [DOI: 10.1002/chem.200902823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
7
|
Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
8
|
Prunkl C, Berndl S, Wanninger-Weiß C, Barbaric J, Wagenknecht HA. Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors. Phys Chem Chem Phys 2010; 12:32-43. [DOI: 10.1039/b914487k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
9
|
Siegmund K, Daublain P, Wang Q, Trifonov A, Fiebig T, Lewis FD. Structure and Photoinduced Electron Transfer in DNA Hairpin Conjugates Possessing a Tethered 5′-Pyrenecarboxamide. J Phys Chem B 2009; 113:16276-84. [DOI: 10.1021/jp907323d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Karsten Siegmund
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Pierre Daublain
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Qiang Wang
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Anton Trifonov
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Torsten Fiebig
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| | - Frederick D. Lewis
- Departments of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Boston College, Chestnut Hill, Massachusetts 02467
| |
Collapse
|
10
|
Barbaric J, Wanninger-Weiß C, Wagenknecht HA. Indole in DNA: Comparison of a Nucleosidic with a Non-Nucleosidic DNA Base Substitution. European J Org Chem 2009. [DOI: 10.1002/ejoc.200800863] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
11
|
Baumstark D, Wagenknecht HA. Fluorescent Hydrophobic Zippers inside Duplex DNA: Interstrand Stacking of Perylene-3,4:9,10-tetracarboxylic Acid Bisimides as Artificial DNA Base Dyes. Chemistry 2008; 14:6640-5. [DOI: 10.1002/chem.200800514] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
12
|
Menacher F, Rubner M, Berndl S, Wagenknecht HA. Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer. J Org Chem 2008; 73:4263-6. [PMID: 18442293 DOI: 10.1021/jo8004793] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.
Collapse
Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, Universitätsstrasse 31, Regensburg, Germany
| | | | | | | |
Collapse
|
13
|
Wagenknecht HA. Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept. Ann N Y Acad Sci 2007; 1130:122-30. [PMID: 18096856 DOI: 10.1196/annals.1430.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There is an increasing need for fluorescent nucleic acid probes that are able to sense genetic variations without the application of enzymes. The incorporation of organic fluorophores either as DNA base modifications or as DNA base substitutions represents a powerful and versatile method for such new fluorescent DNA assays. Multiple labeling of oligonucleotides using several adjacent chromophore-modified DNA bases yields fluorescence enhancement and modulation that are sensitive to single-base mismatches in the complementary oligonucleotide. Charge transfer processes that cause fluorescence quenching are DNA-base mediated and occur over several base pairs distance. Our "DETEQ" setup, consisting of a fluorescence DNA base substitution and the charge acceptor as a second modification two base pairs away, allows the homogeneous detection of single-base mutations simply by fluorescence readout. This could lead to new DNA microarrays which are based on charge transfer processes and can be analyzed by commonly used fluorescence readout techniques.
Collapse
|
14
|
Wagner C, Wagenknecht HA. Perylene-3,4:9,10-tetracarboxylic acid bisimide dye as an artificial DNA base surrogate. Org Lett 2007; 8:4191-4. [PMID: 16956184 DOI: 10.1021/ol061246x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phosphoramidite of the perylene bisimide dye was synthesized as a DNA building block that allows incorporation of this chromophore as an artificial nucleoside surrogate either at the 5'-terminus or at internal positions of duplex DNA. The internally incorporated perylene bisimide chromophore shows strong interactions with the DNA base stack; the 5'-terminally attached perylene bisimide is able to induce dimerization of two whole DNA duplexes.
Collapse
Affiliation(s)
- Clemens Wagner
- University of Regensburg, Institute for Organic Chemistry, Universitätsstr. 31, D-93053 Regensburg, Germany
| | | |
Collapse
|
15
|
Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
Collapse
Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
| |
Collapse
|
16
|
Mayer E, Valis L, Wagner C, Rist M, Amann N, Wagenknecht HA. 1-Ethynylpyrene as a tunable and versatile molecular beacon for DNA. Chembiochem 2005; 5:865-8. [PMID: 15174171 DOI: 10.1002/cbic.200300845] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Elke Mayer
- Chemistry Department, Technical University of Munich, 85747 Garching, Germany
| | | | | | | | | | | |
Collapse
|
17
|
Huber R, Amann N, Wagenknecht HA. Synthesis of DNA with phenanthridinium as an artificial DNA base. J Org Chem 2004; 69:744-51. [PMID: 14750800 DOI: 10.1021/jo0355404] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phenanthridinium-containing DNA building block was synthesized as an ethidium nucleoside analogue starting from 3,8-diamino-6-phenyl-phenanthridine. Using this building block, oligonucleotides bearing the phenanthridinium moiety as an artificial DNA base were prepared via automated solid-phase phosphoramidite chemistry. The modified phenanthridinium-containing DNA duplexes were characterized by UV/vis absorption spectroscopy (including the melting behavior), CD spectroscopy, and steady-state fluorescence spectroscopy. These experiments reveal the expected similarity of the synthetic phenanthridinium moiety with noncovalently bound ethidium. More importantly, the results show clearly that the artificial phenanthridinium base is intercalated within the DNA base stack. The counterbase as part of the complementary strand seems to have only a minor influence on the intercalation properties of the phenanthridinium moiety.
Collapse
Affiliation(s)
- Robert Huber
- Institute for Organic Chemistry and Biochemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany
| | | | | |
Collapse
|