1
|
Xia Z, Kondhare D, Budow-Busse S, Leonard P, Seela F. 7-Deaza-2'-deoxyisoguanosine, a Noncanonical Nucleoside for Nucleic Acid Code Expansion and New DNA Constructs: Nucleobase Functionalization of Inverse Watson-Crick and Purine-Purine Base Pairs. Bioconjug Chem 2024; 35:1233-1250. [PMID: 39088564 DOI: 10.1021/acs.bioconjchem.4c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
7-Deaza-2'-deoxyisoguanosine forms stable inverse Watson-Crick base pairs with 5-methyl-2'-deoxyisocytidine and purine-purine base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine. Both base pairs expand the genetic coding system. The manuscript reports on the functionalization of these base pairs with halogen atoms and clickable side chains introduced at 7-position of the 7-deazapurine base. Oligonucleotides containing the functionalized base pairs were prepared by solid-phase synthesis. To this end, a series of phosphoramidites were synthesized and clickable side chains with short and long linkers were incorporated in oligonucleotides. Fluorescent pyrene conjugates were obtained by postmodification. Functionalization of DNA with a single inverse Watson-Crick base pair by halogens or clickable residues has only a minor impact on duplex stability. Pyrene click adducts increase (long linker) or decrease (short linker) the double helix stability. Stable hybrid duplexes were constructed containing three consecutive purine-purine pairs of 7-functionalized 7-deaza-2'-deoxyisoguanine with guanine or 5-aza-7-deazaguanine in the center and Watson-Crick pairs at both ends. The incorporation of a hybrid base pair tract of 7-deaza-2'-deoxyisoguanosine/5-aza-7-deaza-2'-deoxyguanosine pairs stabilizes the double helix strongly. Fluorescence intensity of pyrene short linker adducts increased when the 7-deazapurine base was positioned opposite to 5-methylisocytosine (inverse base pair) compared to purine-purine base pairs with guanine or 5-aza-7-deazaguanine in opposite positions. For long liker adducts, the situation is more complex. Circular dichroism (CD) spectra of purine DNA differ to those of Watson-Crick double helices and are indicative for the new DNA constructs. The impact of 7-deaza-2'-deoxyisoguanine base pair functionalization is studied for the first time and all experimental details are reported to prepare DNA functionalized at the 7-deazaisoguanine site. The influence of single and multiple incorporations on DNA structure and stability is shown. Clickable residues introduced at the 7-position of the 7-deazaisoguanine base provide handles for Huisgen-Sharpless-Meldal click cycloadditions without harming the stability of purine-pyrimidine and purine-purine base pairs. Other chemistries might be used for bioconjugation. Our investigation paves the way for the functionalization of a new DNA related recognition system expanding the common Watson-Crick regime.
Collapse
Affiliation(s)
- Zhenqiang Xia
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Simone Budow-Busse
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
2
|
Xia Z, Kondhare D, Chandankar SS, Ingale SA, Leonard P, Seela F. Nucleobase-Functionalized 7-Deazaisoguanine and 7-Deazapurin-2,6-diamine Nucleosides: Halogenation, Cross-Coupling, and Cycloaddition. J Org Chem 2024; 89:1807-1822. [PMID: 38227281 DOI: 10.1021/acs.joc.3c02514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The functionalization in position-7 of 7-deazaisoguanine and 7-deazapurin-2,6-diamine ribo- and 2'-deoxyribonucleosides by halogen atoms (chloro, bromo, iodo), and clickable alkynyl and vinyl side chains for copper-catalyzed and copper-free cycloadditions is described. Problems arising during the synthesis of the 7-iodinated isoguanine ribo- and 2'-deoxyribonucleosides were solved by the action of acetone. The impact of side chains and halogen atoms on the pKa values and hydrophobicity of nucleosides was investigated. Halogenated substituents increase the lipophilic character of nucleosides in the order Cl < Br < I and decrease the pK values of protonation. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of azide-alkyne click adducts bearing pyrene as sensor groups were determined. Pyrene fluorescence was solvent-dependent and changed according to the linker lengths. Excimer emission was observed in dioxane for the long linker adduct. Bioorthogonal inverse-electron-demanding Diels-Alder cycloadditions (iEDDA) were conducted on the electron-rich vinyl groups of 7-deazaisoguanine and 7-deazapurin-2,6-diamine nucleosides as dienophiles and 3,6-dipyridyl-1,2,4,5-tetrazine as diene. The initially formed complex reaction mixture of isomers could be easily oxidized with iodine in tetrahydrofuran (THF)/pyridine leading to single aromatic tetrazine adducts within a short time and in excellent yields.
Collapse
Affiliation(s)
- Zhenqiang Xia
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Somnath Shivaji Chandankar
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
3
|
Kondhare D, Leonard P, Seela F. The Base Pairs of Isoguanine and 8-Aza-7-deazaisoguanine with 5-Methylisocytosine as Targets for DNA Functionalization. Bioconjug Chem 2023; 34:422-432. [PMID: 36735859 DOI: 10.1021/acs.bioconjchem.2c00584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The isoguanine-isocytosine base pair (isoG-isoC) represents an important expansion of the DNA coding system. The base pair is more stable than the canonical adenine-thymine or guanine-cytosine pairs. However, nothing is known on the functionalization of the noncanonical isoG-isoC pair at the isoguanine site. In this work, functionalization of the isoG-isoC and the isosteric base pair that contains 8-aza-7-deazaisoguanine in place of isoguanine is studied. Short ethynyl, more space demanding octadiynyl, and dendritic tripropargylamine residues attached to the isoG-isoC base pairs were introduced to oligonucleotides. 12-mer duplexes were formed by hybridization with single base pair modification. The use of the two modified nucleobases gave us the freedom to shift nucleobase substituents within the major groove of double helical DNA. Clickable side chains at position-7 stabilize the base pair, whereas 8-substituents reduce its stability strongly. The weak isoguanine-thymine or 8-aza-7-deazaisoguanine-thymine base pairs show a similar sensitivity to the position of nucleobase functionalization as base pair matches formed with 5-methylisocytosine. CD spectra of all modified duplexes display the typical shape of a B-DNA with only marginal changes. Fluorescent pyrene labeled DNA with long, short, and branched linkers was generated using click chemistry. Pyrene click adducts with long linkers are essential to maintain or to increase base pair stability. Labeled duplexes are more fluorescent than corresponding single strands. For the dendritic linker excimer emission was observed for single strands but only monomer emission in duplexes.
Collapse
Affiliation(s)
- Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
4
|
Zhang A, Kondhare D, Leonard P, Seela F. Purine–Purine Base Pairs in Parallel DNA: β-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with α-D 5-Aza-7-deaza-2′-deoxyguanosine. Bioconjug Chem 2022; 33:1796-1802. [DOI: 10.1021/acs.bioconjchem.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
5
|
Kondhare D, Zhang A, Leonard P, Seela F. DNA with Purine-Purine Base Pairs: Size and Position of Isoguanine and 8-Aza-7-deazaisoguanine Clickable Residues Control the Molecular Recognition of Guanine and 5-Aza-7-deazaguanine. J Org Chem 2022; 87:10630-10650. [PMID: 35948421 DOI: 10.1021/acs.joc.2c00812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Purine-purine base pairs represent an alternative recognition system to the purine-pyrimidine pairing reported by Watson and Crick. Modified purines are the source for non-canonical interactions. To mimic dG-dC interactions, 2'-deoxyisoguanosine (1a) and 8-aza-7-deaza-2'-deoxyisoguanosine (2a) are used to construct base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine (dZ). This work reports the chemical functionalization of 1a and its shape mimic 2a in purine-purine base pairs. Clickable rigid ethynyl and more flexible octadiynyl side chain derivatives of 1a and 2a were synthesized. They were protected and converted into phosphoramidites. Building blocks were employed in the synthesis of base-modified 12-mer oligonucleotides with clickable side chains. Pyrene azide was clicked to the linkers. After hybridization, oligonucleotides with purine-purine base pairs were constructed with linkers and pyrene adducts at position-8 of isoguanine and at position-7 of 8-aza-7-deazaisoguanine. Recognition and stability of purine-purine base pairs were explored using Tm values, thermodynamic data, and CD-spectroscopic changes. Side chains at position-7 of 8-aza-7-deazaisoguanine-guanine base pairs or with 5-aza-7-deazaguanine are well accommodated in DNA, whereas functionalization at 8-position of isoguanine makes the DNA unstable. Pyrene click adducts verified the observation. In conclusion, position-7 is the place of choice for purine-purine base pair functionalization.
Collapse
Affiliation(s)
- Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
6
|
Kondhare D, Leonard P, Seela F. Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties. J Org Chem 2021; 86:14461-14475. [PMID: 34661407 DOI: 10.1021/acs.joc.1c01283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. KTaut values calculated from H2O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H2O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.
Collapse
Affiliation(s)
- Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
7
|
Zhang A, Kondhare D, Leonard P, Seela F. 5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts. Chemistry 2021; 27:7453-7466. [PMID: 33443814 PMCID: PMC8251886 DOI: 10.1002/chem.202005199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/19/2022]
Abstract
The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.
Collapse
Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
| |
Collapse
|
8
|
Chai Y, Guo X, Leonard P, Seela F. Heterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines. Chemistry 2020; 26:13973-13989. [PMID: 32667103 PMCID: PMC7702046 DOI: 10.1002/chem.202002765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Indexed: 02/05/2023]
Abstract
Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the Tm values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7-deazapurines resulted in stable parallel duplexes, thereby confirming Watson-Crick-type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α-d configuration display mirror-like shapes to those with the β-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with a limited number of silver pairs show a B-type double helix almost indistinguishable from natural DNA. Nonmelting silver ion-DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs.
Collapse
Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development LaboratoryWest China HospitalSichuan University610041SichuanP. R. China
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
| |
Collapse
|
9
|
Gate G, Szabla R, Haggmark MR, Šponer J, Sobolewski AL, de Vries MS. Photodynamics of alternative DNA base isoguanine. Phys Chem Chem Phys 2019; 21:13474-13485. [DOI: 10.1039/c9cp01622h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.
Collapse
Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Michael R. Haggmark
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | | | | |
Collapse
|
10
|
Ihegboro GO, Ononamadu CJ, Afor E, Odogiyan GD. Cytotoxic and Hepatocurative Effect of Aqueous Fraction of Tapinanthus bangwensis Against Paracetamol-Induced Hepatotoxicity. J Evid Based Integr Med 2018; 23:2515690X18801577. [PMID: 30261739 PMCID: PMC6166302 DOI: 10.1177/2515690x18801577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Medicinal plants over time have proven to have potential to manage a huge number of
diseases and disorders and thus have become a great source of pharmaceutical drugs. One of
such plants is Tapinanthus bangwensis (African mistletoe). It is a
semiparasitic and epiphytic plant growing on citrus tree, obtaining its food
photosynthetically while its nutrient and water is got from the host plant. The aim of
this study was to determine the cytotoxicological and hepatocurative effect of aqueous
fraction of T bangwensis in acetaminophen (paracetamol)-induced Wistar
rats. The antioxidant potential of the plant was determined by
2,2-diphenyl-1-picrylhydrazine scavenging and ferric reducing power assays. The cytotoxic
effect was determined using Allium cepa test while the liver biochemical
indices were determined by standard protocols. Data obtained were analyzed by 2-way
analysis of variance at 95% confidence level and reported as mean ± standard deviation.
The concentrated aqueous fraction of T bangwensis was found to be 23.3 g
(58.25%). Quantitative determination of some vital phytochemicals revealed the following:
flavonoid (84.6 ± 0.41 mg/100 g), phenol (147.5 ± 1.07 mg/100 g), tannin (31 ± 0.85 mg/
100 g), alkaloid (23.45 ± 0.09 mg/100 g), and saponin (0.146 ± 0.0 mg/100 g). Treatment of
rats with the aqueous extract of T bangwensis significantly decreased
paracetamol-induced elevation of activities of liver function indices, alkaline
phosphatase, alanine aminotransferase, aspartate aminotransferase, triglyceride, total
cholesterol level and increased the albumin, total protein, and high-density lipoprotein
levels. The plant extract also attenuated the paracetamol elevated lipid peroxidation
product, malondialdehyde. The research findings suggest that aqueous extract of T
bangwensis is slightly cytotoxic, possesses appreciable antioxidant property
and exhibited hepatocurative effect against paracetamol-induced hepatoxicity.
Collapse
Affiliation(s)
- Godwin O Ihegboro
- 1 Nigeria Police Academy, Wudil, Kano State, Nigeria.,2 Bayero University, Kano, Kano State, Nigeria
| | - Chimaobi J Ononamadu
- 1 Nigeria Police Academy, Wudil, Kano State, Nigeria.,2 Bayero University, Kano, Kano State, Nigeria
| | - E Afor
- 3 Yaba College of Technology, Yaba, Lagos, Nigeria
| | | |
Collapse
|
11
|
Müller J. Metal-mediated base pairs in parallel-stranded DNA. Beilstein J Org Chem 2017; 13:2671-2681. [PMID: 29564004 PMCID: PMC5753045 DOI: 10.3762/bjoc.13.265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 01/03/2023] Open
Abstract
In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.
Collapse
Affiliation(s)
- Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
| |
Collapse
|
12
|
Zhang W, Gao Q, Wei S, Fu B, Yang Q, Ming X. Synthesis of 8-Substituted 2'-Deoxyisoguanosines via Unprotected 8-Brominated 2-Amino-2'-deoxyadenosine. Chem Biodivers 2017; 15. [PMID: 28853211 DOI: 10.1002/cbdv.201700335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
A variety of applications of 8-alkynylated nucleosides has prompted the synthesis of new purine analogues. Bromination of unprotected 2-amino-2'-deoxyadenosine with Br2 /AcOH/AcONa gives 2-amino-8-bromo-2'-deoxyadenosine (87%). The brominated derivative is converted to 8-alkynylated 2-amino-2'-deoxyadenosines by palladium-catalyzed Sonogashira cross-coupling reaction via microwave assistance (81 - 95%). The resulting compounds are further transformed to 8-alkynylated 2'-deoxyisoguanosines (52 - 70%). The physical properties of new compounds are investigated.
Collapse
Affiliation(s)
- Wen Zhang
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Qian Gao
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Shuxian Wei
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Bicheng Fu
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Qian Yang
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China.,Study on the Structure-Specificity Small Molecule Drug in Sichuan Province Colleges Key Laboratory, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Xin Ming
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China.,Study on the Structure-Specificity Small Molecule Drug in Sichuan Province Colleges Key Laboratory, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| |
Collapse
|
13
|
Zhao H, Schäfer AH, Seela F. Supramolecular Isoguanosine Assemblies Form Hydrogels with Excellent Long-Term Stability. Chempluschem 2017; 82:826-833. [PMID: 31961560 DOI: 10.1002/cplu.201600586] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/16/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Hang Zhao
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan 610041 P. R. China
| | - Andreas H. Schäfer
- nanoAnalytics GmbH; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
| |
Collapse
|
14
|
Ingale SA, Seela F. 7-Deaza-2′-deoxyguanosine: Selective Nucleobase Halogenation, Positional Impact of Space-Occupying Substituents, and Stability of DNA with Parallel and Antiparallel Strand Orientation. J Org Chem 2016; 81:8331-42. [DOI: 10.1021/acs.joc.6b01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin A. Ingale
- Laboratory
of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory
of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
- Laboratorium
für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße
7, 49069 Osnabrück, Germany
| |
Collapse
|
15
|
Jana SK, Leonard P, Ingale SA, Seela F. 2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation. Org Biomol Chem 2016; 14:4927-42. [DOI: 10.1039/c6ob00622a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of 2′-O-alkyl residues on the stability of iCd–dG and iCd–iGd base pairs was studied in DNA with parallel and antiparallel chain orientation.
Collapse
Affiliation(s)
- Sunit K. Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| |
Collapse
|
16
|
Ingale SA, Leonard P, Tran QN, Seela F. Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability. J Org Chem 2015; 80:3124-38. [PMID: 25742047 DOI: 10.1021/acs.joc.5b00040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.
Collapse
Affiliation(s)
- Sachin A Ingale
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Quang Nhat Tran
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- †Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,‡Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
17
|
Pujari SS, Seela F. Parallel stranded DNA stabilized with internal sugar cross-links: synthesis and click ligation of oligonucleotides containing 2'-propargylated isoguanosine. J Org Chem 2013; 78:8545-61. [PMID: 23915305 DOI: 10.1021/jo4012706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.
Collapse
Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | | |
Collapse
|
18
|
Ming X, Ding P, Leonard P, Budow S, Seela F. Parallel-stranded DNA: Enhancing duplex stability by the ‘G-clamp’ and a pyrrolo-dC derivative. Org Biomol Chem 2012; 10:1861-9. [DOI: 10.1039/c2ob06606h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
19
|
Seela F, Jiang D, Budow S. Triplexes with 8-Aza-2'-deoxyisoguanosine replacing protonated dC: probing third strand stability with a fluorescent nucleobase targeting duplex DNA. Chembiochem 2010; 11:1443-50. [PMID: 20544775 DOI: 10.1002/cbic.201000162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The fluorescent 8-aza-2'-deoxyisoguanosine (4) as well as the parent 2'-deoxyisoguanosine (1) were used as protonated dCH(+) surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH(+) are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4. Third-strand binding of oligonucleotides with 4, opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third-strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third-strand binding more flexibility.
Collapse
Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster Germany
| | | | | |
Collapse
|
20
|
Jiang D, Seela F. Oligonucleotide duplexes and multistrand assemblies with 8-aza-2'-deoxyisoguanosine: a fluorescent isoG(d) shape mimic expanding the genetic alphabet and forming ionophores. J Am Chem Soc 2010; 132:4016-24. [PMID: 20192268 DOI: 10.1021/ja910020n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
8-Aza-2'-deoxyisoguanosine (4) is the first fluorescent shape mimic of 2'-deoxyisoguanosine (1a); its fluorescence is stronger in alkaline medium than under neutral conditions. Nucleoside 4, which was synthesized from 8-aza-2'-deoxyguanosine via a 4,6-diamino intermediate after selective deamination, was incorporated in oligodeoxyribonucleotides using phosphoramidite 11. Duplexes with 4 x m(5)iC(d) (5-methyl-2'-deoxyisocytidine) base pairs are more stable than those incorporating dG-dC pairs, thereby expanding the genetic alphabet by a fluorescent orthogonal base pair. As demonstrated by T(m) measurements, the base pair stability decreases in the order m(5)iC(d) x 4 >> dG x 4 > dT x 4 > or = dC x 4 >> dA x 4. A better base pairing selectivity of 4 against the canonical nucleosides dT, dC, dA, and dG is observed than for the degenerated base pairing of 1a. The base pair stability changes can be monitored by nucleobase anion fluorescence sensing. The fluorescence change correlates to the DNA base pair stability. Oligonucleotide 5'-d(T(4)4(4)T(4)) (22), containing short runs of nucleoside 4, forms stable multistranded assemblies (ionophores) with K(+) in the central cavity. They are quite stable at elevated temperature but are destroyed at high pH value.
Collapse
Affiliation(s)
- Dawei Jiang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | | |
Collapse
|
21
|
Arico JW, Calhoun AK, McLaughlin LW. Preparation of the 2′-Deoxynucleosides of 2,6-Diaminopurine and Isoguanine by Direct Glycosylation. J Org Chem 2010; 75:1360-5. [DOI: 10.1021/jo902616s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph W. Arico
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Amy K. Calhoun
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Larry W. McLaughlin
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| |
Collapse
|
22
|
Chiba J, Inouye M. Exotic DNAs Made of Nonnatural Bases and Natural Phosphodiester Bonds. Chem Biodivers 2010; 7:259-82. [DOI: 10.1002/cbdv.200900282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
23
|
Seela F, Shaikh K. Oligonucleotides Containing 7-Deaza-2′-deoxyxanthosine: Synthesis, Base Protection, and Base-Pair Stability. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
24
|
Seela F, Wei C, Melenewski A, He Y, Kröschel R, Feiling E. Parallel-Stranded DNA Formed by New Base Pairs Related to the Isoguanine-Cytosine or Isocytosine-Guanine Motifs. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
25
|
Seela F, Shaikh KI. pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine. Org Biomol Chem 2006; 4:3993-4004. [PMID: 17047881 DOI: 10.1039/b610930f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Triplex-forming oligonucleotides (TFOs) containing 2'-deoxyisoguanosine (2), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) as well as the propynylated 9-deazaguanine N7-(2'-deoxyribonucleoside) were prepared. For this the phosphoramidites 9a, b of the nucleoside 1 and, the phosphoramidites 19, 20 of compound 3b were synthesized. They were employed in solid-phase oligonucleotide synthesis to yield the protected 31-mer oligonucleotides. The deblocking of the allyl-protected oligonucleotides containing 1 was carried out by Pd(0)[PPh3]4-PPh3 followed by 25% aq. NH3. Formation of the 31-mer single-stranded intramolecular triplexes was studied by UV-melting curve analysis. In the single-stranded 31-mer oligonucleotides the protonated dC in the dCH(+)-dG-dC base triad was replaced by 2'-deoxyisoguanosine (1), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) and, 9-deaza-9-propynylguanine N7-(2'-deoxyribonucleoside) (3b). The replacement of protonated dC by compounds 1 and 3b resulted in intramolecular triplexes which are formed pH-independently and are stable under neutral conditions. These triplexes contain "purine" nucleosides in the third pyrimidine rich strand of the oligonucleotide hairpin.
Collapse
Affiliation(s)
- Frank Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.
| | | |
Collapse
|
26
|
Seela F, Wei C, Melenewski A, Feiling E. Parallel-Stranded Duplex DNA and Self-Assembled Quartet Structures Formed by Isoguanine and Related Bases. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004745] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Frank. Seela
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Babarastr 7, D-49069 , Osnabrück , Germany
| | - Changfu. Wei
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Babarastr 7, D-49069 , Osnabrück , Germany
| | - Alexander. Melenewski
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Babarastr 7, D-49069 , Osnabrück , Germany
| | - Elisabeth. Feiling
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Babarastr 7, D-49069 , Osnabrück , Germany
| |
Collapse
|
27
|
Geinguenaud F, Mondragon-Sanchez JA, Liquier J, Shchyolkina AK, Klement R, Arndt-Jovin DJ, Jovin TM, Taillandier E. Parallel DNA double helices incorporating isoG or m5isoC bases studied by FTIR, CD and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 61:579-587. [PMID: 15649787 DOI: 10.1016/j.saa.2004.05.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 05/10/2004] [Indexed: 05/24/2023]
Abstract
FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m5isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A-T and isoG-C or m5isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson-Crick (WC) base pairs) reflect the formation of trans Watson-Crick A-T base pairs. All carbonyl groups of cytosines, m5isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG-C and m5isoC-G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B --> A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type --> N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG-A)/d(C-T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water/trifluoroethanol solutions and its free energy at 0 degrees C was estimated to be 6.6 +/- 0.3 kcal mol(-1).
Collapse
Affiliation(s)
- F Geinguenaud
- Equipe de Spectroscopie Biomoléculaire, UFR de Médecine, Université Paris 13, 74 rue Marcel Cachin, F93017 Bobigny Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Seela F, Kröschel R, He Y. Parallel DNA containing pyrazolo[3,4-D]pyrimidine analogues of isoguanine. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1283-6. [PMID: 11563004 DOI: 10.1081/ncn-100002537] [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
The phosphoramidites of 8-aza-7-deaza-2'-deoxyisoguanosine (1a) and its bromo derivative 1b as well as of 6-aza-2'-deoxyisocytidine and its 5-methyl derivative (3a,b) were synthesized. Parallel-stranded duplexes containing the nucleosides 1a,b show a significantly enhanced duplex stability compared to those containing 2'-deoxyisoguanosine.
Collapse
Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastr. 7, D-49076 Osnabrück, Germany
| | | | | |
Collapse
|
29
|
Bibillo A, Figlerowicz M, Ziomek K, Kierzek R. The nonenzymatic hydrolysis of oligoribonucleotides. VII. Structural elements affecting hydrolysis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:977-94. [PMID: 10893716 DOI: 10.1080/15257770008033037] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Several elements of oligoribonucleotide structure are important for efficient hydrolysis. We have found that the following factors influence oligoribonucleotide hydrolysis: (i) single-stranded structure of RNA flanking the scissile phosphodiester bond, (ii) the substituent on atom C-5 of the uridine adjacent to the cleaved internucleotide bond, (iii) the position of the scissile UA phosphodiester bond within a hairpin loop, (iv) the concentration of formamide, urea, ethanol and sodium chloride.
Collapse
Affiliation(s)
- A Bibillo
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | | | |
Collapse
|
30
|
Seela F, Wei C, Becher G, Zulauf M, Leonard P. The influence of modified purine bases on the stability of parallel DNA. Bioorg Med Chem Lett 2000; 10:289-92. [PMID: 10698456 DOI: 10.1016/s0960-894x(99)00679-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability of the parallel-stranded (ps) DNA duplexes is increased when the dA-residues are replaced by the 7-substituted 7-deaza-2'-deoxyadenosine derivatives 3a,b or the dG-residues by the 8-aza-7-deazapurine 2'-deoxynucleosides 6 and 7a,b. Also the N-7-glycosylated adenine 5 forms stable base pairs in ps-DNA while it destabilizes oligonucleotide duplexes with antiparallel chain orientation. The presence of a 2-amino group as in compound 4b is critical for the DNA-structure, leading to a much greater destabilization of the ps-hybrids than of aps-DNA.
Collapse
Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Germany.
| | | | | | | | | |
Collapse
|
31
|
Seela F, He Y, Wei C. Parallel-stranded oligonucleotide duplexes containing 5-methylisocytosine-guanine and isoguanine-cytosine base pairs. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00511-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
32
|
Lutz S, Burgstaller P, Benner SA. An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudo-thymidine as a substrate for thermostable polymerases. Nucleic Acids Res 1999; 27:2792-8. [PMID: 10373598 PMCID: PMC148490 DOI: 10.1093/nar/27.13.2792] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases are desired that incorporate modified nucleotides into DNA with diminished pausing, premature termination and infidelity. Reported here is a simple in vitro assay to screen for DNA polymerases that accept modified nucleotides based on a set of primer extension reactions. In combination with the scintillation proximity assay (SPA[trade]), this allows rapid and simple screening of enzymes for their ability to elongate oligonucleotides in the presence of unnatural nucleotides. A proof of the concept is obtained using pseudo-thymidine (psiT), the C-nucleoside analog of thymidine, as the unnatural substrate. The conformational properties of psiT arising from the carbon-carbon bond between the sugar and the base make it an interesting probe for the importance of conformational restraints in the active site of polymerases during primer elongation. From a pool of commercially available thermostable polymerases, the assay identified Taq DNA polymerase as the most suitable enzyme for the PCR amplification of oligonucleotides containing psiT. Subsequent experiments analyzing PCR performance and fidelity of Taq DNA polymerase acting on psiT are presented. This is the first time that PCR has been performed with a C-nucleoside.
Collapse
Affiliation(s)
- S Lutz
- Departments of Chemistry and Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611, USA
| | | | | |
Collapse
|
33
|
Abstract
The deoxygenation and 2'-labeling of a C-ribonucleoside by reductive elimination with tri-n-butyltin hydride[3H] in a one-pot reaction is described. The approach is a safe, simple, efficient, and general method for 2'-labeling of nucleosides.
Collapse
Affiliation(s)
- S Lutz
- Department of Chemistry, University of Florida, Gainesville 32611, USA
| | | |
Collapse
|
34
|
Seela F, Melenewski A. 5-Aza-7-deaza-2′-deoxyguanosine: Oligonucleotide Duplexes with Novel Base Pairs, Parallel Chain Orientation and Protonation Sites in the Core of a Double Helix. European J Org Chem 1999. [DOI: 10.1002/(sici)1099-0690(199902)1999:2<485::aid-ejoc485>3.0.co;2-j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Yang XL, Sugiyama H, Ikeda S, Saito I, Wang AH. Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. Biophys J 1998; 75:1163-71. [PMID: 9726918 PMCID: PMC1299791 DOI: 10.1016/s0006-3495(98)74035-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Isoguanine (2-hydroxyladenine) is a product of oxidative damage to DNA and has been shown to cause mutation. It is also a potent inducer of parallel-stranded DNA duplex structure. The structure of the parallel-stranded DNA duplex (PS-duplex) 5'-d(TiGiCAiCiGiGAiCT) + 5'-d(ACGTGCCTGA), containing the isoguanine (iG) and 5-methyl-isocytosine (iC) bases, has been determined by NMR refinement. All imino protons associated with the iG:C, G:iC, and A:T (except the two terminal A:T) basepairs are observed at 2 degrees C, consistent with the formation of a stable duplex suggested by the earlier Tm measurements [Sugiyama, H., S. Ikeda, and I. Saito. 1996. J. Am. Chem. Soc. 118:9994-9995]. All basepairs are in the reverse Watson-Crick configuration. The structural characteristics of the refined PS-duplex are different from those of B-DNA. The PS duplex has two grooves with similar width (7.0 A) and depth (7.7 A), in contrast to the two distinct grooves (major groove width 11.7 A, depth 8.5 A, and minor groove width 5.7 A, depth 7.5 A) of B-DNA. The resonances of the amino protons of iG and C are clearly resolved and observable, but those of the G and iC are very broad and difficult to observe. Several intercalators with different complexities, including ethidium, daunorubicin, and nogalamycin, have been used to probe the flexibility of the backbone of the (iG, iC)-containing PS-duplex. All of them produce drug-induced UV/vis spectra identical to their respective spectra when bound to B-DNA, suggesting that those drugs bind to the (iG, iC)-containing PS-duplex using similar intercalation processes. The results may be useful in the design of intercalator-conjugated oligonucleotides for antisense applications. The study presented in this paper augments our understanding of a growing number of parallel-stranded DNA structures, including the G-quartet, the i-motif, and the unusual homo basepaired parallel-stranded double helix. Their possible relevance is discussed.
Collapse
Affiliation(s)
- X L Yang
- Department of Cell and Structural Biology, University of Illinois, Urbana-Champaign 61801, USA
| | | | | | | | | |
Collapse
|
36
|
Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
37
|
Synthesis of Oligonucleotides Containing 2?-Deoxyisoguanosine and 2?-Deoxy-5-methylisocytidine Using Phosphoramidite Chemistry. Helv Chim Acta 1998. [DOI: 10.1002/hlca.19980810502] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
38
|
Seela F, Melenewski A, Wei C. Parallel-stranded duplex DNA formed by a new base pair between guanine and 5-aza-7-deazaguanine. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00385-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
39
|
Seela F. 7-Deazaisoguanine quartets: self-assembled oligonucleotides lacking the Hoogsteen motif. Chem Commun (Camb) 1997. [DOI: 10.1039/a704866a] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|