1
|
Salihovic A, Ascham A, Taladriz-Sender A, Bryson S, Withers JM, McKean IJW, Hoskisson PA, Grogan G, Burley GA. Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2. Chem Sci 2024:d4sc04938a. [PMID: 39234214 PMCID: PMC11368039 DOI: 10.1039/d4sc04938a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
Nucleosides are pervasive building blocks that are found throughout nature and used extensively in medicinal chemistry and biotechnology. However, the preparation of base-modified analogues using conventional synthetic methodology poses challenges in scale-up and purification. In this work, an integrated approach involving structural analysis, screening and reaction optimization, is established to prepare 2'-deoxyribonucleoside analogues catalysed by the type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii (LlNDT-2). Structural analysis in combination with substrate profiling, identified the constraints on pyrimidine and purine acceptor bases by LlNDT2. A solvent screen identifies pure water as a suitable solvent for the preparation of high value purine and pyrimidine 2'-deoxyribonucleoside analogues on a gram scale under optimized reaction conditions. This approach provides the basis to establish a convergent, step-efficient chemoenzymatic platform for the preparation of high value 2'-deoxyribonucleosides.
Collapse
Affiliation(s)
- Admir Salihovic
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Alex Ascham
- Department of Chemistry, University of York, Heslington York YO10 5DD UK
| | - Andrea Taladriz-Sender
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Samantha Bryson
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Jamie M Withers
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Iain J W McKean
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde 161 Cathedral Street Glasgow G4 0RE UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington York YO10 5DD UK
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| |
Collapse
|
2
|
Caldero-Rodríguez NE, Arpa EM, Cárdenas DJ, Martínez-Fernández L, Jockusch S, Seth SK, Corral I, Crespo-Hernández CE. 2-Oxopurine Riboside: A Dual Fluorescent Analog and Photosensitizer for RNA/DNA Research. J Phys Chem B 2022; 126:4483-4490. [PMID: 35679327 DOI: 10.1021/acs.jpcb.2c01113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
There is significant interest in developing suitable nucleoside analogs exhibiting high fluorescence and triplet yields to investigate the structure, dynamics, and binding properties of nucleic acids and promote selective photosensitized damage to DNA/RNA, respectively. In this study, steady-state, laser flash photolysis, time-resolved IR luminescence, and femtosecond broad-band transient absorption spectroscopies are combined with quantum chemical calculations to elucidate the excited-state dynamics of 2-oxopurine riboside in aqueous solution and to investigate its prospective use as a fluorescent or photosensitizer analog. The Franck-Condon population in the S1 (ππ*) state decays through a combination of solvent and conformational relaxation to its minimum in 1.9 ps. The population trapped in the 1ππ* minimum bifurcates to either fluoresce or intersystem cross to the triplet manifold within ca. 5 ns, while another fraction of the population decays nonradiatively to the ground state. It is demonstrated that 2-oxopurine riboside exhibits both high fluorescent (48%) and significant triplet (between 10% and 52%) yields, leading to a yield of singlet oxygen generation of 10%, making this nucleoside analog a dual fluorescent and photosensitizer analog for DNA and RNA research.
Collapse
Affiliation(s)
| | - Enrique M Arpa
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain
| | - Diego J Cárdenas
- Departamento de Química Orgánica, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lara Martínez-Fernández
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Steffen Jockusch
- Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Sourav Kanti Seth
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Inés Corral
- Departamento de Química, Universidad Autónoma de Madrid, c/Francisco Tomás y Valiente 7, Cantoblanco, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | |
Collapse
|
3
|
Budow-Busse S, Jana SK, Kondhare D, Daniliuc C, Seela F. 8-Furylimidazolo-2'-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence. Acta Crystallogr C Struct Chem 2022; 78:141-147. [PMID: 35245210 PMCID: PMC8896525 DOI: 10.1107/s2053229622001000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/28/2022] [Indexed: 11/10/2022] Open
Abstract
8-Furylimidazolo-2'-deoxycytidine (furImidC), C14H14N4O5, is a fluorescent analogue of 2'-deoxycytidine, also displaying the same recognition face. As a constituent of DNA, furImidC forms extraordinarily strong silver-mediated self-pairs. Crystal structure determination revealed that furImidC adopts two types of disordered residues: the sugar unit and the furyl moiety. The disorder of the sugar residue amounts to an 87:13 split. The disorder of the furyl ring results from axial chirality at the C8-C2'' bond connecting the nucleobase to the heterocycle. The two atropisomers are present in unequal proportions [occupancies of 0.69 (2) and 0.31 (2)], and the nucleobase and the furyl moiety are coplanar. Considering the atomic sites with predominant occupancy, an anti conformation with χ = - 147.2 (7)° was found at the glycosylic bond and the 2'-deoxyribosyl moiety shows a C2'-endo (S, 2T1) conformation, with P = 160.0°. A 1H NMR-based conformational analysis of the furanose puckering revealed that the S conformation predominates also in solution. In the solid state, two neighbouring furImidC molecules are arranged in a head-to-tail fashion, but with a notable tilt of the molecules with respect to each other. Consequently, one N-H...N hydrogen bond is found for neighbouring molecules within one layer, while a second N-H...N hydrogen bond is formed to a molecule of an adjacent layer. In addition, hydrogen bonding is observed between the nucleobase and the sugar residue. A Hirshfeld surface analysis was performed to visualize the intermolecular interactions observed in the X-ray study. In addition, the fluorescence spectra of furImidC were measured in solvents of different polarity and viscosity. furImidC responds to microenvironmental changes (polarity and viscosity), which is explained by a hindered rotation of the furyl residue in solvents of high viscosity.
Collapse
Affiliation(s)
- Simone Budow-Busse
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Sunit K. Jana
- 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
| | - Constantin Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 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, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
| |
Collapse
|
4
|
Notomi R, Wang L, Sasaki S, Taniguchi Y. Design and synthesis of purine nucleoside analogues for the formation of stable anti-parallel-type triplex DNA with duplex DNA bearing the 5mCG base pair. RSC Adv 2021; 11:21390-21396. [PMID: 35478801 PMCID: PMC9034152 DOI: 10.1039/d1ra02831f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
We herein demonstrated for the first time the direct recognition of duplex DNA bearing the 5-methyl-2′-deoxycytosine and 2′-deoxyguanosine base pair by triplex DNA formation. Triplex-forming oligonucleotides contained the novel artificial nucleoside analogues 2-amino-2′-deoxy-nebularine derivatives, and their molecular design, synthesis, and functional evaluation are described. We herein demonstrated for the first time the direct recognition of duplex DNA bearing the 5-methyl-2′-deoxycytosine and 2′-deoxyguanosine base pair by triplex DNA formation.![]()
Collapse
Affiliation(s)
- Ryotaro Notomi
- Graduate School of Pharmaceutical Sciences
- Kyushu University
- Fukuoka 812-8582
- Japan
| | - Lei Wang
- Graduate School of Pharmaceutical Sciences
- Kyushu University
- Fukuoka 812-8582
- Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences
- Nagasaki International University
- Sasebo
- Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences
- Kyushu University
- Fukuoka 812-8582
- Japan
| |
Collapse
|
5
|
Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
Collapse
Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
| |
Collapse
|
6
|
Mei H, Ingale SA, Seela F. Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link. Chemistry 2014; 20:16248-57. [PMID: 25336305 DOI: 10.1002/chem.201404422] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 12/13/2022]
Abstract
8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). The silver-mediated (ph) ImidC-(ph) ImidC base pair fits well into the DNA double helix and has the stability of a covalent cross-link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.
Collapse
Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857; Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | | | | |
Collapse
|
7
|
Yang F, Zhu Y, Yu B. A dramatic concentration effect on the stereoselectivity of N-glycosylation for the synthesis of 2′-deoxy-β-ribonucleosides. Chem Commun (Camb) 2012; 48:7097-9. [DOI: 10.1039/c2cc33155a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Tung YS, Coumar MS, Wu YS, Shiao HY, Chang JY, Liou JP, Shukla P, Chang CW, Chang CY, Kuo CC, Yeh TK, Lin CY, Wu JS, Wu SY, Liao CC, Hsieh HP. Scaffold-Hopping Strategy: Synthesis and Biological Evaluation of 5,6-Fused Bicyclic Heteroaromatics To Identify Orally Bioavailable Anticancer Agents. J Med Chem 2011; 54:3076-80. [DOI: 10.1021/jm101027s] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yen-Shih Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Yu-Shan Wu
- Department of Chemistry, Tunghai University, 181 Taichung Harbor Road Section 3, Taichung 407, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Jing-Ping Liou
- College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - Paritosh Shukla
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Wei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chi-Yen Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Ching-Chuan Kuo
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chin-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Chun-Chen Liao
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
- Department of Chemistry, Chung Yuan Christian University, Chungli 320, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| |
Collapse
|
9
|
Liu Z, Li D, Yin B, Zhang J. Highly stereoselective synthesis of 2′-deoxy-β-ribonucleosides via a 3′-(N-acetyl)-glycyl-directing group. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
10
|
Seela F, Jiang D, Xu K. 8-Aza-2′-deoxyguanosine: Base pairing, mismatch discrimination and nucleobase anion fluorescence sensing in single-stranded and duplex DNA. Org Biomol Chem 2009; 7:3463-73. [DOI: 10.1039/b908017a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Seela F, Sirivolu VR. Pyrrolo-dC oligonucleotides bearing alkynyl side chains with terminal triple bonds: synthesis, base pairing and fluorescent dye conjugates prepared by the azide-alkyne "click" reaction. Org Biomol Chem 2008; 6:1674-87. [PMID: 18421402 DOI: 10.1039/b719459e] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-(Octa-1,7-diynyl)-2'-deoxyuridine was converted into the furano-dU derivative 7 by copper-catalyzed cyclization; the pyrolodC-derivative 3 was formed upon ammonolysis. The bicyclic nucleosides 3 and 7 as well as the corresponding non-cyclic precursors 4 and 6 all containing terminal C[triple bond]C bonds were conjugated with the non-fluorescent 3-azido-7-hydroxycoumarin 5 employing the copper(I)-catalyzed Huisgen-Sharpless-Meldal cycloaddition "click reaction". Strongly fluorescent 1H-1,2,3-triazole conjugates (30-33) are formed incorporating two fluorescent reporters-the pyrdC nucleoside and the coumarin moiety. Oligonucleotides incorporating 6-alkynyl and 6-alkyl 7H-pyrrolo[2,3-d]pyrimidin-2(3H)-one nucleosides (3 and 2f) have been prepared by solid-phase synthesis using the phosphoramidite building blocks 10 and 13 ; the pyrrolo-dC oligonucleotides are formed during ammonia treatment. The duplex stability of oligonucleotides containing 3 and related derivatives was studied. Oligonucleotides with terminal triple bonded nucleosides such as 3 are more stabilizing than those lacking a side chain with terminal unsaturation; open-chain derivatives (4) are even more efficient. The click reaction was also performed on oligonucleotides containing the pyrdC-derivative and the fluorescence properties of nucleosides, oligonucleotides and their coumarin conjugates were studied.
Collapse
Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 4814, Münster, Germany.
| | | |
Collapse
|
12
|
1,N6-Etheno-2′-deoxytubercidin and pyrrolo-C: synthesis, base pairing, and fluorescence properties of 7-deazapurine nucleosides and oligonucleotides. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.09.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
13
|
Rolland V, Kotera M, Lhomme J. Convenient Preparation of 2-Deoxy-3,5-di-O-p-toluoyl-α-D-erythro-pentofuranosyl Chloride. SYNTHETIC COMMUN 2006. [DOI: 10.1080/00397919708007071] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Valérie Rolland
- a LEDSS , UMR 5616, CNRS, BP53, Université Joseph Fourier, 38041, GRENOBLE, France
| | - Mitsuharu Kotera
- a LEDSS , UMR 5616, CNRS, BP53, Université Joseph Fourier, 38041, GRENOBLE, France
| | - Jean Lhomme
- a LEDSS , UMR 5616, CNRS, BP53, Université Joseph Fourier, 38041, GRENOBLE, France
| |
Collapse
|
14
|
Seela F, Jawalekar AM, Sun L, Leonard P. Oligonucleotides containing pyrazolo[3,4-d]pyrimidines: 8-Aza-7-deazaadenines with bulky substituents in the 2- or 7-position. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:1485-505. [PMID: 16438030 DOI: 10.1080/15257770500265745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The synthesis of the 2'-deoxyadenosine analogues 1b, 2b, and 3c modified at the 7- and/or 2-position is described. The effect of 7-chloro and 2-methylthio groups on the duplex stability is evaluated. For that, the nucleosides 1b, 2b, and 3c were converted to the corresponding phosphoramidites 15, 19, and 22, which were employed in the solid-phase oligonucleotide synthesis. In oligonucleotide duplexes, compound 1b forms stable base pairs with dT, of which the separated 1b-dT base pairs contribute stronger than that of the consecutive base pairs. Compound 2b shows universal base pairing properties while its N8 isomer 3c forms duplexes with lower stability.
Collapse
Affiliation(s)
- Frank Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universitdät Osnabrück, Osnabrück, Germany.
| | | | | | | |
Collapse
|
15
|
Seela F, Peng X. Synthesis and Properties of 7‐Substituted 7‐Deazapurine (Pyrrolo[2,3‐d]pyrimidine) 2′‐Deoxyribonucleosides. ACTA ACUST UNITED AC 2005; Chapter 1:Unit 1.10. [DOI: 10.1002/0471142700.nc0110s21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Frank Seela
- Universität Osnabrück Osnabrück Germany
- Center for Nanotechnology (CeNTech) Münster Germany
| | - Xiaohua Peng
- Universität Osnabrück Osnabrück Germany
- Center for Nanotechnology (CeNTech) Münster Germany
| |
Collapse
|
16
|
Wang K, Stringfellow S, Dong S, Yu H. Synthesis and fluorescence study of 7-azaindole in DNA oligonucleotides replacing a purine base. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002; 58:2595-603. [PMID: 12396042 PMCID: PMC3764495 DOI: 10.1016/s1386-1425(02)00004-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The fluorescence spectroscopy of 7-azaindole (7aIn) incorporated in DNA oligonucleotides is investigated. Incorporation of 7aIn into DNA oligonucleotides is accomplished through standard solid-phase phosphoramidite chemistry. Fluorescence emission of the 7aIn chromophore shifts slightly to the red (from 386 nm to 388 nm) upon glycosylation at the N-1 position, but its relative fluorescence quantum yield increases 23 times, from 0.023 to 0.53. Upon incorporation into DNA, the fluorescence emission of 7aIn is greatly quenched with fluorescence quantum yields of 0.020 and 0.016 in single and double strand DNA, respectively. The fluorescence emission for 7aIn in DNA oligonucleotides shifts to the blue with an emission maximum at 379 nm. Both the strong fluorescence quenching and the blue shift of the emission spectrum signify that 7aIn is stacked with neighboring DNA bases in both single and double strand DNA. As the duplex DNA melts due to temperature increase, the fluorescence of the 7aIn chromophore increases, indicating the transition from the less fluorescent duplex DNA to the more fluorescent single strand DNA. Since this fluorescent 7aIn is a structural analog of purine, its fluorescence property may be utilized as a probe for studying nucleic acid structure and dynamics.
Collapse
Affiliation(s)
- Ke Wang
- Polymer Research Institute, Sichuan Union University, Chengdu, China
| | | | - Shiming Dong
- Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
| | - Hongtao Yu
- Department of Chemistry, Jackson State University, Jackson, MS 39217, USA
| |
Collapse
|
17
|
Seela F, Becher G, Chen Y. Fluorescence properties and base pair stability of oligonucleotides containing 8-aza-7-deaza-2'-deoxyisoinosine or 2'-deoxyisoinosine. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1581-98. [PMID: 11200261 DOI: 10.1080/15257770008045448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The fluorescence and the base pairing properties of 8-aza-7-deaza-2'-deoxyisoinosine (1) are described and compared with those of 2'-deoxyisoinosine (2). The corresponding phosphoramidites (11, 12) are synthesized using the diphenylcarbamoyl (DPC) residue for the 2-oxo group protection. The nucleosides 1 and 2 base pair with 2'-deoxy-5-methylisocytidine in DNA duplexes with antiparallel chain orientation and with 2'-deoxycytidine in a parallel DNA. These base pairs are less stable than the canonical dA-dT pair and that of 2'-deoxyinosine (4) with 2'-deoxycytidine. The fluorescence of the nucleosides 1 and 2 is quenched (approximately 95%) in duplex DNA. The residual fluorescence is used to determine the Tm-values, which are found to be the same as determined UV-spectrophotometrically.
Collapse
Affiliation(s)
- F Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Germany.
| | | | | |
Collapse
|
18
|
Rappaport HP. Synthesis of 9-(2-deoxy-beta-D-ribofuranosyl)purine-2-thione. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:839-43. [PMID: 10960040 DOI: 10.1080/15257770008035029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A synthesis of 9-(2-deoxy-beta-D-ribofuranosyl)purine-2-thione was performed by desulfurization of 2'-deoxy-6-thioguanine to give 2-amino-9-(2-deoxy-beta-D-ribofuranosyl)purine, diazotization with chloride replacement to give 2-chloro-9-(2-deoxy-beta-D-ribofuranosyl)purine, and the replacement of chloride with sulfur using thiolacetic acid and deacetylation.
Collapse
Affiliation(s)
- H P Rappaport
- Biology Department, Temple University, Philadelphia, PA 19122, USA
| |
Collapse
|
19
|
Seela F, Mittelbach C. 7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908043087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
20
|
Thermal stability studies of the non canonical base pair between 5-methyl-isocytosine and isohypoxanthine. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00820-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
21
|
De Napoli L, Messere A, Montesarchio D, Piccialli G, Varra M. 6-Chloroxanthosine, a Useful Intermediate for the Efficient Syntheses of [6-15N]-Isoguanosine, Isoinosine and Other Purine Nucleoside Analogues. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
22
|
Burmeister J, Azzawi A, Kiedrowski GV. Synthesis of novel phosphoramidite derivatives bearing pyrenyl and dansyl groups. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00598-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|