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Search for "oligodeoxynucleotide" in Full Text gives 7 result(s) in Beilstein Journal of Organic Chemistry.
Double-headed nucleosides: Synthesis and applications
- Vineet Verma,
- Jyotirmoy Maity,
- Vipin K. Maikhuri,
- Ritika Sharma,
- Himal K. Ganguly and
- Ashok K. Prasad
Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98
- 11 was dimethoxytritylated and phosphitylated following the standard procedures and incorporated once into a 13-mer oligodeoxynucleotide and an LNA-modified oligodeoxynucleotide sequence, and four-times in the middle of a 12-mer oligodeoxynucleotide sequence in order to study the effect of the
Graphical Abstract
Figure 1: Double-headed nucleosides. B1 and B2 = nucleobases or heterocyclic/carbocyclic moieties; L = linker....
Scheme 1: Synthesis of 2′-(pyrimidin-1-yl)methyl- or 2′-(purin-9-yl)methyl-substituted double-headed nucleosi...
Scheme 2: Synthesis of double-headed nucleoside 7 having two cytosine moieties.
Scheme 3: Synthesis of double-headed nucleoside 2′-deoxy-2′-C-(2-(thymine-1-yl)ethyl)-uridine (11).
Scheme 4: Double-headed nucleosides 14 and 15 obtained by click reaction.
Scheme 5: Synthesis of the double-headed nucleoside 19.
Scheme 6: Synthesis of the double-headed nucleosides 24 and 25.
Scheme 7: Synthesis of double-headed nucleosides 28 and 29.
Scheme 8: Synthesis of double-headed nucleoside 33.
Scheme 9: Synthesis of double-headed nucleoside 37.
Scheme 10: Synthesis of the double-headed nucleoside 1-(5′-O-(4,4′-dimethoxytrityl)-2′-C-((4-(pyren-1-yl)-1,2,...
Scheme 11: Synthesis of triazole-containing double-headed ribonucleosides 46a–c and 50a–e.
Scheme 12: Synthesis of double-headed nucleosides 54a–g.
Scheme 13: Synthesis of double-headed nucleosides 59 and 60.
Scheme 14: Synthesis of the double-headed nucleosides 63 and 64.
Scheme 15: Synthesis of double-headed nucleosides 66a–c.
Scheme 16: Synthesis of benzoxazole-containing double-headed nucleosides 69 and 71 from 5′-amino-5′-deoxynucle...
Scheme 17: Synthesis of 4′-C-((N6-benzoyladenin-9-yl)methyl)thymidine (75) and 4′-C-((thymin-1-yl)methyl)thymi...
Scheme 18: Synthesis of double-headed nucleosides 5′-(adenine-9-yl)-5′-deoxythymidine (79) and 5′-(adenine-9-y...
Scheme 19: Synthesis of double-headed nucleosides 85–87 via reversed nucleosides methodology.
Scheme 20: Double-headed nucleosides 91 and 92 derived from ω-terminal-acetylenic sugar derivatives 90a,b.
Scheme 21: Synthesis of double-headed nucleosides 96a–g.
Scheme 22: Synthesis of double-headed nucleosides 100 and 103.
Scheme 23: Double-headed nucleosides 104 and 105 with a triazole motif.
Scheme 24: Synthesis of the double-headed nucleosides 107 and 108.
Scheme 25: Synthesis of double-headed nucleoside 110 with additional nucleobase in 5′-(S)-C-position joined th...
Scheme 26: Synthesis of double-headed nucleosides 111–113 with additional nucleobases in the 5′-(S)-C-position...
Scheme 27: Synthesis of double-headed nucleoside 114 by click reaction.
Scheme 28: Synthesis of double-headed nucleosides 118 with an additional nucleobase at the 5′-(S)-C-position.
Scheme 29: Synthesis of bicyclic double-headed nucleoside 122.
Scheme 30: Synthesis of double-headed nucleosides 125a–c derived from 2′-amino-LNA.
Scheme 31: Double-headed nucleoside 127 obtained by click reaction.
Scheme 32: Synthesis of double-headed nucleoside 130.
Scheme 33: Double-headed nucleosides 132a–d and 134a–d synthesized by Sonogashira cross coupling reaction.
Scheme 34: Synthesis of double-headed nucleosides 137 and 138 via Suzuki coupling.
Scheme 35: Synthesis of double-headed nucleosides 140 and 141 via Sonogashira cross coupling reaction.
Scheme 36: Synthesis of double-headed nucleoside 143.
Scheme 37: Synthesis of the double-headed nucleoside 146.
Scheme 38: Synthesis of 5-C-alkynyl-functionalized double-headed nucleosides 151a–d.
Scheme 39: Synthesis of 5-C-triazolyl-functionalized double-headed nucleosides 154a, b.
Scheme 40: Synthesis of double-headed nucleosides 157a–c.
Scheme 41: Synthesis of double-headed nucleoside 159, phosphoramidite 160 and the corresponding nucleotide mon...
Scheme 42: Synthesis of double-headed nucleoside 163, phosphoramidite 164 and the corresponding nucleotide mon...
Scheme 43: Synthesis of double-headed nucleoside 167, phosphoramidite 168, and the corresponding nucleotide mo...
Scheme 44: Synthesis of double-headed nucleoside 171, phosphoramidite 172, and the corresponding nucleotide mo...
Scheme 45: Synthesis of double-headed nucleoside 175, phosphoramidite 176, and the corresponding nucleotide mo...
Scheme 46: Synthesis of double-headed nucleoside 178.
Scheme 47: Synthesis of the double-headed nucleosides 181 and 183.
Scheme 48: Alternative synthesis of the double-headed nucleoside 183.
Scheme 49: Synthesis of double-headed nucleoside 188 through thermal [2 + 3] sydnone–alkyne cycloaddition reac...
Scheme 50: Synthesis of the double-headed nucleosides 190 and 191.
Scheme 51: Synthesis of 1-((5S)-2,3,4-tri-O-acetyl-5-(2,6-dichloropurin-9-yl)-β-ᴅ-xylopyranosyl)uracil (195).
Scheme 52: Synthesis of hexopyranosyl double-headed pyrimidine homonucleosides 200a–c.
Figure 2: 3′-C-Ethynyl-β-ᴅ-allopyranonucleoside derivatives 201a–f.
Scheme 53: Synthesis of 3′-C-(1,4-disubstituted-1,2,3-triazolyl)-double-headed pyranonucleosides 203–207.
Scheme 54: Synthesis of 3′-C-(1,4-disubstituted-1,2,3-triazolyl)-double-headed pyranonucleosides 208 and 209.
Scheme 55: Synthesis of 3′-C-(1,4-disubstituted-1,2,3-triazolyl)-double-headed pyranonucleoside 210.
Scheme 56: Synthesis of double-headed acyclic nucleosides (2S,3R)-1,4-bis(thymine-1-yl)butane-2,3-diol (213a) ...
Scheme 57: Synthesis of double-headed acyclic nucleosides (2R,3S)-1,4-bis(thymine-1-yl)butane-2,3-diol (213c) ...
Scheme 58: Synthesis of double-headed acetylated 1,3,4-oxadiazino[6,5-b]indolium-substituted C-nucleosides 218b...
Scheme 59: Synthesis of double-headed acyclic nucleoside 222.
Scheme 60: Synthesis of functionalized 1,2-bis(1,2,4-triazol-3-yl)ethane-1,2-diols 223a–f.
Scheme 61: Synthesis of acyclic double-headed 1,2,4-triazino[5,6-b]indole C-nucleosides 226–231.
Scheme 62: Synthesis of double-headed 1,3,4-thiadiazoline, 1,3,4-oxadiazoline, and 1,2,4-triazoline acyclo C-n...
Scheme 63: Synthesis of double-headed acyclo C-nucleosides 240–242.
Scheme 64: Synthesis of double-headed acyclo C-nucleoside 246.
Scheme 65: Synthesis of acyclo double-headed nucleoside 250.
Scheme 66: Synthesis of acyclo double-headed nucleoside 253.
Scheme 67: Synthesis of acyclo double-headed nucleosides 259a–d.
Scheme 68: Synthesis of acyclo double-headed nucleoside 261.
Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection
- Shahien Shahsavari,
- Dhananjani N. A. M. Eriyagama,
- Bhaskar Halami,
- Vagarshak Begoyan,
- Marina Tanasova,
- Jinsen Chen and
- Shiyue Fang
Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108
- 60 years of intensive research, the challenges for chemical oligodeoxynucleotide (ODN) synthesis have been considered largely overcome [1][2][3][4]. However, this is only true for unmodified ODNs at limited synthesis scales. For modified ODNs that contain sensitive functionalities including those
Graphical Abstract
Scheme 1: Comparison of Dmoc and dM-Dmoc as nucleobase protecting groups for ODN synthesis.
Figure 1: dM-Dmoc phosphoramidite monomers and CPG with Dmoc linker.
Scheme 2: Synthesis of compound 5 [44], nucleoside phosphoramidite monomers 3a–c and phosphoramidite capping agen...
Figure 2: Structure of phosphoramidites containing electrophilic groups.
Scheme 3: Synthesis of ester-containing phosphoramidite 26a.
Figure 3: ODN sequences 30a–e. Their 5'-tritylated versions are labeled as 30a-tr, 30b-tr, 30c-tr, 30d-tr, an...
Figure 4: RP HPLC profiles of (a) crude 30a-tr, (b) pure 30a-tr, (c) crude 30a, (d) pure 30a, (e) crude 30c-tr...
Figure 5: PAGE analyses of ODNs 30a–e. Lanes 1–5 are ODNs 30a–e, respectively.
Figure 6: MALDI–TOF MS of (a) ODN 30a and (b) 30c.
Scheme 4: ODN deprotection and cleavage under non-nucleophilic conditions.
An amine protecting group deprotectable under nearly neutral oxidative conditions
- Shahien Shahsavari,
- Chase McNamara,
- Mark Sylvester,
- Emily Bromley,
- Savannah Joslin,
- Bao-Yuan Lu and
- Shiyue Fang
Beilstein J. Org. Chem. 2018, 14, 1750–1757, doi:10.3762/bjoc.14.149
- Dmoc group for amine protection in automated solid-phase oligodeoxynucleotide (ODN) synthesis [18]. For deprotection, we found that sodium periodate could effectively oxidize multiple Dmoc functions in the ODNs to achieve complete deprotection. Under these oxidative conditions, oxidation of the ODN was
Graphical Abstract
Scheme 1: Dmoc and dM-Dmoc protection and deprotection of amines.
Scheme 2: Selective deprotection of dM-Dmoc-, Boc- and Fmoc-protected amines.
Fluorogenic PNA probes
- Tirayut Vilaivan
Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17
- transduction and readout strategies have been developed, even for fluorescence-based detection alone, the recognition element of the probe is almost always an oligodeoxynucleotide. During the past few decades, there have been continuous developments of unnatural oligonucleotides with superior properties that
- make them worthwhile alternatives to the traditionally used oligodeoxynucleotide probes. In this respect, peptide nucleic acids (PNA) [5] have been one of the most widely used alternative oligonucleotide probes in addition to locked and morpholino nucleic acids [6][7]. Although many review articles on
Graphical Abstract
Figure 1: The design of classical DNA molecular beacons.
Figure 2: Structures of DNA and selected PNA systems.
Figure 3: Various binding modes of PNA to double stranded DNA including triplex formation, triplex invasion, ...
Figure 4: The design and working principle of the PNA beacons according to (A) Ortiz et al. [41] and (B) Armitage...
Figure 5: The design of "stemless" PNA beacons.
Figure 6: The applications of PNA openers to facilitate the binding of PNA beacons to double stranded DNA [40,47].
Figure 7: The working principle of snap-to-it probes that employed metal chelation to bring the dyes in close...
Figure 8: Examples of pre-formed dye-labeled PNA monomers and functionalizable PNA monomers.
Figure 9: Dual-labeled PNA beacons with end-stacking or intercalating quencher.
Figure 10: The working principle of hybrid PNA-peptide beacons for detection of (A) proteins [80] and (B) protease...
Figure 11: The working principle of binary probes.
Figure 12: The working principle of nucleic acid templated fluorogenic reactions leading to a (A) ligated prod...
Figure 13: Catalytic cycles in fluorogenic nucleic acid templated reactions [90].
Figure 14: The working principle of strand displacement probes.
Figure 15: (A) Examples of CPP successfully used with labeled PNA probes. (B) The use of single-labeled PNA pr...
Figure 16: The concept of PNA–GO platform for DNA/RNA sensing.
Figure 17: Single-labeled fluorogenic PNA probes.
Figure 18: Examples of environment sensitive fluorescent labels that have been incorporated into PNA probes as...
Figure 19: The mechanism of fluorescence change in TO dye.
Figure 20: Fluorescent nucleobases capable of hydrogen bonding that have been incorporated into PNA probes.
Figure 21: Comparison of the designs of the (A) light-up PNA probe and (B) FIT PNA probe.
Figure 22: The structures of TO and its analogues that have successfully been used in FIT PNA probes.
Figure 23: The working principle of dual-labeled FIT PNA probes [222,223].
Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes
- Christine Beuck and
- Elmar Weinhold
Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239
- ; DNA methyltransferase; nucleic acids; oligodeoxynucleotide; thionucleoside; Introduction Covalent interstrand DNA cross-links have long sparked clinical and biochemical interest. The cytotoxicity of bisfunctional alkylating agents like nitrogen mustards or chloroethyl nitrosourea (CENU) derivatives
Graphical Abstract
Figure 1: Covalent cross-linking of a I6S/U4S or G6S/U4S base pair within duplex ODN 1∙2 (a) by bis-alkylatio...
Figure 2: Characterization of HPLC-purified cross-linked duplex 1I6S-Et-S4U2 (a) by denaturing anion exchange...
Figure 3: Characterization of HPLC-purified cross-linked duplex 1G6S-Et-S4U2 (a) by denaturing anion exchange...
Figure 4: Opening and traceless linker removal of the cross-linked duplexes 1I6S-Et-S4U2 and 1G6S-Et-S4U2 by ...
Figure 5: UV time course of opening of the cross-link in duplex 1I6S-Et-S4U2 with the thiol nucleophiles DTT ...
Figure 6: Competition binding of M.TaqI to DNA with unlocked and locked target base pairs. Increasing amounts...
Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach
- Tatyana V. Abramova,
- Olga B. Morozova,
- Vladimir N. Silnikov and
- Alexandra V. Yurkovskaya
Beilstein J. Org. Chem. 2013, 9, 2898–2909, doi:10.3762/bjoc.9.326
- -elimination. It is worthy to notice that the TBAF treatment is essential when the phosphotriester group contains the aromatic residue (p-chlorophenyl in our case), which is much more stable to ammonia than the 2-cyanoethyl group usually used in the phosphoramidite oligodeoxynucleotide synthesis. After the
Graphical Abstract
Figure 1: Model compounds for the TR NMR photo-CIDNP experiments: conjugates of 4-benzoylbenzoic acid, 2’-deo...
Scheme 1: Synthesis of functionalized derivatives of 4-benzoylbenzoic acid (9), L-tryptophan (11, 16) and L-t...
Scheme 2: Synthesis of conjugates 1–3: i) 2,4,6-triisopropylbenzenesulfonyl chloride (TPSCl), 1-methylimidazo...
Scheme 3: Synthesis of conjugates 4 and 5: i) TPSCl, MeIm, Py; ii) AcOH/H2O; iii) p-chlorophenyl dichlorophos...
Scheme 4: Synthesis of conjugates 6–8. i) TPSCl, MeIm, Py; ii) TBAF in Py/H2O, then NH3/H2O; iii) TBAF in Py/H...
Synthesis, reactivity and biological activity of 5-alkoxymethyluracil analogues
- Lucie Brulikova and
- Jan Hlavac
Beilstein J. Org. Chem. 2011, 7, 678–698, doi:10.3762/bjoc.7.80
- the 3',5'-hydroxyl groups, the 5'-hydroxyl group was dimethoxytritylated and the 3'-hydroxyl group phosphitylated to afford phosphoramidite 134. The final phosphoramidite 134 was incorporated into oligodeoxynucleotide sequences via solid-phase synthesis by an automated DNA synthesizer. Modified
- styrene to afford nucleoside 147. The oxidation of alkene function in 147 with OsO4 led to a mixture of diastereomers of vicinal diols 148. For the introduction of the oligodeoxynucleotide 146, the dihydroxynucleoside 147 was converted to the corresponding phosphoramidite. This was carried out as follows
- protection groups at the sugar ring were removed by the reaction with TBAF. Finally, the 5'-hydroxyl groups were tritylated and the 3'-hydroxy group converted to the corresponding phosphoramidite 150. The resulting phosphoramidite was incorporated into a 12-mer oligodeoxynucleotide via automated solid-phase
Graphical Abstract
Figure 1: Investigated derivatives.
Figure 2: Modifications of uracil ring.
Figure 3: 5-(3,3,3-Trifluoro-1-methoxypropyl)-2'-deoxyuridine (1).
Scheme 1: Synthesis of 5-(3,3,3-trifluoro-1-methoxypropyl)-2'-deoxyuridine (1) and 5-(3,3,3-trifluoro-1-(2-pr...
Scheme 2: Synthesis of 5-(3,3,3-trifluoro-1-methoxyprop-1-yl)-5,6-dihydro-2'-deoxyuridine (8).
Scheme 3: Synthesis of 5-(methoxy-2-haloethyl)-2'-deoxyuridines 12 and 13.
Scheme 4: Synthesis of 5-(1-methoxy-2-iodoethyl) nucleosides 28–30.
Figure 4: [125I] radiolabelled 5-(1-methoxy-2-iodoethyl)-2'-deoxyuridine 31.
Scheme 5: Synthesis of 5-(1-alkoxy-2-iodoethyl) 34–36 and 5-(1-ethoxy-2,2-diiodoethyl)-2'-deoxyuridine (33).
Scheme 6: Synthesis of 5-(1-methoxy-2-iodoethyl)-3',5'-di-O-acetyl-2'-deoxyuridine (38) and 5-(1-ethoxy-2-iod...
Figure 5: 5-(1-Hydroxy(or ethoxy)-2-haloethyl)-3',5'-di-O-acetyl-2'-deoxyuridines 43–46.
Scheme 7: 5-(1-Methoxy-2,2-dihaloethyl)-2'-deoxyuridines 47–49.
Scheme 8: Synthesis of 5-[1-(2-haloethyl(or nitro)ethoxy)-2-iodoethyl]-2'-deoxyuridines 50–54.
Scheme 9: Synthesis of alkoxyuracil analogues 56–61.
Figure 6: 5-(Methoxy-2-haloethyl)uracils 62–64.
Scheme 10: Synthesis of perfluoro derivatives 70–74.
Scheme 11: Synthesis of 1-β-D-arabinofuranosyl-5-(1-methoxy-2-iodoethyl)uracil (79).
Scheme 12: Synthesis of 1-β-D-arabinofuranosyl-5-(2,2-dibromo-1-methoxyethyl)uracil 82 and uridine analogue 83....
Scheme 13: Synthesis of methoxy derivative 87.
Scheme 14: Synthesis of 5-(1-methoxy-2-azidoethyl)-2'-deoxyuridine (93).
Scheme 15: Synthesis of methoxyalkyl derivatives 96 and 97.
Scheme 16: Synthesis of 5-(1-methoxyethyl)-2'-deoxyuridine (100).
Scheme 17: Synthesis of 2'-deoxy-5-(1-methoxyethyl)-4'-thiouridine (104).
Figure 7: 5-(1-Butoxyethyl)uracil 105 and 5-(1-butoxyethyl)-2'-deoxyuridine (106).
Scheme 18: Synthesis of β- and α-anomer of 5-(1-ethoxy-2-methylprop-1-yl)-2'-deoxyuridine.
Scheme 19: Synthesis of 5-(1-acyloxyethyl)-1-(tetrahydrofuran-2-yl)uracils 117 and 118.
Scheme 20: Synthesis of 5-(1,2-diacetoxyethyl)-3',5'-di-O-acetyl-2'-deoxyuridine 120.
Scheme 21: Synthesis of 5-[alkoxy-(4-nitrophenyl)methyl]uracils 124.
Scheme 22: Synthesis of 5-[alkoxy-(4-nitrophenyl)methyl]uridines 126 and 127.
Scheme 23: Synthesis of phosphoramidite 134. Reaction conditions 1: (a) TBDMSCl, imidazole, pyridine, 33 h, 99...
Scheme 24: Synthesis of phosphoramidite 145. (a) B(OCH3)3, CH(OCH3)3, Na2CO3, MeOH, 150 °C; (b) I2, (0.6 equiv...
Figure 8: Oligonucleotide 146.
Scheme 25: Synthesis of phosphoramidite 150.
Figure 9: 2'-Deoxyuridine derivatives 151–154.
Scheme 26: Synthesis of 2'-deoxyuridine derivatives 151–152.
Scheme 27: Synthesis of 5-[3-(2'-deoxyuridin-5-yl)-1-methoxyprop-1-yl]-2'-deoxyuridine (163).
Scheme 28: Synthesis of “metallocenonucleosides” 164 and 167.
Scheme 29: Synthesis of 5-(2,4:3,5-di-O-benzylidene-D-pentahydroxypentyl)-2,4-di-tert-butoxy-pyrimidine 172 an...
Figure 10: α- and β-pseudouridine (174 and 175).
Figure 11: 5'-Modified pseudouridine 176 and secopseudouridines 177, 178.
Figure 12: Methoxy derivatives 12, 13 and 28.
Figure 13: 5-(1-Methoxy-2,2-dihaloethyl)-2'-deoxyuridines 47–49.
Figure 14: 5-(1-Methoxyethyl)-2'-deoxyuridine 100.
Figure 15: 2'-Deoxy-5-(1-methoxyethyl)-4'-thiouridine (104).
Figure 16: 5-(1-Methoxy-2-azidoethyl)-2'-deoxyuridine (93).
Figure 17: 5-[1-(2-Halo(or nitro)ethoxy-2-iodoethyl)]-2'-deoxyuridines 50–54.
Figure 18: 5-[Alkoxy-(4-nitrophenyl)-methyl] uracil analogues 124, 126 and 127.
Figure 19: Methoxyiodoethyl pyrimidine nucleoside 79.
Figure 20: 5-[alkoxy-(4-nitro-phenyl)-methyl]uridines 126 and 127.
