Nucleic acid chemistry

Editor: Prof. Hans-Achim Wagenknecht
Karlsruhe Institute of Technology

Since the discovery of the structure of the DNA double helix in 1953, we know that DNA is of critical importance, carrying the genetic information for all living organisms. Only a few years later the first reports on the chemical synthesis of oligonucleotides appeared. During the past years the field of nucleic acid chemistry has expanded dramatically: natural and artificial functionalities, as well as probes, markers or other biologically active molecules, can be synthetically introduced into DNA (as well as RNA) by preparing the corresponding artificial DNA and RNA building blocks. Although nucleic acid chemistry appears to be a mature part of organic and bioorganic chemistry, the many questions that are still being raised give sufficient motivation to continue to synthesize new nucleic acid probes. Moreover, in addition to their biological functionality, DNA and RNA are considered as increasingly important architectures and scaffolds for two- and three-dimensional objects, networks and materials for nanosciences.

Nucleic acid chemistry

Hans-Achim Wagenknecht

Editorial
Published 10 Dec 2014

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Beilstein J. Org. Chem. 2014, 10, 2928–2929, doi:10.3762/bjoc.10.311

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A new building block for DNA network formation by self-assembly and polymerase chain reaction

Holger Bußkamp,
Sascha Keller,
Marta Robotta,
Malte Drescher and
Andreas Marx

Full Research Paper
Published 07 May 2014

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1. Graphical Abstract
2. Scheme 1: Reagents and conditions: (a) PdCl₂(PPh₃)₂, DMF, CuI, NEt₃, 55 °C, microwave, 82%; (b) PdCl₂(PPh₃)₂,...
  
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3. Scheme 2: Stepwise solid-phase synthesis for branched oligonucleotides. (I): The first oligonucleotide branch...
  
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4. Figure 1: (A) Depiction of synthesized branched oligonucleotides; (B) Sequences of all synthesized branched o...
  
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5. Figure 2: Thermal denaturating studies of self-complementary branched oligonucleotides. Different conditions ...
  
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6. Figure 3: Generation of DNA networks with Taq DNA polymerase from 1062 nt template using primer ODN I and ODN...
  
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7. Figure 4: AFM analysis of DNA structures: (A) Overview-scan 10 × 10 µm showing DNA networks generated after 2...
  
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8. Figure 5: EPR spectra with corresponding spectral simulations (red line) of (A) dT*TP, (B) PCR reaction produ...
  
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Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

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Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

Alex Manicardi,
Lucia Guidi,
Alice Ghidini and
Roberto Corradini

Full Research Paper
Published 02 Jul 2014

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1. Graphical Abstract
2. Figure 1: (a) TAT triplet structure showing Watson–Crick and Hoogsteen base pairing; the binding can be reinf...
  
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3. Scheme 1: Synthesis of the PNA monomer 1: i) 1. PPh₃, H₂O, THF; 2. TFA, 71%; ii) 1-pyreneacetic acid, HBTU, D...
  
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4. Figure 2: Fluorescence spectra at 347 nm excitation, recorded at 20 °C of: (a) PNA1, (b) PNA2, (c) PNA3, (d) ...
  
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5. Figure 3: (a) Increase in fluorescence intensity of the excimer band for PNA2 upon addition of complementary ...
  
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6. Figure 4: Ratio of the intensities of the pyrene excimer (F₄₇₄) and monomer emission (F₃₇₉) for the PNA probe...
  
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Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

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Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

Christian B. Winiger,
Simon M. Langenegger,
Oleg Khorev and
Robert Häner

Full Research Paper
Published 11 Jul 2014

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1. Graphical Abstract
2. Figure 1: (A) Structures of 1,8-dialkynylpyrene (Y) and PDI (E); (B) illustration of the electrostatic potent...
  
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3. Figure 2: A plot of melting temperature (T_m) versus the number of pyrene–PDI interactions for duplexes 1*2 to ...
  
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4. Figure 3: UV–vis absorption spectra (scaled) of duplexes 1*2 (blue) and 1*6 (red) at 20 °C. Conditions: see Table 1.
  
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5. Figure 4: UV–vis absorption spectra (scaled) of duplexes 1*2 to 1*6 at 20 °C. Conditions: see Table 1.
  
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6. Figure 5: Temperature-dependent UV–vis absorption spectrum of 1*2. Conditions: see Table 1.
  
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7. Figure 6: Fluorescence spectra of oligomer 1 (black), duplex 1*2 (blue) and duplex 1*6 (red) at 20 °C. Excita...
  
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8. Figure 7: PAGE experiment. All oligomers were used in a total amount of 150 pmol in 10 mM sodium phosphate bu...
  
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Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

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Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

Branislav Dugovic,
Michael Wagner and
Christian J. Leumann

Full Research Paper
Published 12 Aug 2014

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1. Graphical Abstract
2. Figure 1: Chemical structures and carbon numbering scheme of tricyclo(tc)-DNA (top, left), bicyclo(bc)-DNA (t...
  
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3. Scheme 1: Conditions: (a) NaBH₄, CeCl₃·7H₂O, MeOH, −78 °C → rt, 1.5 h, 73% (+9% of C6-epimer); (b) TBS-Cl, im...
  
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4. Scheme 2: Conditions: (a) thymine, BSA, TMSOTf, TMSCl, CH₃CN, rt, 2.5 h; (b) DMTrCl, pyridine, rt, 16 h, 29% ...
  
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5. Figure 2: X-ray structure of top row: nucleosides 8β (left), 11β (center) and overlay of both structures (rig...
  
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6. Scheme 3: Pathways for elimination of the modified nucleotides during the oxidation step in oligonucleotide a...
  
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Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

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Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

Nico Rublack and
Sabine Müller

Full Research Paper
Published 15 Aug 2014

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1. Graphical Abstract
2. Figure 1: Retrosynthetic analysis of the bifunctional cytidine derivative 1 for functionalization of a period...
  
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3. Figure 2: Introduction of the triazolyl moiety into the uridine derivative 7 generating synthon 3. I: 4 equiv...
  
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4. Figure 3: Preparation of synthon 4 and substitution of the triazolyl moiety of 3 to form the fully protected ...
  
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5. Figure 4: Synthesis of 2',3'-bis-O-(tert-butyldimethylsilyl)-1-[4-(N'-biotinyl-3,6-dioxaoctane-1,8-diamine)py...
  
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6. Figure 5: Formation of the phosphoramidite 2 from amino alcohol 13, and subsequent coupling to the 5'-O-depro...
  
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7. Figure 6: A) Reversed-phase HPLC purification of 1 after complete deprotection of 16. A represents the absorp...
  
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8. Figure 7: Reaction scheme of periodate oxidation of a 20mer model RNA followed by coupling of cytidine deriva...
  
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9. Figure 8: Reversed-phase HPLC analysis. A: Crude product of the coupling reaction between the 20mer model RNA...
  
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Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

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Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

Jasmin Levic and
Ronald Micura

Full Research Paper
Published 18 Aug 2014

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1. Graphical Abstract
2. Scheme 1: The hypermodified nucleoside queuosine (Q) and the synthetic targets of preQ₁ bases 1 to 3 with com...
  
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3. Scheme 2: Synthesis of [¹⁵N1,¹⁵N3,H₂¹⁵N(C2)]-preQ₁ base (1). a) CH₃ONa (10 equiv) CH₃OH, reflux, 10 h, RP C18...
  
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4. Scheme 3: Synthesis of [¹⁵N9]-preQ₁ base (2). a) [¹⁵N]-KCN (1 equiv), Na₂CO₃, H₂O, pH 9, 80 °C, 3 h, then roo...
  
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5. Scheme 4: Synthesis of [H₂¹⁵N(C7')] preQ₁ base (3). a) K₂CO₃ (1.5 equiv), DMF, 70 °C, 14 h, 47%. b) Dess–Mart...
  
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6. Figure 1: Comparison of ¹H NMR spectra of the preQ₁ bases 1, 2 and 3 with complementary ¹⁵N labeling patterns...
  
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Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

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Pyrrolidine nucleotide analogs with a tunable conformation

Lenka Poštová Slavětínská,
Dominik Rejman and
Radek Pohl

Full Research Paper
Published 22 Aug 2014

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1. Graphical Abstract
2. Figure 1: Examples of biologically active acyclic and cyclic nucleotide analogs.
  
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3. Figure 2: The pyrrolidine nucleotide analogs investigated in this study.
  
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4. Scheme 1: The synthesis of pyrrolidine nucleotides 7–14.
  
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5. Figure 3: The numbering of the pyrrolidine ring, the nucleobase and the endocyclic phase angles for the purpo...
  
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6. Figure 4: The aliphatic part (pyrrolidine protons) of the ¹H NMR spectra of 9 measured in D₂O at different pD...
  
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7. Figure 5: Changes of selected ¹H and ¹³C chemical shifts of 9 upon pD change.
  
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8. Figure 6: The deuteration equilibria of phosphonomethyl derivatives 7–10.
  
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9. Figure 7: The aliphatic part (pyrrolidine protons) of the ¹H NMR spectra of 13 measured in D₂O at different p...
  
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10. Figure 8: Amide rotamers of phosphonoformyl derivatives 11–14.
  
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11. Figure 9: The ³¹P NMR spectra (202.3 MHz) of 14 measured (the black curve) and simulated (the red curve) at v...
  
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12. Figure 10: A part of the H,C-HSQC spectrum of derivative 13, showing the assignment of rotamers A and B.
  
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13. Figure 11: The pseudorotation pathway of the pyrrolidine ring in the compounds studied. The sign B stands for ...
  
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14. Figure 12: An example of the stereospecific assignment of pyrrolidine-ring protons of 14 in the H,H-ROESY spec...
  
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15. Figure 13: The energy profile of the five-membered pyrrolidine ring pseudorotation for adenine derivatives 9 a...
  
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16. Figure 14: The most stable conformations of adenine derivatives 9 and 13A calculated by the B3LYP/6-31++G* met...
  
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Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

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Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Keunsoo Kim,
Venkateshwarlu Punna,
Phaneendrasai Karri and
Ramanarayanan Krishnamurthy

Full Research Paper
Published 08 Sep 2014

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1. Graphical Abstract
2. Figure 1: A constitutional and conformational (idealized) representation of isoGNA, an isomer of glycerol nuc...
  
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3. Scheme 1: Initial routes towards the synthesis of iso-glycerol nucleosides.
  
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4. Scheme 2: Preparation of thymine and adenine containing phosphoramidites of isoGNA.
  
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5. Scheme 3: Preparation of guanine- and cytosine-containing phosphoramidites of isoGNA.
  
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6. Scheme 4: Preparation of adenine containing phosphoramidite of isoGNA.
  
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7. Scheme 5: Mitsunobu reaction with the di-Boc-adenine.
  
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8. Scheme 6: An attempt to remove both Boc and silyl groups simultaneously.
  
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9. Scheme 7: The synthesis of 26 via tritylation and benzoylation.
  
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Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

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Second generation silver(I)-mediated imidazole base pairs

Susanne Hensel,
Nicole Megger,
Kristina Schweizer and
Jens Müller

Full Research Paper
Published 09 Sep 2014

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1. Graphical Abstract
2. Scheme 1: Schematic representation of an imidazole–Ag(I)–imidazole base pair (top) and a thyminate–Hg(II)–thy...
  
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3. Figure 1: Different views of a DNA duplex comprising three neighbouring imidazole–Ag(I)–imidazole base pairs....
  
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4. Scheme 2: Schematic representation of silver(I)-mediated imidazole homo base pairs involving 2-methylimidazol...
  
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5. Scheme 3: Synthesis of methylimidazole-based nucleosides and their corresponding phosphoramidites required fo...
  
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6. Scheme 4: Oligonucleotide sequences under investigation (X = 2-methylimidazole 2a or 4-methylimidazole 2b).
  
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7. Figure 2: Melting curves based on normalized UV absorbance at 260 nm of a) duplex I with X = 4-methylimidazol...
  
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8. Figure 3: CD spectra of a) duplex I with X = 4-methylimidazole and b) duplex II with X = 2-methylimidazole in...
  
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Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

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Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

Nattawut Yotapan,
Chayan Charoenpakdee,
Pawinee Wathanathavorn,
Boonsong Ditmangklo,
Hans-Achim Wagenknecht and
Tirayut Vilaivan

Full Research Paper
Published 11 Sep 2014

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1. Graphical Abstract
2. Scheme 1: Synthesis of propargylated Nile red 1.
  
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3. Scheme 2: Synthesis of azidobutyl- and Nile red-modified acpcPNA.
  
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4. Figure 1: MALDI–TOF mass spectra of the crude 10mer acpcPNA before (top) (calcd m/z 3688.0), and after functi...
  
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5. Figure 2: Normalized absorption (---) and fluorescence (––) spectra of (a) propargyl Nile red 1 and (b) Nile ...
  
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6. Figure 3: (a) Normalized absorption (---) and fluorescence (––) spectra and (b) fluorescence spectra of Nile ...
  
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Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

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Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

Marijana Radić Stojković,
Marko Škugor,
Łukasz Dudek,
Jarosław Grolik,
Julita Eilmes and
Ivo Piantanida

Full Research Paper
Published 12 Sep 2014

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1. Graphical Abstract
2. Scheme 1: Studied DBTAA–adenine conjugates (AP3, AP3am, AP5, AP6) [11], and the reference compounds lacking adeni...
  
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3. Scheme 2: Preparations of the products AP3am and AP5. Starting compounds were synthesized according to previo...
  
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4. Figure 1: Changes in the UV–vis spectrum of AP3am (c = 1.0 × 10⁻⁵ mol dm⁻³) upon titration with poly dA–poly ...
  
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5. Figure 2: Induced CD bands observed for AP3, AP3am, AP6 for poly dA–poly dT and poly (dAdT)₂ (c = 3.0 × 10⁻⁵ ...
  
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6. Figure 3: Comparison of AP3 ICD bands for ss-DNA (dA and dT) with alternating- and homo-AT ds-polynucleotides...
  
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7. Figure 4: Self-folding of AP5 (upper left – note the stacking of DBTAA and adenine) and AP3 (lower left – not...
  
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8. Figure 5: Schematic presentation of self-folded AP5 (free AP5 see Figure 4; upper left) in the minor groove of poly d...
  
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Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

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Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

Alejandro Gimenez Molina,
Amit M. Jabgunde,
Pasi Virta and
Harri Lönnberg

Full Research Paper
Published 29 Sep 2014

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1. Graphical Abstract
2. Scheme 1: Synthesis of building blocks of the oligoribonucleotide synthesis. (i) TFA, aq THF, 0 °C; (ii) 2-me...
  
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3. Scheme 2: (i) 6a, CuI, sodium ascorbate, DMAc; (ii) HCl in dioxane/MeOH 2:1, (iii) 5a', 4,5-dicyanoimidazole,...
  
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4. Figure 1: HPLC traces referring to precipitation of the tetrapodal support bearing fully protected UU-dimers (...
  
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5. Figure 2: HPLC traces referring to precipitation of the tetrapodal support bearing 5'-O-deprotected UU-dimers...
  
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6. Figure 3: Negative ion ESIMS and HPLC traces of the isolated 3'-UUGCA-5'. For the MS over a wider mass range,...
  
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Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

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Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

Christine Beuck and
Elmar Weinhold

Full Research Paper
Published 01 Oct 2014

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1. Graphical Abstract
2. Figure 1: Covalent cross-linking of a I^6S/U^4S or G^6S/U^4S base pair within duplex ODN 1∙2 (a) by bis-alkylatio...
  
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3. Figure 2: Characterization of HPLC-purified cross-linked duplex 1^I6S-Et-S4U2 (a) by denaturing anion exchange...
  
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4. Figure 3: Characterization of HPLC-purified cross-linked duplex 1^G6S-Et-S4U2 (a) by denaturing anion exchange...
  
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5. Figure 4: Opening and traceless linker removal of the cross-linked duplexes 1^I6S-Et-S4U2 and 1^G6S-Et-S4U2 by ...
  
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6. Figure 5: UV time course of opening of the cross-link in duplex 1^I6S-Et-S4U2 with the thiol nucleophiles DTT ...
  
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7. Figure 6: Competition binding of M.TaqI to DNA with unlocked and locked target base pairs. Increasing amounts...
  
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Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

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Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

Emma Werz and
Helmut Rosemeyer

Full Research Paper
Published 02 Oct 2014

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1. Graphical Abstract
2. Figure 1: Chemical formulae and lipo-oligonucleotide sequences.
  
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3. Figure 2: Schematic illustrations (experiments A–F) of the specific DNA duplex formation at artificial lipid ...
  
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4. Figure 3: Experimental setup. Schematic drawing of the laser scanning microscope, the optical transparent mic...
  
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5. Figure 4: Chronological protocol of duplex formation of the lipo-oligonucleotide 4 with the complementary Cy5...
  
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6. Figure 5: Comparison of the bilayer brightness intensity with either Cy5 (irradiation: 635 nm) or Sybr Green ...
  
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7. Figure 6: Scheme of a z-scan of a lipid bilayer showing two locations for measurements of the diffusion times...
  
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8. Figure 7: Experiment B (4 + 6 + SG). Bilayer brightness as function of the various events (addition of oligon...
  
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9. Figure 8: Experiment D (4 + 9 + SG). Bilayer brightness as function of time and the various events [addition ...
  
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10. Figure 9: Conceivable geometry of the complex at the bilayer surface (cis compartment).
  
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11. Figure 10: Experiment E (10 + 6 + SG). Bilayer brightness as a function of time as well as of various events [...
  
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12. Figure 11: Experiment E (10 + 6 + SG). Bilayer brightness as function of the incubation time (A), of the perfu...
  
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13. Figure 12: Z-scans of the experiment E before and after the addition of Sybr Green I. A) Z-scan after the addi...
  
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14. Figure 13: Experiment E in reversed order of component addition; SG + 10 + 6.
  
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15. Figure 14: Bilayer brightness as a function of perfusion number and incubation periods for the experiment E in...
  
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16. Figure 15: Bilayer brightness as a function of perfusion number and incubation periods for the experiment F (SG...
  
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17. Figure 16: Kinetics of the tertiary complex formations of various lipo-DNA/DNA with Sybr Green I during incuba...
  
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18. Figure 17: Trafficking of a siRNA by a lipophilized DNA.
  
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19. Figure 18: A) Stage unit of the ‘Ionovation Explorer’ mounted on a standard inverted fluorescence microscope. ...
  
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Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

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Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

Vicky Gheerardijn,
Jos Van den Begin and
Annemieke Madder

Full Research Paper
Published 04 Nov 2014

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1. Graphical Abstract
2. Figure 1: Amino acid functionalized nucleosides.
  
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3. Scheme 1: Reagents and conditions: a) i. Et₃N, Pd(PPh₃)₄, THF, CO (4 bar), 70 °C, 48 h, ii. Et₃N, di-tert-but...
  
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4. Scheme 2: Reagents and conditions: a) Et₃N, Pd(PPh₃)₄, THF, CO (4 bar), 48 h, 70 °C (68%); b) Et₃N·3HF, Et₃N,...
  
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5. Scheme 3: Reagents and conditions: a) Et₃N, Pd(PPh₃)₄, THF, CO (4 bar), 48 h, 70 °C (90%); b) Et₃N·3HF, Et₃N,...
  
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Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

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Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

Lidija-Marija Tumir,
Marijana Radić Stojković and
Ivo Piantanida

Review
Published 10 Dec 2014

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1. Graphical Abstract
2. Scheme 1: The Grignard-based synthesis of 6-alkyl phenanthridine.
  
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3. Scheme 2: Radical-mediated synthesis of 6-arylphenanthridine [14].
  
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4. Scheme 3: A t-BuO^• radical-assisted homolytic aromatic substitution mechanism proposed for the conversion of ...
  
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5. Scheme 4: Synthesis of 5,6-unsubstituted phenanthridine starting from 2-iodobenzyl chloride and aniline [17].
  
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6. Scheme 5: Phenanthridine synthesis initiated by UV-light irradiation photolysis of acetophenone O-ethoxycarbo...
  
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7. Scheme 6: PhI(OAc)₂-mediated oxidative cyclization of 2-isocyanobiphenyls with CF₃SiMe₃ [19,20].
  
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8. Scheme 7: Targeting 6-perfluoroalkylphenanthridines [21,22].
  
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9. Scheme 8: Easily accessible biphenyl isocyanides reacting under mild conditions (room temp., visible light ir...
  
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10. Scheme 9: Microwave irradiation of Diels–Alder adduct followed by UV irradiation of dihydrophenanthridines yi...
  
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11. Scheme 10: A representative palladium catalytic cycle.
  
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12. Scheme 11: The common Pd-catalyst for the biphenyl conjugation results simultaneously in picolinamide-directed...
  
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13. Scheme 12: Pd(0)-mediated cyclisation of imidoyl-selenides forming 6-arylphenanthridine derivatives [16]. The inse...
  
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14. Scheme 13: Palladium-catalysed phenanthridine synthesis.
  
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15. Scheme 14: Aerobic domino Suzuki coupling combined with Michael addition reaction in the presence of a Pd(OAc)₂...
  
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16. Scheme 15: Rhodium-catalysed alkyne [2 + 2 + 2] cycloaddition reactions [36].
  
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17. Scheme 16: The O-acetyloximes derived from 2′-arylacetophenones underwent N–O bond cleavage and intramolecular ...
  
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18. Scheme 17: C–H arylation with aryl chloride in the presence of a simple diol complex with KOt-Bu (top) [39]; for s...
  
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19. Scheme 18: The subsequent aza-Claisen rearrangement, ring-closing enyne metathesis and Diels–Alder reaction – ...
  
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20. Scheme 19: Phenanthridine central-ring cyclisation with simultaneous radical-driven phosphorylation [42].
  
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21. Scheme 20: Three component reaction yielding the benzo[a]phenanthridine core in excellent yields [44].
  
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22. Scheme 21: a) Reaction of malononitrile and 1,3-indandione with BEP to form the cyclised DPP products; b) pH c...
  
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23. Figure 1: Schematic presentation of the intercalative binding mode by the neighbour exclusion principle and i...
  
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24. Figure 2: Urea and guanidine derivatives of EB with modified DNA interactions [57].
  
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25. Figure 3: Structure of mono- (3) and bis-biguanide (4) derivative. Fluorescence (y-axis normalised to startin...
  
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26. Scheme 22: Bis-phenanthridinium derivatives (5–7; inert aliphatic linkers, R = –(CH₂)₄– or –(CH₂)₆–): rigidity...
  
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27. Figure 4: Series of amino acid–phenanthridine building blocks (general structure 10; R = H; Gly) and peptide-...
  
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28. Figure 5: General structure of 45 bis-ethidium bromide analogues. Reproduced with permission from [69]. Copyright...
  
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29. Scheme 23: Top: Recognition of poly(U) by 12 and ds-polyAH⁺ by 13; bottom: Recognition of poly(dA)–poly(dT) by ...
  
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30. Figure 6: The bis-phenanthridinium–adenine derivative 15 (LEFT) showed selectivity towards complementary UMP;...
  
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31. Figure 7: The neomycin–methidium conjugate targeting DNA:RNA hybrid structures [80].
  
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32. Figure 8: Two-colour RNA intercalating probe for cell imaging applications: Left: Chemical structure of EB-fl...
  
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33. Figure 9: The ethidium bromide nucleosides 17 (top) and 18 (bottom). DNA duplex set 1 and 2 (E = phenanthridi...
  
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34. Figure 10: Left: various DNA duplexes; DNA1 and DNA2 used to study the impact on the adjacent basepair type on...
  
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35. Figure 11: Structure of 4,9-DAP derivative 19; Rright: MIAPaCa-2 cells stained with 10 μM 19 after 60 and 120 ...
  
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36. Figure 12: Examples of naturally occurring phenanthridine analogues.
  
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Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

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A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

Darinka Dzubiel,
Heiko Ihmels,
Mohamed M. A. Mahmoud and
Laura Thomas

Full Research Paper
Published 11 Dec 2014

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1. Graphical Abstract
2. Scheme 1: Equilibrium between single-stranded ILPR-DNA a2 and its parallel and antiparallel quadruplex form.
  
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3. Figure 1: Structures of ligands 1–6 used in this study.
  
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4. Figure 2: A) CD spectra of ILPR-DNA a2 (20 μM) at different temperatures in potassium phosphate buffer (95 mM...
  
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5. Figure 3: CD spectra of ILPR-sequence a2 (20 µM) in potassium phosphate buffer (95 mM, pH 7.0; ^__ : immediate...
  
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6. Figure 4: Fluorimetric monitoring of thermal DNA-denaturation of the ILPR quadruplex Fa2T (0.2 μM DNA concent...
  
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7. Figure 5: Fluorimetric titration of 1a (A), 1b (B), 1c (C), 1d (D) and 1e (E) with a2 in potassium phosphate ...
  
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8. Figure 6: Fluorimetric titration of 2 (A), 3 (B), 4 (C), 5 (D) and 6 (E) with a2 in potassium phosphate buffe...
  
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9. Figure 7: Job plot from fluorimetric analysis of mixtures of ligands 1e (A), 4 (B) and 6 (C) with ILPR-DNA a2...
  
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10. Figure 8: CD spectra of ILPR-DNA a2 in the presence of 1d (A), 1e (B), 2 (C), 4 (D), 5 (E) and 6 (F) at LDR =...
  
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Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

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NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

Boris Schmidtgall,
Claudia Höbartner and
Christian Ducho

Full Research Paper
Published 13 Jan 2015

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1. Graphical Abstract
2. Figure 1: Design concept of nucleosyl amino acid (NAA)-modified oligonucleotides 5 formally derived from stru...
  
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3. Scheme 1: Retrosynthetic analysis of target phosphoramidites (S)-7 and (R)-7 (BOM = benzyloxymethyl).
  
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4. Scheme 2: Synthesis of N-Fmoc-protected thymidine-derived nucleosyl amino acids (S)-9 and (R)-9; details on t...
  
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5. Scheme 3: Synthesis of protected 3'-amino-2',3'-dideoxyadenosine 8.
  
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6. Scheme 4: Synthesis of target phosphoramidites (S)-7 and (R)-7 and of two NAA-modified DNA oligonucleotides 30...
  
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Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

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Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

William H. Hersh

Full Research Paper
Published 30 Jan 2015

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1. Graphical Abstract
2. Figure 1: Acyl phosphorus compounds.
  
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3. Scheme 1: Synthesis of a dinucleoside acylphosphonate (3b) and a formate diester (1a).
  
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4. Scheme 2: Reaction of an H-phosphonodiamidite with acid chlorides.
  
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5. Figure 2: ORTEP [52] drawing of 9. Selected distances (Å) and angles (°): P–N1 1.687(1), P–N2 1.679(1), P–C1 1.87...
  
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6. Scheme 3: Synthesis of dinucleosides.
  
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7. Scheme 4: Calculated phosphine, acylphosphine, phosphite, and acylphosphonite inversion barriers.
  
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Beilstein J. Org. Chem. 2015, 11, 184–191, doi:10.3762/bjoc.11.19

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TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

Dnyaneshwar B. Gophane and
Snorri Th. Sigurdsson

Full Research Paper
Published 09 Feb 2015

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1. Graphical Abstract
2. Figure 1: Base pairing of ^TC with G (A), ^TA with T (B), ^UC with G (C) and ^UA with T (D).
  
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3. Scheme 1: Synthesis of nucleoside ^TA and its corresponding phosphoramidite 5. TPS = 2,4,6-triisopropylbenzene...
  
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4. Scheme 2: Synthesis of nucleoside ^UA and its corresponding phosphoramidite 10.
  
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5. Scheme 3: Synthesis of nucleoside ^UC and its corresponding phosphoramidite 14.
  
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6. Figure 2: EPR spectra of 14-mer DNA duplexes 5′-d(GACCTCG^TAATCGTG)•5′-d(CACGATYCGAGGTC), (10 mM phosphate, 10...
  
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7. Figure 3: Possible base pairing of ^TAH⁺ with C (A) and G (B) at pH 5.
  
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8. Figure 4: Possible base pairing of ^UA and ^UC with C.
  
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9. Figure 5: EPR spectra of 14-mer DNA duplex 5′-d(GACCTCG^UAATCGTG)•5′-d(CACGATYCGAGGTC) (A), and 5′-d(GACCTCG^UC...
  
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Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

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C-5’-Triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides: Synthesis and biological evaluation

Roberto Romeo,
Caterina Carnovale,
Salvatore V. Giofrè,
Maria A. Chiacchio,
Adriana Garozzo,
Emanuele Amata,
Giovanni Romeo and
Ugo Chiacchio

Full Research Paper
Published 09 Mar 2015

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1. Graphical Abstract
2. Figure 1: 2’-Oxa-3’-aza-modified nucleosides and 2’-oxa-3’-aza-modified nucleotides.
  
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3. Figure 2: Triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides.
  
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4. Scheme 1: Synthesis of triazolyl isoxazolidinyl-nucleosides 13 and 14. Reagents and conditions: a) Tosyl chlo...
  
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5. Figure 3: α–β Epimerization.
  
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Beilstein J. Org. Chem. 2015, 11, 328–334, doi:10.3762/bjoc.11.38

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A procedure for the preparation and isolation of nucleoside-5’-diphosphates

Heidi J. Korhonen,
Hannah L. Bolt and
David R. W. Hodgson

Letter
Published 10 Apr 2015

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1. Graphical Abstract
2. Scheme 1: PPN pyrophosphate.
  
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3. Scheme 2: Preparation of NDPs.
  
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4. Scheme 3: ³¹P NMR spectrum of TDP 2a after precipitation from reaction mixture.
  
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5. Scheme 4: Attempted use of an isopropylidene-protected 5’-tosylnucleoside.
  
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Beilstein J. Org. Chem. 2015, 11, 469–472, doi:10.3762/bjoc.11.52

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Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

Friederike Danneberg,
Alice Ghidini,
Plamena Dogandzhiyski,
Elisabeth Kalden,
Roger Strömberg and
Michael W. Göbel

Full Research Paper
Published 16 Apr 2015

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1. Graphical Abstract
2. Scheme 1: Formation of the 2-aminobenzimidazole moiety.
  
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3. Scheme 2: Synthesis of tris(2-aminobenzimidazole). Conditions: a: Boc-ON, THF, 0 °C to rt, 46 h, 45%; b: 1) 1...
  
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4. Scheme 3: Synthesis of PNA conjugates. Conditions: a: 1) 9, HOBt, DIC, DMF, rt, 24 h; 2) piperidine, DMF, rt,...
  
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5. Figure 1: Sequences of PNA conjugates 10–14 and oligonucleotides 15–20. Lysines are attached to the C-terminu...
  
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6. Figure 2: Cleavage of RNA by their corresponding PNA conjugates (150 nM substrate, 750 nM conjugate, 50 mM Tr...
  
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7. Figure 3: Substrate specificity of conjugates 12 and 14 (150 nM substrate, 750 nM conjugate, 50 mM Tris-HCl, ...
  
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8. Figure 4: Cleavage of RNA substrates 15, 16, and 17 by their matching conjugates as a function of conjugate c...
  
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9. Figure 5: Cleavage kinetics of 15 in the presence and absence of conjugate 12. Conditions: 150 nM substrate, ...
  
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Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

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Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties

Emma Werz and
Helmut Rosemeyer

Full Research Paper
Published 01 Jun 2015

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1. Graphical Abstract
2. Figure 1: General structure of the fluorophore-labeled lipo-oligonucleotides and positions of lipophilization...
  
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3. Figure 2: Chemical formulae 1–9 and lipo-oligonucleotide sequences 10–15.
  
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4. Figure 3: Energy-minimized 3D structures of the lipophilic nucleoside headgroups 4a–9a. All 3D structures wer...
  
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5. Figure 4: Schematic display of the three main equilibria existing on the cis side of the bilayer chamber.
  
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6. Figure 5: Bilayer brightness vs event graph of 5’-d(4a-Cy5-TAG GTC AAT ACT) (10).
  
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7. Figure 6: Bilayer brightness vs event graph of 5’-d(5a-Cy5-TAG GTC AAT ACT) (11).
  
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8. Figure 7: Bilayer brightness vs event graph of 5’-d(6a-Cy5-TAG GTC AAT ACT) (12).
  
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9. Figure 8: Bilayer brightness vs event graph of 5’-d(7a-Cy5-TAG GTC AAT ACT) (13).
  
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10. Figure 9: Infiltration of lipo-oligonucleotide (13) aggregates from the buffer into the lipid bilayer. Z-dire...
  
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11. Figure 10: Bilayer brightness vs event graph of 5’-d(8a-Cy5-TAG GTC AAT ACT) (14).
  
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12. Figure 11: Bilayer brightness vs event graph of 5’-d(9a-Cy5-TAG GTC AAT ACT) (15).
  
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13. Figure 12: Summarizing the bilayer brightness for LONs 10–15 depending on the incubation time up to the maximu...
  
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14. Figure 13: Diffusion time measurements of LON 10 (5 µL, 50 nM). A) Z-direction scan directly after the additio...
  
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15. Figure 14: Hydrodynamic models of lipophilic oligonucleotides 10–15. Views are perpendicular (right) or parall...
  
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16. Figure 15: Scheme of a stretched rotation ellipsoid with the semi-major axes a and b.
  
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17. Figure 16: Schematic structure of a Cy5-labeled lipo-oligonucleotide.
  
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18. Figure 17: Fluorescence lifetime τ_F values of the LONs 10–15. A) Logarithmic imaging of fluorescence intensity...
  
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Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

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