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

Beilstein J. Org. Chem. 2015, 11, 913–929, doi:10.3762/bjoc.11.103

• lipophilicity but mainly the chemical structure and topology of the head group is of decisive importance for the optimal interaction of a lipo-oligonucleotide with an artificial lipid bilayer. Moreover, fluorescence half-live and diffusion time values were measured to determine the diffusion coefficients of the

• , equimolar amounts of complementary and non-complementary DNA strands as well as a SYBR Green I solution were added to the bilayer-bound lipo-oligonucleotide. The kinetics of the ternary complex formation at the bilayer surface as well as the stability of the complexes against perfusion was measured by

• the amphiphilic head group but preserved the oligonucleotide DNA sequence. This sequence [5’-d(NL-(Cy5) TAG GTC AAT ACT); NL = nucleolipid] was chosen because it forms neither a hairpin structure nor a self-complementary duplex [9]. Particularly, for a successful delivery of siRNAs [10][11][12] their

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• the geometry of the oligomeric interactions provided an important precedent [10] and has stimulated intense research in glycomimetics, glycodendrimers, and glycopolymers [11][12]. Over the past decade, there has been a growing interest in using oligonucleotide hybridization [13][14][15] to scaffold

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

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• or miRNAs. Although most site-selective artificial ribonucleases consist of a catalytic unit (both with and without metal ions) attached to a DNA oligonucleotide or 2’-O-methyloligoribonucleotide complementary to the targeted RNA [1][2][3], possible future in cell applications suggest the conjugation

• of RNA cleavers to oligonucleotide analogues such as peptide nucleic acids (PNA) [4]. The benefits of oligonucleotide analogues are higher affinity towards RNA [5] as well as improved resistance against biodegradation [6]. Furthermore, PNA can be applied to block miRNA functions in cell culture

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

Beilstein J. Org. Chem. 2015, 11, 328–334, doi:10.3762/bjoc.11.38

• -carbanucleoside. However, in order to maintain the six-bond periodicity of the oligonucleotides and thus the flexibility of the oligonucleotide chain the methylene bridge at the pseudo-5’-position was retained. The obtained compounds have shown to be endowed with an interesting antitumor activity: most of them

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

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

• . 50% reduction of the nitroxide during oligonucleotide synthesis, which utilized dichloroacetic acid for the removal of the trityl groups. However, in spite of low yields, the spin-labeled oligonucleotides were readily separated from those containing the reduced spin label by denaturing polyacrylamide

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

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction

• to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. Keywords: backbone modifications; DNA; nucleic acids; oligonucleotides; stereoselective synthesis; zwitterions; Introduction

• their high polarity represents a significant hurdle for cellular uptake and leads to problematic pharmcokinetics. Furthermore, they are prone to nuclease-mediated degradation. As a consequence, it is of utmost importance to modify oligonucleotide structures using chemical or enzymatic methods in order

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

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• fluorimetric analysis. CD spectra were obtained from a solution of the ILPR quadruplex-forming oligonucleotide a2 in K+-containing buffer (95 mM) in a temperature range from 20 to 95 °C. The oligonucleotide a2 showed CD signals that are characteristic of a mixture of parallel (λmax = 265 nm; λmin = 235 nm) and

• only two stacked G-quartets that are stabilized upon association of the ligands 2, 4, 5 and 6. Nevertheless, this proposed folding pattern of the oligonucleotide a2 needs to be confirmed in a more detailed structure analysis by high-resolution NMR spectroscopy. Conclusion This study represents the

• first comparative investigation of the interaction of different quadruplex ligands with an oligonucleotide sequence from the ILPR. In summary, it is demonstrated that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming

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

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• DNA was used to study photoinducible charge transfer processes [87]. Upon attachment to the DNA chain the phenanthridinium base (E, Figure 9) was efficiently intercalated into the DNA oligonucleotide, not disturbing the position of adjacent basepairs nor the complementary oligonucleotide strand

Galactan synthesis in a single step via oligomerization of monosaccharides

• Marius Dräger and
• Amit Basu

Beilstein J. Org. Chem. 2014, 10, 2658–2663, doi:10.3762/bjoc.10.279

• : arabinogalactan protein; glycosyl fluoride; glycosylation; oligosaccharides; Introduction Despite numerous recent advances in the synthesis of complex oligosaccharides, unlike polypeptide or oligonucleotide assembly, their preparation remains far from a routine endeavor. The critical step in oligosaccharide

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

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• is often a problem. Moreover achieving control in terms of number, positioning and exact location of the desired catalytic moieties is far from straightforward. In contrast to the existing variety of rather complicated and unpredictable RNA based ribozyme-like structures, oligonucleotide duplexes

• unprotected histidine methyl ester, we decided to protect the imidazole functionality immediately after the reaction with the tert-butyloxycarbonyl (t-Boc) protecting group [53], which is compatible with the reagents used during nucleoside- and oligonucleotide synthesis [45][54]. While the t-Boc group can be

• removed with a 10% TFA solution [54], the acid labile DNA can suffer from depurination after treatment with acid. According to literature, the t-Boc group can also be cleaved during standard deprotection procedures with saturated ammonia after oligonucleotide synthesis [41][55]. In view of all these

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• systems; solid-phase DNA synthesis; synthetic biology; Introduction It has been nearly 50 years since the first solid-phase synthesis of DNA by Letsinger and Mahadevan [1][2]. This work laid the platform for new strategies in oligonucleotide synthesis, culminating in the development of phosphoramidite

• -letter DNA alphabet. This choice reflected simpler conversion rules, to be discussed elsewhere. AEGIS-guided oligonucleotide assembly yields a kanamycin resistance gene The actual sequences designed by OligArch and used here are shown in Figure 4, with overlaps. These were prepared by automated DNA

• errors were found most frequently at the ends of the reads, as expected for sequencing errors, rather than errors in the primary synthesis, polymerase extension, or conversion PCR. Standard oligonucleotide assembly attempts without AEGIS components fail While these results show that synthetic DNA

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

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion. Keywords: artificial lipid bilayers; lipo-oligonucleotide duplexes; nucleic acids; Sybr Green I; Introduction The post

• (2b) – prepared by using compound 2a – was proven by fluorescence microscopy. Now, we simplify this technique by hybridizing an unlabelled DNA target strand to the bilayer-immobilized lipo-oligonucleotide and by using Sybr Green I (3, SG) [20][21][22] as a fluorescent double strand indicator [20][21

• ) as well as the lipo-oligonucleotide sequences the paper is dealing with are shown in Figure 1. Results and Discussion Figure 2 displays the six DNA duplexes which have been assembled at the artificial lipid bilayer and visualized by addition of Sybr Green I. In the following the results of these

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

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

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• this was then used for the 3'-O-acylation of 4a in pyridine in the presence of 4-dimethylaminopyridine. Experimental details for the preparation of all the building blocks and NMR and MS data for their characterization are given in Supporting Information File 1. Oligonucleotide synthesis Previously

• . Upon completion of the assembly of 3'-UUGCA-5', the oligonucleotide was released from the support and deprotected by treatment with triethylamine, ammonia and finally with TBAF. The deprotected pentamer was precipitated from EtOH with NaOAc, The overall yield of the pentamer was 54% (according to the

• a linear gradient from MeCN 25% at t = 0 min to MeCN 100% at t = 25min (for the HPLC traces, see Supporting Information File 1). Oligonucleotide synthesis. Support 8b (0.151 g; 0.056 mmol) and 6 equiv of the phosphoramidite building block 5a' (200 mg; 0.35 mmol; 1.5 equiv per branch) were dissolved

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

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• in the appearance of a strong negative band at 350 nm, characteristic for ds-DNA. This band could be used to probe the efficiency of pairing oligo dT sequences with complementary dA or rA structures, for instance, in any (antisense strategy) developed oligonucleotide, which relies on efficient and

Second generation silver(I)-mediated imidazole base pairs

• Susanne Hensel,
• Nicole Megger,
• Kristina Schweizer and
• Jens Müller

Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

• processing metal-mediated base pairs [26][27], resulting, e.g., in the formation of cytosine–Ag(I)–adenine base pairs [28]. Structural analyses of short oligonucleotide duplexes comprising one or more metal-mediated base pairs indicate that the large conformational space of nucleic acids exists also for

• creating long contiguous metal-containing sections within oligonucleotide duplexes [35]. A closer inspection of the experimental NMR structure reveals that the silver(I) ions, despite being lined up inside the duplex along the helical axis, still appear to be accessible from the outside of the duplex

• the two hydroxy functions with the dimethoxytrityl and the 2-cyanoethyl-N,N-diisopropylphosphoramidite moieties, finally resulting in the formation of 4a/4b suitable for automated solid-phase oligonucleotide synthesis. The pKa values of the free nucleosides 2a/2b were determined by pD-dependent 1H NMR

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

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability. Keywords: acyclic nucleic acids; glycerol

• recently reported on the base-pairing properties of isoGNA, an isomer of glycerol derived nucleic acid (Figure 1) [8]. Our motivation was driven by the question “how structurally simple and minimal can an oligonucleotide be and still exhibit base-pairing?” When we studied isoGNA we were surprised to find

• compound was found to be highly unstable for isolation and handling (one of the N6-benzoyl group falls off very easily). The third option was the use of the N6,N6-di-Boc-adenine derivative, even though this entails the difficulty in removing these Boc groups, which are incompatible with the oligonucleotide

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• nucleoside, nucleotide and oligonucleotide spatial structure. The conformation predefines, for example, the stability of DNA:RNA duplexes – complexes between oligodeoxyribonucleotide and a complementary RNA strain [7] or an overall shape of oligonucleotide. It is also well known that the structure of DNA may

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

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• bifunctionalized cytidine derivative 1 as the final product was isolated by reversed-phase chromatography with a yield of 83% over the last three steps (Figure 6). To set-up conditions for conjugation of the bifunctional cytidine derivative 1 to RNA, we synthesized a short model oligonucleotide (GUC AGC CGU CAG

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

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• of single modifications with nucleosides of the bicyclo-/tricyclo-DNA platform within deoxyoligonucleotides are not predictive for the stability of fully modified oligonucleotides. Keywords: DNA/RNA affinity; nucleic acids; nucleosides; oligonucleotides; oligonucleotide therapy; X-ray structures

• this a gain in the free energy of duplex formation and, hence, more stable duplexes are expected [24]. Over the years we became interested in determining the structure/RNA affinity relationship of the underlying sugar scaffold and to develop them into a molecular platform for oligonucleotide

• arrangement of γ and a somewhat attenuated but clear preference for an S-type furanose conformation. Oligonucleotide synthesis The dodecamers ON1–4, shown in Table 2, containing one to two modifications, were synthesized in order to test the consequences of the two modified bicyclic nucleotides on RNA and DNA

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now

• available as parts of artificially expanded genetic information systems (AEGIS), and tools are now available to generate entirely standard DNA from AEGIS DNA during PCR amplification. Here, we describe the OligArch (for "oligonucleotide architecting") software, an application that permits synthetic

• software product to assist in the design of the fragments to be assembled. That product, OligArch (for “oligonucleotide architecting”) is described here. While other packages exist that output designed oligonucleotides for large-scale synthesis, such as GeneGenie [11], DNAWorks [12], and Gene2Oligo [13

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

Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

• total of four PDIs (blue) and/or pyrenes (green). Oligomers 1–7 consisting of varying numbers of pyrene or PDI moieties covalently linked to complementary DNA strands were prepared by automated oligonucleotide synthesis using the previously described phosphoramidite pyrene [53] and PDI [55] building

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

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• oligonucleotide probes [34], the effect of single- or multiple pyrene units on PNA in the formation of triplex structures has still to be addressed. We have recently reported the modification of uracil at C5 by hydroxymethylation, followed by substitution with chloride and then with azide, which can be used for

Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

• Tatyana V. Abramova,
• Sergey S. Belov,
• Yulia V. Tarasenko and
• Vladimir N. Silnikov

Beilstein J. Org. Chem. 2014, 10, 1151–1158, doi:10.3762/bjoc.10.115

• efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits

• . Keywords: labile linker; morpholino oligomers; oligonucleotide mimics; solid-phase-supported peptide synthesis (SPPS); Introduction The phosphorodiamidate morpholino oligomers (PMO) and peptide conjugated PMO (PPMO) are currently promising candidates for antisense therapy of a number of infectious and

• . An attractive feature of these new morpholino oligonucleotide analogues is the absence of additional chiral centers. Unlike commercially available PMO and PPMO, which are mixtures of diastereomers, oligomers constructed with the use of phosphoromonoamidate [7], oxalyl diamide [8], amidine [9] and

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

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• 4 [42] yielding 5 in acceptable yields (Scheme 1). Finally, compound 5 was transformed into 6 by phosphitylation resulting in a building block that bears protection groups and reactive groups that are standard in solid phase DNA oligonucleotide synthesis. Synthesis of branched oligonucleotides. DNA

• oligonucleotide synthesis was performed at 0.2 µmol scale (trityl-on mode) employing the standard phosphoramidites and 6 which was diluted in a mixture containing 10% CH2Cl2 in CH3CN to a final concentration of 0.12 M. 3000 Å LCAA-CPG support was used, derivatized with the respective 3'-nucleotide of the

• respective DNA oligomers. Since we later intended to investigate whether the oligonucleotide branches are used as primers in PCR (vide infra), the oligonucleotides have to terminate with a free 3'-hydroxy group. This requires a particular synthesis strategy (Scheme 2). The synthesis strategy was adapted in a

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

• phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates. Keywords: CIDNP; nucleotide–amino acid conjugates

• ; oligonucleotide synthesis; phosphotriester approach; Introduction Maintaining the integrity of the genome is of paramount biological importance, since the damage of DNA is considered to cause aging and various degenerative diseases. To prevent the pathological DNA damage, cells evolve the DNA repair machinery

• strategy for obtaining the model conjugates should provide a synthetic versatility, easy scaling up, and high purity of the title compounds. Although there is a number of well-developed methods of the automatic solid phase supported synthesis (SPSS) of oligonucleotide–peptide conjugates [8], this strategy