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

• an ever-greater focus [5][6][8][9][10][11]. The study of the interactions of single- and double-stranded nucleic acids with lipid bilayers is, therefore, of significant importance, particularly for the following reasons: 1. for the optimization of the in vivo delivery of lipophilic siRNAs [12][13][14

• ], 2. for the development of analytical techniques for the detection of nucleic acids [15][16][17], 3. for structure elucidation of complex aggregates formed by such natural nanostructures [5][6] and 4. for cell-surface engineering [18]. In a preceding manuscript [19] we reported the lipid bilayer

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

• nucleic acids. The CD spectrum of duplex ODN 1I6S-Et-S4U2 retains the characteristic shape of B-DNA, showing that the ethyl cross-link does not significantly distort the DNA helix (data not shown). The cross-linked duplexes were further characterized by thermal denaturation monitoring the UV absorption at

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

• in high yields. Keywords: nucleic acids; oligoribonucleotides; phosphoramidite; soluble support; synthesis; Introduction Recognition of short noncoding RNAs as regulatory elements of gene expression [1][2][3][4][5] has attracted interest in their physico-chemical properties, including structure

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

• recognition; circular dichroism; DBTAA-adenine conjugate; ds-DNA/RNA; minor groove binding; nucleic acids; Introduction The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several non-covalent binding modes. Typical examples are double-stranded (ds) DNA

• . Nevertheless, the dynamic nature of nucleic acids, combined with structural differences between various DNA/RNA sequences, offer numerous highly interesting targets. Within the last two decades, the design of small binding molecules has mostly relied on the three-dimensional recognition of various targeted DNA

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

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany 10.3762/bjoc.10.224 Abstract DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work

• insertion are suggestive of different interactions between the Nile red label and the duplexes. Keywords: click chemistry; deoxyribonucleic acid; DNA bulge; fluorescence; nucleic acids; solvatochromism; Introduction Fluorescent labels are important tools for investigating the structure and dynamics of

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

• ; metal-mediated base pairs; nucleic acids; nucleosides; Introduction Nucleic acids with their evolutionary optimized self-assembling properties represent an ideal basis for the generation of artificial, site-specifically functionalized supramolecular aggregates [1][2][3][4]. In this context, numerous

• -called metal-mediated base pairs between two complementary ligand-derived artificial nucleobases can be formed. Accordingly, metal-based functionality can be introduced site-specifically into nucleic acids. Various applications have been reported for such metal-modified nucleic acids [5], including

• increased charge transfer capability [10][11] and DNA-based logic gates [12][13]. Applying the concepts of coordination chemistry, a wide range of metal-specific ligands have been incorporated successfully into nucleic acids and nucleic acid derivatives. Most recently, even coordination patterns of the [2

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

• ) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of

• 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

• nucleic acids; isoGNA; oligonucleotides; phosphoramidites; Introduction Acyclic nucleic acids have garnered a lot of attention and are becoming an important component in nucleic acid chemistry [1][2][3]. Lately, there has been an explosion in the number of investigated candidates [4][5][6][7]. We have

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

• of a conformational analysis show that the alkylation/acylation can be effectively used for tuning the pyrrolidine conformation over the whole pseudorotation cycle. Keywords: conformation; NMR; nucleic acids; nucleotide analog; phosphonic acid; pseudorotation; pyrrolidine; Introduction Nucleotides

Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

• Jasmin Levic and
• Ronald Micura

Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

• . Keywords: heterocycles; ligands; nucleic acids; nucleobases; nucleosides; pyrrolopyrimidinones; Introduction The small pyrrolo[2,3-d]pyrimidine 7-(aminomethyl)-7-deazaguanine is a natural product, also termed prequeuosine base (preQ1 base) [1][2]. This guanine derivative is involved in the complex

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

• derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated. Keywords: cytidine deaminase; modified nucleoside; nucleic acids; ribozyme; RNA world

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

• has been replaced by a charge neutral peptide backbone, such as the peptide nucleic acids (PNAs) [15] or by a nucleotide derived phosphorodiamidate backbone, such as the morpholino oligonucleotides (PMOs) [16]. Of particular interest is the class of conformationally constrained oligonucleotides

• . Members of this class are amongst others the locked nucleic acids (LNA) [17][18], the hexose nucleic acids (HNAs) [19] and the family of bi- and tricyclo-DNA (Figure 1) [20][21][22][23]. These analogues aim at increasing RNA affinity by structurally preorganizing single strands for duplex formation. Bc

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• educts contribute the majority of the novel skeleton of the product” [44]. In this review, we understand educts as compounds that contribute carbon atoms to the MCR product [45]. By the analogy to nucleosides included in the DNA/RNA nucleic acids, this review is limited to MCRs involving furanosyl

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

• interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions. Keywords: DNA; hybridization; nucleic acids; perylenediimide; pyrene; Introduction When two aromatic molecules are in close proximity they often have a tendency to interact non-covalently in a face

• molecular scaffold for arranging various types of chromophores [39][40][41][42][43][44]. Recently, we reported that oligoarenotides (oligomers with an alternating phosphodiester-aromatic hydrocarbon motif) exhibit similar structural properties as nucleic acids, and although the aromatic hydrocarbons cannot

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

• 7, 14183, Huddinge, Sweden 10.3762/bjoc.10.154 Abstract Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a

• positioning of the pyrene units along the chain. An increase in triplex stability and a very high mismatch-selectivity, derived from combined stacking and base-pairing interactions, were found for PNA2, bearing two distant pyrene units. Keywords: modified nucleobase; nucleic acids; PNA; pyrene excimer; SNP

Postsynthetic functionalization of glycodendrons at the focal point

• Thisbe K. Lindhorst and
• Katharina Elsner

Beilstein J. Org. Chem. 2014, 10, 1482–1487, doi:10.3762/bjoc.10.152

• etherification, thiol-ene reaction and in particular olefin cross metathesis. Keywords: amphiphilic glycomimetics; cross metathesis; glycodendrons; multivalent glycoconjugates; multivalent glycosystems; Introduction In addition to nucleic acids and proteins, molecular life is based on a third important class

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• glycosystems; peptides; Introduction In comparison to proteins and nucleic acids, carbohydrates have traditionally received less attention in the scientific community. However, it is increasingly apparent that carbohydrates and glycoconjugates are involved in a multitude of physiological and pathological

• processes and offer an enormous potential to encrypt biological information [1][2][3][4]. In contrast to the linear nucleic acids and proteins, carbohydrates usually form branched oligomers or polymers which are joined together by a variety of linkages. The vast amount of resulting carbohydrate oligomers

• of carbohydrates in cell biology is still lagging far behind our knowledge of proteins and nucleic acids. This backlog is mainly due to the complexity of biological carbohydrates. Additionally, established analytical and synthetic methods in protein and nucleic acid research such as automated

Stereoselective synthesis of carbocyclic analogues of the nucleoside Q precursor (PreQ₀)

• Sabin Llona-Minguez and
• Simon P. Mackay

Beilstein J. Org. Chem. 2014, 10, 1333–1338, doi:10.3762/bjoc.10.135

• ; stereoselective amine synthesis; triol synthesis; Introduction 7-Deazapurine (pyrrolo[2,3-d]pyrimidine) nucleosides are commonly found in nature playing a variety of roles such as building blocks of nucleic acids and tRNA, metabolites or antimetabolites [1]. Deazapurine ribonucleosides also show interesting

Atherton–Todd reaction: mechanism, scope and applications

• Stéphanie S. Le Corre,
• Mathieu Berchel,
• Hélène Couthon-Gourvès,
• Jean-Pierre Haelters and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2014, 10, 1166–1196, doi:10.3762/bjoc.10.117

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

• positively charged centers in oligonucleotide analogues results in increased water solubility and higher thermal stability of complementary duplexes of such oligonucleotide mimics with nucleic acids [14][15]. Some conformationally restricted protonated PNA or pyrrolidine oligonucleotide mimics exhibit

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

• hydrogels. Keywords: AFM; branched DNA; DNA; DNA polymerase; nanotechnology; nucleic acids; PCR; self-assembly; Introduction DNA has found applications in the field of nanotechnology due to its inherent properties. The simplicity and predictability of DNA secondary structure are of outstanding potential

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• presentation of recognition units since incorporation of artificial β-amino acids allows positioning of side chains on one side of the helix in equidistant 5 Å intervals. This concept was proven to be beneficial for base-pair recognition of β-peptide nucleic acids leading to high duplex stabilities of

An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles

• Marcus Baumann and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2013, 9, 2265–2319, doi:10.3762/bjoc.9.265

• terminating biosynthesis of nucleic acids eventually interrupting the division of virally infected cells. Most commonly the pyrimidine/pyrimidone substructure has been introduced as a preassembled unit. Thymine (3.3), cytosine (3.4) and uracil (3.5) are all industrially accessed on large scale utilising

A new synthetic access to 2-N-(glycosyl)thiosemicarbazides from 3-N-(glycosyl)oxadiazolinethiones and the regioselectivity of the glycosylation of their oxadiazolinethione precursors

• El Sayed H. El Ashry,
• El Sayed H. El Tamany,
• Mohy El Din Abdel Fattah,
• Mohamed R. E. Aly,
• Ahmed T. A. Boraei and
• Axel Duerkop

Beilstein J. Org. Chem. 2013, 9, 135–146, doi:10.3762/bjoc.9.16

• : glycosyloxadiazolinethiones; glycosylsulfanyloxadiazoles; glycosylthiosemicarbazides; thermal rearrangement; X-ray crystallography; Introduction Modified nucleosides are versatile motifs for studying the relationship between the structure and functions of nucleic acids and problems of metabolism, besides their main

Peptoids and polyamines going sweet: Modular synthesis of glycosylated peptoids and polyamines using click chemistry

• Daniel Fürniss,
• Timo Mack,
• Frank Hahn,
• Sidonie B. L. Vollrath,
• Katarzyna Koroniak,
• Ute Schepers and
• Stefan Bräse

Beilstein J. Org. Chem. 2013, 9, 56–63, doi:10.3762/bjoc.9.7

• either polyamines or peptoids. In addition, functionalized nucleic acids were attached to polyamines via the same route. Based on a modular solid-phase synthesis of peralkynylated peptoids with up to six alkyne groups, the latter were modified with azidosugar building blocks by using copper-catalyzed

• the treatment of a variety of diseases. However, the rendering of nucleic acids and oligosaccharides as therapeutically active substances often requires a derivatization or a chemical coupling reaction that permits the selective and simple formation of covalent adducts. Some modifications permit the

• functional structures. Likewise, the coupling reaction should be permitted in hydrophilic solvents such as water or DMSO, since both unprotected nucleic acids and oligosaccharides, as well as many other biomacromolecules, prefer a hydrophilic reaction environment. With the advent of mild and biocompatible

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• illumination, by means of the direct regulation of enzymatic activity [64][65][66][67], peptides, proteins, nucleic acids [68][69][70][71][72][73][74][75][76], receptors [77][78][79][80][81][82], or ion channels [83][84][85], or by modulation of the concentration of several labelled molecules. This strategy is