Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by

• application in metal-mediated base pairing [6][7]. Structural analyses have shown that their formation is possible without major conformational changes of the nucleic acid [8], even though metal-modified nucleic acids may very well adopt non-helical topologies [9]. It is even possible to create DNA duplexes

• , even though their formation is in principle also compatible with cisoid glycosidic bonds. Hence, metal-mediated base pairs that require a transoid orientation of the glycosidic bonds may be ideally generated in a parallel-stranded double helix. This section summarizes base pairing patterns established

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• solution. In respect to the complementary oligothymidine T10 template in water, compounds 3 and 5 both show a self-assembling behavior according to canonical base–base pairing. However, in buffer solution, derivative 5 was much more effective than 3 in binding to the T10 template. Furthermore the adenine

• was prehybridized, so that canonical base pairing of the chromophore–nucleoside conjugates with the template could be excluded. After centrifugation, compound 3 shows no effective self-assembly to single or double-stranded templates in buffer; only in water an assembly occurring to both single

• stranded templates (Table 3). Compound 5 shows a significantly higher self-assembly ratio to T10 than to (dA)10, indicating canonical base pairing. Furthermore, the self-assembly ratio (number of assembled pyrene moieties with respect to the number of binding sites at the template, e.g., 10 for T10) of 112

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• in one (very low yielding) or in four steps from D-mannose in a straightforward manner (Scheme 13a). In the proposed mechanism (Scheme 13b), the anomeric oxygen self-displaces the bromide (hard Lewis base, soft Lewis base pairing) at the 4-position to form a THF ring. The ring oxygen then displaces

• fashion [58][59]. Therefore, they postulated that by using the correct divalent cation and suitable Lewis acid/Lewis base pairing, the necessary transition-state organization to favor glycosylation of a glycosyl fluoride would outcompete hydrolysis in the aqueous medium. This would lead to a simple non

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• amplification of mutations. The introduction of mutations can lead to a weaker base pairing between the template molecule and its copy, thus increasing the efficiency of the separation of this particular template duplex. Considering the proposed abundance of amino acids, it is natural to assume the presence of

• E1 to E12 and are shown in Figure 8c. It is important to note that mutations between enzymes are such that the stability of the ligase duplex due to base pairing is not altered, but only the catalytic activity and replication rate are affected. All these enzymes were shown to cross-replicate, with

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• possibilities for variation are indeed a requirement for systems to undergo open-ended evolution [66]. The storage of genetic information as a sequence in a polymer associated with template replication through base-pairing constitutes an efficient system to ensure evolvability. It is that evolvability which

• replication by von Kiedrowski [67], leads to sub-exponential growth. It turns out, at least at this time, that no isolated system able to reproduce itself, presents all of the qualities required for the emergence of life: i.e., the replication of nucleic acids through base-pairing is limited by parabolic

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was

• analogue. Keywords: base-pairing; base-pair mismatch; DNA functionalization; DNA templates; dynamic combinatorial chemistry; D-threoninol based scaffolds; Introduction The well-defined duplex structure, self-assembling by base-pair recognition, and the accessibility by solid-phase synthesis make DNA

• , we generated the libraries of reversibly interconverting building blocks – dynamic combinatorial libraries (DCL) (Figure 1). The abasic strand and its complementary template strand are spontaneously assembled into a double helix through Watson–Crick base-pairing and the incoming nucleobase monomer

Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• critically about the fundamental principles behind split aptamer assembly. We quickly recognized that the function of split aptamers relies on a thermodynamic balancing act in which the enthalpic gain of base pairing and base stacking in the assembled state is weighed against the entropic cost of assembly

• first divided the sequence by removing one of the loop regions, and then systematically truncated the base-pairing stems until we achieved the desired assembly properties. As predicted by our thermodynamic model, we found that split aptamer sequences having fewer base pairs could function in high ionic

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• switching [15] applications, a variety of specific and site selective binding properties are available [16]. In particular, the specificity of Watson–Crick base pairing of DNA nucleotides can be used for the directed and predictable self-assembly of nanoparticles [17]. The DNA mediated assembly of

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

• Information File 1), which proves that cleavage in the examined concentration range fully depends on Watson–Crick base pairing. Cleavage experiments with varying amounts of conjugates (Figure 4) show that – at concentrations below 1.5 µM – RNA cleavage by PNAs 10–12 and 14 obeys saturation kinetics. Full

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

• in the melting temperature, while UA destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label TA varied with different base-pairing partners in duplex DNA, with the TA•T pair

• ][41][42], non-native base-pairing properties of nucleobases [43][44][45][46] and their dynamics [42][47][48]. Fluorescence spectroscopy, using environmentally sensitive fluorescent nucleosides has been used for detection of local structural perturbations [49][50][51][52][53][54][55][56][57], including

• duplex DNA [69]. In other words, this label could not only distinguish between pairing with guanine and a mismatch but was also able to pinpoint the base-pairing partner. Furthermore, TC revealed a flanking-base dependent variation in the EPR spectra, showing that minor structural variations in the local

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• molecular recognition as well. The most important natural example of sequence specific, multivalent molecular recognition is the hybridization of complementary DNA strands via the base pairing of adenosine and thymine respectively guanine and cytosine. Within the last years these binding motifs have been

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

• fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson–Crick base

• -pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here

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

• values of ≈5 × 104 kHz. Further experiments concerning a multiple compartment chamber with a common aqueous sub-phase, as well as a thermostated device for a suppression of nonspecific base pairing are underway [15]. Moreover, ab initio molecular-dynamics- (AIMD)- and ab initio Monte-Carlo- (AIMC

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

• 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

• that the base-pairing properties were unpredictably different from other closely related acyclic nucleic acids [8]. This indicated that the nature of the backbone exerts a strong influence on the disposition of the nucleobases, and there seems to be no straightforward correlation between the nature of

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

• 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

• stable triplexes of the type PNA/DNA/PNA with poly-purine DNA, via both Watson–Crick and Hoogsteen base pairing (Figure 1). These structures are so stable that dsDNA undergoes displacement of the non-complementary strand [4][5][6][7]. However, the formation of triplex structures is limited to

• stabilize PNA2DNA triplex structures by additional stacking interactions which combine with Watson–Crick and Hoogsteen base pairing; these interactions are clearly detectable by the formation of the excimer band of pyrene in the fluorescence spectra. Thus this work makes a significant step toward the

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• base pairing. In the case of the pyrimidines the modification at position 5 should not significantly interfere with the preferred anti-conformation of the nucleosidic bond. Thus, the Watson–Crick base pairing of the corresponding modified oligonucleotides should be maintained. Over the past few years

Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

• Daniel Lachmann,
• Sina Berndl,
• Otto S. Wolfbeis and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2010, 6, No. 13, doi:10.3762/bjoc.6.13

• similar within each duplex set, DNA1Y or DNA2Y. This is typical for chromophores as base surrogates [26][27][28][29][30][31][32][33][34][35][36] since they do not exhibit any preferential base pairing properties. The UV–vis absorption properties of all Nile Blue-modified duplexes are remarkably different

Crystal engineering of analogous and homologous organic compounds: hydrogen bonding patterns in trimethoprim hydrogen phthalate and trimethoprim hydrogen adipate

• Packianathan Thomas Muthiah,
• Savarimuthu Francis,
• Urszula Rychlewska and
• Beata Warżajtis

Beilstein J. Org. Chem. 2006, 2, No. 8, doi:10.1186/1860-5397-2-8

• leading to base-pairing, quadruple hydrogen bonded arrays, DDAA and DADA (D- donor, A = acceptor), etc. C-H...π, π-π stacking, etc are further stabilizing the crystal structures. The quadruple hydrogen bonded arrays have been observed in the crystal structures of TMP m-chlorobenzoate, [11] TMP-sorbate

• identical with TMP-dicarboxylate salts such as TMP-hydrogen glutarate [17] and TMP-succinate [29] but differ only in the number of carbon atoms of the chain. Such cyclic hydrogen-bonded ring formation blocks the base-pairing interaction between the pyrimidine moieties. Hence base-pairing has not been