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

• . In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base

• shows several unique properties [26][27][28]. Its potential applications as a probe for DNA sensing are well-established. For example, we have developed singly labeled acpcPNA probes that can give a fluorescence change in response to hybridization to DNA [29][30][31]. Due to its solvatochromic

• properties, Nile red is a potential candidate to be used in combination with PNA to develop a hybridization probe which not only differentiates between complementary and non-complementary DNA, but can also report on local structural variations. Except for an example from our group on the conformation control

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

• just the four standard nucleotides. Natural DNA's peculiar combination of strong and weak G:C and A:T pairs, the context-dependence of the strengths of those pairs, unimolecular strand folding that competes with desired interstrand hybridization, and non-Watson–Crick interactions available to standard

• form additional nucleobase pairs orthogonally to the A:T and G:C pairs. In principle, adding extra nucleotides in the genetic alphabet can mitigate the hybridization problems in highly complex mixtures of single-strand DNA fragments simply by increasing the information density of the resulting DNA

• against all other AEGIS spans being used in the current assembly set, with those that might hybridize with an unintended target being excluded. Potential hybridization is defined as any complementarity with a Tm of ≥50% of the minimum span Tm that can be designed. Further, spans that will result in

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

• dialkynylpyrenes (Y) results in a pronounced excimer fluorescence [53]. Hybridization of single strands 1 and 2 increases the intensity of the excimer (Figure 6), whereas hybridization of single strands 1 and 6 results in an extinction of excimer fluorescence. Such behaviour was also observed in previous work and

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

• alone, and in the presence of DNA no clear-cut transition was detected, suggesting a pyrene-mediated strong aggregation of the probe itself. As described below, all the probes showed excimer emission in the 460–480 nm range upon hybridization (Figure 2). The temperature dependence of the excimer band in

• ), probably due to the quenching effect of nucleobase units; however, the most important data are related to changes in the fluorescence spectrum upon hybridization with DNA, since this property is strongly related to the environment around the fluorophores [38] and can reveal interactions between pyrene

• hybridization with the templating DNA, though lower than for PNA2. PNA6 has already a strong excimer emission as single-strand, but this band was slightly enhanced upon interaction with the full-match DNA1, whereas it was slightly reduced in the presence of DNA2. For all PNAs, very similar results were obtained

Preparation of phosphines through C–P bond formation

• Iris Wauters,
• Wouter Debrouwer and
• Christian V. Stevens

Beilstein J. Org. Chem. 2014, 10, 1064–1096, doi:10.3762/bjoc.10.106

• ligands in the field of metal-catalysis. This has spurred the development of new routes toward functionalized phosphines. Some of the most important C–P bond formation strategies were reviewed and organized according to the hybridization of carbon in the newly formed C–P bond. Keywords: cross-coupling

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

• ][35]. Furthermore, it has been shown that branched DNA constructs can form materials by self-assembly [36]. Richert et al. were able to generate DNA based materials based on branched DNA molecules which are non-covalently bound to each other by only hybridization of 2 nucleotides [37]. Interestingly

• surfaces and in solution. Results and Discussion Design and synthesis of the branching molecule. In order to investigate the impact of rigidity of the branching core on DNA hybridization and usage of the constructs for network formation by PCR, we aimed at synthesizing a branching molecule based on the

• branches in 5'–3' direction using inverse protected phosphoramidites. Thermal denaturation studies comparing linear and branched oligonucleotides hybridization. Incorporated phosphoramidite 6 is depicted as Bp for branched ODN I.a Supporting Information Experimental procedures and full characterization

Theoretical studies on the intramolecular cyclization of 2,4,6-t-Bu₃C₆H₂P=C: and effects of conjugation between the P=C and aromatic moieties

• Masaaki Yoshifuji and
• Shigekazu Ito

Beilstein J. Org. Chem. 2014, 10, 1032–1036, doi:10.3762/bjoc.10.103

• calculation, as the Mes*–P–C angle was considerably bent at the level, such as B3LYP/6-31G(d) [14]. The bent structure optimized by the DFT method might reflect overestimation of the sp2-type hybridization of the phosphorus atom because of the sterically encumbered Mes* group [19]. Figure 1 displays the DFT

Allenylphosphine oxides as simple scaffolds for phosphinoylindoles and phosphinoylisocoumarins

• G. Gangadhararao,
• Ramesh Kotikalapudi,
• M. Nagarjuna Reddy and
• K. C. Kumara Swamy

Beilstein J. Org. Chem. 2014, 10, 996–1005, doi:10.3762/bjoc.10.99

• at δ ~ 4.78 (2J(P–H) = 18.0 Hz, PCH) which is absent in the latter set; the difference in the value of 1J(P–C) in the two sets is also consistent with the hybridization at the corresponding α-carbon (to phosphorus). Finally, the X-ray structure was determined for 20 (Figure 4). The above reaction is

Site-selective covalent functionalization at interior carbon atoms and on the rim of circumtrindene, a C₃₆H₁₂ open geodesic polyarene

• Hee Yeon Cho,
• Ronald B. M. Ansems and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2014, 10, 956–968, doi:10.3762/bjoc.10.94

• mixing of s-orbital character with the p-orbitals in the π-system. This hybridization lowers the energy of each atomic orbital in the π-system and thereby lowers the energy of all the derived π-MOs, i.e., both the HOMO (highest occupied molecular orbital) and the LUMO (lowest unoccupied molecular orbital

• ) [5]. This lowering of the HOMO offsets the raising of the HOMO caused by poorer π overlap; however, lowering the LUMO as a consequence of orbital hybridization amplifies the lowering caused by the weaker π-bond. The major electronic consequence of π-system curvature, therefore, is a substantial

Polyglycerol-functionalized nanodiamond as a platform for gene delivery: Derivatization, characterization, and hybridization with DNA

• Li Zhao,
• Yuki Nakae,
• Hongmei Qin,
• Tadamasa Ito,
• Takahide Kimura,
• Hideto Kojima,
• Lawrence Chan and
• Naoki Komatsu

Beilstein J. Org. Chem. 2014, 10, 707–713, doi:10.3762/bjoc.10.64

• , Lys8 and His8) through click chemistry followed by hybridization with plasmid DNA (pDNA) and its characterization by electrophoresis is reported. Results and Discussion Preparation and characterization of ND50-PG In view of actual cancer therapy utilizing the enhanced permeation and retention (EPR

• synthesized by the central research laboratory of Shiga University of Medical Science and G*Arg8 was purchased from GL Biochem Ltd. in Shanghai, China. The pBluescript II KS (Agilent Technologies, Inc., Tokyo, Japan) was used as a test pDNA for the hybridization with ND-PG-BPP. Dialysis was carried out by use

• -PG-BPP were characterized by FTIR (Figure 1d–f). Decent NMR spectra of the ND-PG-BPP were not obtained because of lower dispersibility of the ND-PG-BPP than the above ND-PG derivatives. Gel retardation assay The hybridization of ND-PG-BPP with DNA was studied by means of an agarose gel retardation

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

• Helge Klare,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

• ring is slightly distorted (angle between [PNN] planes 6.3° and 6.5°, Figure 7 and Figure 8). The angular sum around N3/N4 (15: 354.8°/353.6°, 16: 356.9°/349.2°) is ambiguous with respect to the hybridization of nitrogen (nominal sp3/sp2: 328° and 360°, respectively) but suggests a hybridization with

Elucidation of the regio- and chemoselectivity of enzymatic allylic oxidations with Pleurotus sapidus – conversion of selected spirocyclic terpenoids and computational analysis

• Verena Weidmann,
• Mathias Schaffrath,
• Holger Zorn,
• Julia Rehbein and
• Wolfgang Maison

Beilstein J. Org. Chem. 2013, 9, 2233–2241, doi:10.3762/bjoc.9.262

• BDH298 values are more subtle and might be referred to additional steric strain imposed by a change in hybridization of the carbon atom from sp3 to sp2 upon radical formation and hyperconjugation effects (Table 2). Correlating the experimental observations with the computational results, one can deduce

Activation of cryptic metabolite production through gene disruption: Dimethyl furan-2,4-dicarboxylate produced by Streptomyces sahachiroi

• Dinesh Simkhada,
• Huitu Zhang,
• Shogo Mori,
• Howard Williams and
• Coran M. H. Watanabe

Beilstein J. Org. Chem. 2013, 9, 1768–1773, doi:10.3762/bjoc.9.205

• . The S. sahachiroi/ΔaziA2 disruptants were confirmed by PCR and Southern hybridization of thiostrepton resistant and apramycin sensitive colonies. Direct comparison of HPLC profiles of the wild-type and ΔaziA2 crude organic extracts were striking (Figure 2). The ΔaziA2 mutant gave a single major peak

• . sahachiroi/ΔaziA2) and PCR performed. The AziA2UF/TsrR and TsrF/AziA2DR primer set was utilized: initial denaturation at 98 °C for 30 s; 30 total cycles of denaturation for 10 s; annealing at 64.5 °C for 40 s; polymerization at 72 °C for 60 s and finally gap filing at 72 °C for 10 min. Southern hybridization

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• the py orbital. This hybridization takes place so that the orbital is directed away from the three ligands toward the empty coordination site, making this position suitable for the approach of an incoming ligand. This simple picture has been corroborated by DFT calculations on T-shaped [Pt(alkyl)(PMe3

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• only provides reliable results if the donor atoms that coordinate to the metal center are the same and in an equal hybridization state in both cases. Therefore, we will compare the distances obtained in this work against [M(pyridine)n]m+ and [M(NH3)n]m+ (n = 4 for Li+ and Be2+ and 6 for all others

Stereogenic boron in 2-amino-1,1-diphenylethanol-based boronate–imine and amine complexes

• Sebastian Schlecht,
• Walter Frank and
• Manfred Braun

Beilstein J. Org. Chem. 2011, 7, 615–621, doi:10.3762/bjoc.7.72

• /hexane and the result of the X-ray analysis is shown in Figure 1. A comparison of the boron–nitrogen distance in the imine complex 8 (156.3 pm) and the amine complex 10 (159.5 pm) reveals a small elongation of the bond upon saturation of the imine group that results from the change in hybridization at

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• studies showed that hybridization of DNG-Hoechst conjugates 64 and 65 to dsDNA enhances the stability of the triple helix through simultaneous minor groove binding by the tethered Hoechst 33258 ligand. Furthermore, Hoechst 33258 is able to enhance the stability of the duplex DNG·DNA with a flexible minor

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

• and the corresponding modified oligonucleotides in the visible range are the loss of one absorption band and a red-shift from 633 nm to 653 nm for the second absorption signal. A further small bathochromic shift of ca. 5 nm is observed upon hybridization of the modified single strands DNA1 and DNA2 to

The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

• Kari Raatikainen,
• Massimo Cametti and
• Kari Rissanen

Beilstein J. Org. Chem. 2010, 6, No. 4, doi:10.3762/bjoc.6.4

• atoms (C–X where X = F, Cl, Br or I) and nucleophilic atoms (S, O or N, in their various hybridization states). The analysis was based on intermolecular contact distances shorter than 1.26 times the sum of the van der Waals (VDW) radii of the two interacting atoms. The analysis showed that the

• ], following the polarizability of halogen atom. The hybridization of the C–X carbon atom on the XB donor molecule has also an effect on the strength and directionality of the halogen bond. The order C(sp3) < C(sp2) < C(sp) is generally followed [24][25][26] and for example haloalkynes are found to be

Novel banana-discotic hybrid architectures

• Hari Krishna Bisoyi,
• H. T. Srinivasa and
• Sandeep Kumar

Beilstein J. Org. Chem. 2009, 5, No. 52, doi:10.3762/bjoc.5.52

• , liquid crystal oligomers provide and stabilize a variety of fluid phases with fascinating functions and oligomeric approach provides a wide flexibility in the molecular design. The hybridization of above mentioned two varieties of liquid crystals may lead to novel nanostructured materials with

Synthesis of novel photochromic pyrans via palladium- mediated reactions

• Christoph Böttcher,
• Gehad Zeyat,
• Saleh A. Ahmed,
• Elisabeth Irran,
• Thorben Cordes,
• Cord Elsner,
• Wolfgang Zinth and
• Karola Rueck-Braun

Beilstein J. Org. Chem. 2009, 5, No. 25, doi:10.3762/bjoc.5.25

• the rise of an intense band centered at ~460 nm (Figure 1a/b). The spectral signature of this band allows an assignment to the open forms with a more planar structure due to the sp2-hybridization at the formerly sp3-hybridized carbon carrying the aryl residues. The π-system now extends over a