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

• transferred to artificial systems like peptide nucleic acids (PNA) [33] and extensively used to mimic biological processes [34][35] or to generate functional materials [36]. Host–guest chemistry has been studied in the field of sequence-specific molecular recognition as well. The selective recognition of

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

• – has also been incorporated into DNA as a base replacement, again without showing significant structure-induced fluorescence change [22]. Peptide nucleic acid or PNA is an electrostatically neutral analogue of DNA which can form very stable duplexes with DNA and RNA in a highly sequence specific

• fashion. PNA–DNA duplexes have different structural morphology and electrostatic potential surfaces from DNA–DNA duplexes and therefore they are interacting differently with DNA-binding dyes [23][24][25]. We had recently introduced a new conformationally constrained pyrrolidinyl PNA known as acpcPNA that

• 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

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

• + 1] type could be obtained [14][15]. While most examples focus on the use of DNA, other systems such as RNA [16], GNA [17][18] (glycol nucleic acid), PNA [19][20][21], and other nucleic acid derivatives [22] have been modified as well. It is interesting to note that metal-mediated base pairs do not

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

• recognition; triplex stabilization; Introduction Peptide nucleic acid (PNA) probes are very selective in the recognition of DNA and have been used in a large variety of diagnostic methods, easily allowing the detection of point mutations at very low concentrations [1][2][3]. Poly-pyrimidine PNA can form very

• 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

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

• of the SPR signal is certainly due to the low molecular weight of HisHis which limits any further SPR investigations. Additionally, bifunctionalized carbohydrate surfaces were incubated simultaneously with FITC-HisHis, TRITC-ConA, and FITC-PNA to elucidate whether selective binding of the synthetic

• lectin to glycosides is also observed in the presence of natural lectins. In Figure 6, the overlays of fluorescence images are shown. In each experiment, FITC-HisHis is detected exclusively on the NANA and the Gal areas, whereas TRITC-ConA binds to Man and FITC-PNA binds to Gal only. These observations

• demonstrate that selective recognition between HisHis and NANA or Gal is not in any way disturbed by the presence of a second lectin and that the synthetic lectin HisHis and the natural lectins ConA and PNA operate orthogonally. Additionally, the selectivity of the FITC-HisHis was tested with a set of

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

• previously used in the synthesis of PMO in the 2→4 direction [23]. This corresponds to the 5’→3’ direction of native oligonucleotides. In our case, the MorGly oligomers were synthesized in the opposite direction (4→2) [20] similar to the standard direction (3’→5’) of native ODN and peptide nucleic acid (PNA

Mannose-decorated cyclodextrin vesicles: The interplay of multivalency and surface density in lectin–carbohydrate recognition

• Ulrike Kauscher and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2012, 8, 1543–1551, doi:10.3762/bjoc.8.175

• to the average spacing of mannose at 50% surface coverage of guest 1. These observations are entirely consistent with our previous investigation of an artificial glycocalyx of lactose and maltose and its interaction with ConA and peanut agglutinin (PNA) [28][29]. Interestingly, if guests 2–4 (0.1 mM

A novel high-yield synthesis of aminoacyl p-nitroanilines and aminoacyl 7-amino-4-methylcoumarins: Important synthons for the synthesis of chromogenic/fluorogenic protease substrates

• Xinghua Wu,
• Yu Chen,
• Herve Aloysius and
• Longqin Hu

Beilstein J. Org. Chem. 2011, 7, 1030–1035, doi:10.3762/bjoc.7.117

• -nitroaniline (aminoacyl-pNA) and aminoacyl 7-amino-4-methylcoumarin (aminoacyl-AMC) are important synthons for the synthesis of chromogenic/fluorogenic protease substrates. A new efficient method was developed to synthesize aminoacyl-pNA and aminoacyl-AMC derivatives in excellent yields starting from either

• acid/peptide conjugates liberates the free chromophore or fluorophore, allowing the convenient determination of the rate of enzyme catalysis with a UV or fluorescence spectrophotometer. p-Nitroaniline (pNA) is one of the most commonly used chromogenic reagents. The synthesis of peptide-pNAs usually

• aminoacyl-pNA and aminoacyl-AMC derivatives through the selenocarboxylate/azide amidation strategy, under aqueous or alcoholic reaction conditions, with excellent yields. Results and Discussion An efficient method was developed to synthesize aminoacyl-pNAs and aminoacyl-AMCs in excellent yields as shown in

Symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated systems

• Sławomir Boncel,
• Maciej Mączka,
• Krzysztof K. K. Koziol,
• Radosław Motyka and
• Krzysztof Z. Walczak

Beilstein J. Org. Chem. 2010, 6, No. 34, doi:10.3762/bjoc.6.34

• ]. Moreover, α,ω-nucleobase amide-conjugated molecules possess the tendency to form meta-stable complexes with DNA and thus can perturb the cell replication. For example, amide-linked heterodimer synthons consisting of acyclic nucleoside units and 5′-amino-2′,5′-dideoxythymidine are PNA/DNA chimeras (V) [4