One-pot synthesis of hybrid macrocyclic pentamers with variable functionalizations around the periphery

Rather than four- or six-residue macrocylces, one-pot macrocyclization allows for the highly selective formation of five-residue macrocycles rigidified by intramolecular hydrogen bonds. Variable functionalizations around the pentameric periphery were achieved by reacting monomers with higher oligomers bearing different exterior side chains. The formation of these hybrid pentamers suggests a chain-growth mechanism for the one-pot macrocyclization where the successive addition of monomers onto higher oligomers is faster than those between two monomers or two higher oligomers.     

Changes of flavan-3-ols with different degrees of polymerization in seeds of 'Shiraz', 'Cabernet Sauvignon' and 'Marselan' grapes after veraison

Flavan-3-ols consist of flavan-3-ol monomers and polymers with different degrees of polymerization (DP). In this study, flavan-3-ol extracts from grape seeds were well separated into three fractions including monomers, oligomers (2 < DP < 10) and polymers (DP > 10), by means of normal-phase HPLC-MS. The different patterns of these three fractions were analyzed in three Vitis vinifera cultivars ('Shiraz', 'Cabernet Sauvignon' and 'Marselan') seeds from veraison to harvest. The results showed: (1) polymers were the main form of flavan-3-ols in grape seeds and monomers accounted for only a small proportion; (2) the contents of flavan-3-ol monomers in the seeds of three grape cultivars all exhibited a gradually decreasing trend with a little fluctuation, whereas the patterns of the change of contents of oligomers and polymers were extremely different among grape cultivars; the contents of flavan-3-ol oligomers were enhanced in the seeds of 'Cabernet Sauvignon', but were reduced in the other two cultivars; (3) with regard to the proportion of flavan-3-ols with a certain DP to total flavan-3-ols, both flavan-3-ol monomers and flavan-3-ols with low DP fell in proportion, while the flavan-3-ols with high DP increased correspondingly. These findings indicate that flavan-3-ol polymerization in developing seeds is variety-dependent and may be genetically regulated.     

Modeling procyanidin self-association processes and understanding their micellar organization: a study by diffusion NMR and molecular mechanics

The colloidal behavior of eight synthetic procyanidins (three monomers, four dimers, and a trimer) has been investigated in water or in a winelike medium using DOSY NMR spectroscopy and molecular dynamics simulations. Different behavior was observed for monomers and oligomers. Monomers self-associate with a high affinity constant (37-53 M(-1)) to form micelles at low cmc (critical micelle concentration) values (1-5 g.L(-1)). These micelles undergo a time-dependent coalescence process to form hazes and precipitates. As for dimers and the trimer, self-association also occurs but with a lower affinity (approximately 6 M(-1)) and at higher cmc values (10-20 g.L(-1)) to form small micelles (<5 nm) that remain stable throughout the experiment. The presence of 10% ethanol does not significantly affect the self-association constant for monomers and oligomers but increases their cmc values by approximately 50% and decreases the micelle size by a factor 2. However, the presence of 20 mM NaCl appears to negate the effect of ethanol. This study helps to clarify the role of procyanidin monomers versus oligomers in wine turbidity and demonstrates that procyanidin oligomers are fully available to interact with saliva proteins.     

Rapid Synthesis of Propargyl-γ-Modified Peptide Nucleic Acid Monomers for Late-Stage Functionalization of Oligomers

The exceptional hybridization properties of peptide nucleic acids (PNAs) coupled with the ease of their synthesis has made this artificial nucleic acid mimetic a desirable platform for diagnostics, therapeutics and supramolecular engineering. PNA backbone modifications have been extensively explored to finetune physicochemical properties and for conjugation of functional molecules. Here, we detail the synthesis of a universal γ-propargyl-PNA backbone from serine, and its acylation with the four DNA canonical nucleobases. The availability of serine as d or l enantiomer provide simple accesses to PNA oligomers for hybridization with natural oligonucleotides or for orthogonal hybridization circuitry. We show that late-stage conjugation enables optimization of the physicochemical properties. This approach is appealing due to its orthogonality to Fmoc-SPPS, its flexibility and ease for introducing diversity by on-resin copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). We exemplified the utility of these novel monomers with PNA based hybridization chain reactions (HCRs).     

Analysis of disulphide linkages in bovine kappa-casein oligomers using two-dimensional electrophoresis

Disulphide bonds play an important role in protein structure and function. Bovine kappa-casein (kappa-csn), an important glycoprotein in milk, contains two cysteines that can form disulphide bonds. On 2-D gels run under nonreducing conditions the kappa-csn in milk presented a complex pattern of monomers and disulphide-linked oligomers. Trains of spots corresponding to monomers to hexamers were observed as a result of the participation of different glycoforms and phosphoforms in oligomer formation. The dimers and trimers ran as doublets on the gel and analysis of the disulphide-linked peptides released from them after in-gel tryptic digestion showed they were the result of different disulphide linkages. The linkages were confirmed by MSMS. When milks with electrophoretically distinct genetic variants of kappa-csn were mixed and run on 2-D gels, they retained their distinct patterns indicating that disulphide exchange reactions or disulphide 'scrambling' was not occurring during 2-D analysis. The patterns observed represent the native distribution of kappa-csn in milk at harvest. The role and significance of the disulphide bonding of kappa-csn are discussed.     

Solid-phase synthesis of peptide ribonucleic acids (PRNA)

The range of available peptide ribonucleic acid (PRNA) monomers was fully expanded for the use in solid-phase synthesis of PRNA oligomers, which were designed to reversibly control the recognition and complexation behavior of the complementary DNA/RNA by external factors. A couple of PRNA 12-mers with desired purine-pyrimidine mixed sequences were prepared indeed in high yields by the solid-phase synthesis.     

Oxy-peptide nucleic acid with a pyrrolidine ring that is configurationally optimized for hybridization with DNA

Four stereoisomers of oxy-peptide nucleic acids containing ether linkages in the main chain and conformationally-restricted pyrrolidine rings (pyrrolidine-based oxy-PNA = POPNA) were newly synthesized and investigated for binding to DNA. cis-l-POPNA with 9 adenine bases formed the most stable hybrid with dT(9). The POPNA showed high sequence specificity similar to that of the Nielsen-type PNA and sharper melting behavior in hybridization with DNA than the Nielsen-type PNA.     

Detection of Aβ Monomers and Oligomers: Early Diagnosis of Alzheimer's Disease

Alzheimer's disease (AD), as the most common progressive neurodegenerative disorder, is pathologically characterized by deposition of extracellular plaque composed of amyloid‐β peptide (Aβ). Different assembled states of Aβ have been considered as both important biomarkers and drug targets for the diagnosis and therapy of AD. Recent studies demonstrate that small, diffusible Aβ oligomers formed by aggregation of Aβ monomers are the major toxic agents in AD. Therefore, the development of reliable assays for Aβ (both monomers and oligomers) will be important for the early differential diagnosis of dementia, predicting the progression of AD, as well as monitoring the effectiveness of novel anti‐Aβ drugs for AD. In this review, we summarize the recent progress made in the development of techniques for detection of Aβ monomers and oligomers. In particular, the principles governing the design of these sensors are classified and summarized. Moreover, the advantages and disadvantages of the assays are evaluated. This review also discusses the improvements and challenges for application of these assays in the early diagnosis of AD.     

Co‐existence of Two Different α‐Synuclein Oligomers with Different Core Structures Determined by Hydrogen/Deuterium Exchange Mass Spectrometry

Neurodegenerative disorders are characterized by the formation of protein oligomers and amyloid fibrils, which in the case of Parkinson’s disease involves the protein α‐synuclein (αSN). Cytotoxicity is mainly associated with the oligomeric species, but we still know little about their assembly and structure. Hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is used to analyze oligomers formed by wild‐type (wt) αSN and also three familial αSN mutants (A30P, E46K, and A53T). All four variants show co‐existence of two different oligomers. The backbone amides of oligomer type I are protected from exchange with D₂O until they dissociate into monomeric αSN by EX1 exchange kinetics. Fewer residues are protected against exchange in oligomer type II, but this type does not revert to αSN monomers. Both oligomers are protected in the core sequence Y39–A89. Based on incubation studies, oligomer type I appears to form straight fibrils, while oligomer type II forms amorphous clusters that do not directly contribute to the fibrillation process.     

Cryoscopy on sulfuric acid solutions of a heterocyclic polymer (BBB) and related compounds

Cryoscopic measurements have been carried out on solutions in sulfuric acid of a heterocyclic polymer, its monomers, and certain of its oligomers. The polymer, BBB, is prepared by the polycondensation of 1,4,5,8-naphthalenetetracarboxylic acid (NTC) with 3,3′-diaminobenzidine (DAB). The results show that the polymer, its oligomers and one of its monomers, DAB, are all extensively protonated in sulfuric acid, whereas its other monomer is not. The degree of protonation appears to be greater for the polymer than for its low molecular weight oligomers.     

Development of an efficient and low-cost protocol for the manual PNA synthesis by Fmoc chemistry

An efficient and low-cost protocol for the manual synthesis of Peptide Nucleic Acids is reported here. The protocol relies on coupling reactions carried out with 2.5 equiv of PNA monomers activated with HOBT/HBTU, in the presence of pyridine/NMM. The protocol has been tested on four PNA oligomers with a length ranging from 9 to 12 bases and a purine content up to 67%.     

DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer

A series of polyaniline (PANI) oligomers was constructed from monomer units covalently linked to duplex DNA through N-(2-aminoethyl) groups bonded through cytosines. DNA oligomers containing the aniline monomers were treated with horseradish peroxidase (HRP) and H2O2 under conditions known to cause polymerization of aniline. No change in the absorption spectrum of the DNA was observed for samples containing fewer than four contiguous aniline groups. However, for oligomers containing four, five, or six aniline units, treatment with HRP and H2O2 led to the appearance of absorption features characteristic of the conducting "proton doped" emeraldine oxidation state of PANI. Molecular modeling shows that the DNA is distorted in the region of the PANI, but flanking regions of the DNA maintain their B-form structure. These findings provide a method to exploit the self-recognition, self-assembly, and sequence programmability of DNA for the formation of conducting polymers.     

From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives

Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using ¹³C, ¹⁵N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.     

Cyclic versus linear siloxane liquid crystalline oligomers: phase behaviour

The phase behaviour of cyclic and linear liquid crystalline polysiloxanes containing two different cholesteric mesogens is reported. The thermal properties of the synthesized monomers and oligomers were investigated by polarizing optical microscopy and differential scanning calorimetry. The influence of the structure of cyclic siloxane on the mesomorphic properties of cyclic liquid crystalline polysiloxanes is discussed. Similar trends in the thermal transitions of cyclic and linear compounds containing the same mesogenic composition were observed, though the cyclic oligomers showed poorer mesomorphic properties as compared with their linear analogues.     

In situ AFM study of amelogenin assembly and disassembly dynamics on charged surfaces provides insights on matrix protein self-assembly

Because self-assembly of matrix proteins is a key step in hard tissue mineralization, developing an understanding of the assembly pathways and underlying mechanisms is likely to be important for successful hard tissue engineering. While many studies of matrix protein assembly have been performed on bulk solutions, in vivo these proteins are likely to be in contact with charged biological surfaces composed of lipids, proteins, or minerals. Here we report the results of an in situ atomic force microscopy (AFM) study of self-assembly by amelogenin--the principal protein of the extracellular matrix in developing enamel--in contact with two different charged substrates: hydrophilic negatively charged bare mica and positively charged 3-aminopropyl triethoxysilane (APS) silanized mica. First we demonstrate an AFM-based protocol for determining the size of both amelogenin monomers and oligomers. Using this protocol, we find that, although amelogenin exists primarily as ~26 nm in diameter nanospheres in bulk solution at a pH of 8.0 studied by dynamic light scattering, it behaves dramatically differently upon interacting with charged substrates at the same pH and exhibits complex substrate-dependent assembly pathways and dynamics. On positively charged APS-treated mica surfaces, amelogenin forms a relatively uniform population of decameric oligomers, which then transform into two main populations: higher-order assemblies of oligomers and amelogenin monomers, while on negatively charged bare mica surfaces, it forms a film of monomers that exhibits tip-induced desorption and patterning. The present study represents a successful attempt to identify the size of amelogenin oligomers and to directly monitor assembly and disassembly dynamics on surfaces. The findings have implications for amelogenin-controlled calcium phosphate mineralization in vitro and may offer new insights into in vivo self-assembly of matrix proteins as well as their control over hard tissue formation.     

Cyclic versus linear siloxane liquid crystalline oligomers: phase behaviour

The phase behaviour of cyclic and linear liquid crystalline polysiloxanes containing two different cholesteric mesogens is reported. The thermal properties of the synthesized monomers and oligomers were investigated by polarizing optical microscopy and differential scanning calorimetry. The influence of the structure of cyclic siloxane on the mesomorphic properties of cyclic liquid crystalline polysiloxanes is discussed. Similar trends in the thermal transitions of cyclic and linear compounds containing the same mesogenic composition were observed, though the cyclic oligomers showed poorer mesomorphic properties as compared with their linear analogues.     

Prospering the biphen[n]arenes family by tailoring reaction modules

Reported here is the comprehensive investigation on the formation of biphen[n]arenes by tailoring reaction modules. Five new macrocyclic arenes and four oligomers were synthesized by the condensation of monomers possessing different multimethoxyphenyl reaction modules and paraformaldehyde. We proved that the number and sites of methoxy on reaction modules greatly affected the reaction activity, shape, and connection mode of macrocycles. Moreover, the triangular and saddle-shaped configuration of macrocycles were revealed by single crystal structures. The results provided a typical and fundamental guidance in designing new macrocyclic arenes.     

Chimeric (aeg-pyrrolidine)PNAs: synthesis and stereo-discriminative duplex binding with DNA/RNA

The design and facile conversion of naturally occurring 4-hydroxyproline to all four diastereomers of thymine pyrrolidine PNA monomer, (2R,4S)-adenine, -guanine and -cytosine monomers and their incorporation into duplex forming PNA oligomers is reported. The interesting results of the hybridization studies with complementary DNA/RNA sequences in either parallel or antiparallel orientation reveal the stereochemistry-dependent DNA vs. RNA discriminations and parallel/antiparallel orientation selectivity.     

Synthesis and characterization of thiol–ene functionalized siloxanes and evaluation of their crosslinked network properties

Three types of linear thiol‐functionalized siloxane oligomers and three types of ene‐functionalized oligomers were synthesized and subsequently photopolymerized. Within each type of thiol‐functionalized oligomer, the ratio of mercaptan repeat units to nonreactive phenyl repeat units was varied to manipulate both the crosslink density and the degree of secondary interactions through π–π stacking. Similarly, the repeat units of the three ene‐functionalized oligomers are composed of allyl‐functional monomers, benzene‐functional monomers, and octyl‐functional monomers in varying ratios of benzene:octyl but with a constant fraction of allyl moieties. The structural composition of the siloxane oligomers plays a pivotal role in the observed material properties of networks formed through thiol–ene photopolymerization. Networks with a high concentration of thiol functionalities exhibit higher rubbery moduli, ultimate strengths, and Young's moduli than networks with lower thiol concentrations. Moreover, the concentration of functionalities capable of participating in secondary interactions via hydrogen bonding or π–π stacking directly impacts the network glass transition temperature and elasticity. The combination of low crosslink density and high secondary interactions produces networks with the greatest toughness. Finally, the fraction of octyl repeats correlates with the hydrophobic nature of the network. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

DNA-directed synthesis of aniline and 4-aminobiphenyl oligomers: programmed transfer of sequence information to a conjoined polymer nanowire

A new class of materials was prepared from aniline-containing oligomers that are covalently linked to the nucleobases of duplex DNA. Oligomers composed of repeating aniline (PANI) or 4-aminobiphenyl (PAB) units having the properties of conducting polymers conjoined to the DNA were prepared by the reaction of horseradish peroxidase and H2O2 with DNA having the appropriate monomers aligned within the major groove. These oligomers exhibit the spectral and chemical properties typical of para-linked polyanilines. This method of preparation enables utilization of the unique self-recognizing properties and sequence programmability of DNA to create tailored oligomers. This ability was demonstrated experimentally by preparation of PAB oligomers from alternating benzene and aniline monomers. Conjoined conducting polymers carrying the sequence information of DNA may have applicability as nanowires.