DNA-, RNA- and self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone

A new pyrrolidinyl peptide nucleic acid (PNA) comprising of an alternate sequence of 4′-nucleobase-modified proline with (2′R,4′S) configuration and a (1S,2S)-2-aminocyclopentanecarboxylic acid [(2′R,4′S)-acpcPNA] backbone was synthesized and its DNA-, RNA- and self-pairing properties studied. T_m and CD studies suggested that the (2′R,4′S)-acpcPNA forms antiparallel hybrids to DNA and RNA with high sequence and direction specificity. The stability of these hybrids is comparable to those of the (2′R,4′R)-acpcPNA hybrids previously reported by our group. On the other hand, experiments with a self-complementary sequence indicated that the new (2′R,4′S)-acpcPNA forms a more stable antiparallel self-hybrid than (2′R,4′R)-acpcPNA.     

PNA分子一阶超极化率溶剂效应的研究

运用超瑞利散射(HRS)方法对PNA分子在不同溶剂中的一阶超极化率进行了实验研究.基于外参法我们提出了用于研究HRS溶剂效应的数据处理方法.实验结果表明PNA分子在不同溶液中的一阶超极化率随着溶剂极性的增强而增加.还对该实验结果进行了初步的理论分析和解释.     

Synthetic,Structural, and RNA Binding Studies on 2-Aminopyridine-Modified Triplex-Forming Peptide Nucleic Acids

The development of new RNA-binding ligands is attracting increasing interest in fundamental science and the pharmaceutical industry. The goal of this study was to improve the RNA binding properties of triplex-forming peptide nucleic acids (PNAs) by further increasing the pK_a of 2-aminopyridine ( M ). Protonation of M was the key for enabling triplex formation at physiological pH in earlier studies. Substitution on M by an electron-donating 4-methoxy substituent resulted in slight destabilization of the PNA–dsRNA triplex, contrary to the expected stabilization due to more favorable protonation. To explain this unexpected result, the first NMR structural studies were performed on an M -modified PNA–dsRNA triplex which, combined with computational modeling identified unfavorable steric and electrostatic repulsion between the 4-methoxy group of M and the oxygen of the carbonyl group connecting the adjacent nucleobase to PNA backbone. The structural studies also provided insights into hydrogen-bonding interactions that might be responsible for the high affinity and unusual RNA-binding preference of PNAs.     

The effect of structure on improvement of the PNA Young modulus: A study of steered molecular dynamics

Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accordingly, this paper investigates the elastic properties of the Prefoldin nano-actuator (PNA), specifically its Young modulus and the structural changes on a microscopic scale. For this purpose, three structurally different PNAs obtained from Protein Data Bank (PDB) and previous studies of our research team have been used. The selected three-tentacles Prefoldin are analyzed via the series of steered molecular dynamics simulations (SMD) based on the theory of Two Springs in Series. The simulation is applied in the velocity of 0.1, 0.05, and 0.01. Due to differences in the structure of the Prefoldin, PNAs exhibited different behaviours at various pull rates. Also, the analysis showed different values of Young's modulus for the PNA tentacles in the interval of (2.5–4 GPa). Understanding the mechanical properties of a Prefoldin nano actuator allows for a closer examination of its application in transportation the pathogenic cargos and intelligent drug delivery.     

A Peptide Nucleic Acid (PNA)‐DNA Ferrocenyl Intercalator for Electrochemical Sensing

A ferrocenyl intercalator was investigated to develop an electrochemical DNA biosensor employing a peptide nucleic acid (PNA) sequence as capture probe. After hybridization with single strand DNA sequence, a naphthalene diimide intercalator bearing ferrocene moieties (FND) was introduced to bind with the PNA‐DNA duplex and the electrochemical signal of the ferrocene molecules was used to monitor the DNA recognition. Electrochemical impedance spectroscopy was used to characterize the different modification steps. Differential pulse voltammetry was employed to evaluate the electrochemical signal of the FND intercalator related to its interaction with the complementary PNA‐DNA hybrid. The ferrocene oxidation peaks were utilised for the target DNA quantification. The developed biosensor demonstrated a good linear dependence of FND oxidation peak on DNA concentration in the range 1 fM to 100 nM of target DNA, with a low detection limit of 11.68 fM. Selectivity tests were also investigated with a non‐complementary DNA sequence, indicating that the FND intercalator exhibits a selective response to the target PNA‐DNA duplex.     

New Synthetic Route to γ-Mercaptomethyl PNA Monomers

Peptide nucleic acids (PNAs) are oligonucleotide mimics widely used as antisense, antigene molecules, and biotechnological tools. Recently, several microarrays and other biosensors based on PNAs have been developed. The construction of PNA molecular beacons or light-up probes for DNA detection requires the labelling of the PNA moiety. Labels are usually attached at the C or N terminal end by a flexible linker or in the middle of a PNA sequence, substituting one PNA base with an artificial base or by attaching fluorophores to a modified PNA backbone. The need to develop simple protocols to label PNAs encouraged us to design a new procedure for the synthesis of γ-mercaptomethyl-modified PNA. Here we propose a new strategy for the synthesis of modified PNAs, bearing amino acid side chains. The synthesis is straightforward and is an improvement to the procedures reported so far, as it uses stable intermediates and proceeds with better yields.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 28

The protected hydrazide‐linked uracil‐ and adenine‐derived tetranucleoside analogues 17, 19 , and 21 were synthesized in solution by coupling the dimeric hydrazines 6 and 10 with the carboxylic acids 7, 11 , and 16 . These hydrazines and acids were obtained by partially deprotecting the hydrazines 5, 9 , and 15 , and these were prepared by coupling the hydrazines 3 and 14 with the carboxylic acids 4 and 8 . The crystal structure analysis of the fully protected UU dimer 5 showed the formation of an antiparallel cyclic duplex with the uracil units H‐bonded via H? N(3) and O?C(2). Stacking interactions were observed between the uracil units with a buckle twist of 30.9°, and between the uracil unit II and the fluoren‐9‐yl group of Fmoc (=9H‐fluoren‐9‐yl)methoxycarbonyl). The hydrazide H? N(3′) and the C?O group of Fmoc form an intramolecular H‐bond. The uracil‐ and adenine‐derived, water‐soluble hydrazide‐linked self‐complementary octamers 23 – 32 and the non‐self‐complementary uracil derived decamer 33 were obtained by coupling the carboxylic acids 4 and 8 on a solid support. ¹H‐NMR Analysis in CDCl₃, mixtures of CDCl₃ and (D₆)DMSO, and (D₈)THF showed that the partially deprotected dimers 5, 6, 12 , and 13 form weakly associated linear duplexes. The partially deprotected tetramers 17 and 18 do not associate. The hydrazide‐linked octamers 23 – 32 do not stack in aqueous solution, and the non‐self‐complementary decamer 33 does not stack with the complementary strands of DNA 43 and RNA 42 . The Cbz‐protected amide‐linked octamers 51 – 56 derived from uracil, adenine, cytosine, and guanine were obtained as the main products by solid‐phase synthesis from the carboxylic acids 46 – 49 . The fully deprotected amide‐linked octamers proved insoluble, and could neither be purified nor analysed.     

Biosensors and rapid diagnostic tests on the frontier between analytical and clinical chemistry for biomolecular diagnosis of dengue disease: a review

The past decades have witnessed enormous technological improvements towards the development of simple, cost-effective and accurate rapid diagnostic tests for detection and identification of infectious pathogens. Among them is dengue virus, the etiologic agent of the mosquito-borne dengue disease, one of the most important emerging infectious pathologies of nowadays. Dengue fever may cause potentially deadly hemorrhagic symptoms and is endemic in the tropical and sub-tropical world, being also a serious threat to temperate countries in the developed world. Effective diagnostics for dengue should be able to discriminate among the four antigenically related dengue serotypes and fulfill the requirements for successful decentralized (point-of-care) testing in the harsh environmental conditions found in most tropical regions. The accurate identification of circulating serotypes is crucial for the successful implementation of vector control programs based on reliable epidemiological predictions. This paper briefly summarizes the limitations of the main conventional techniques for biomolecular diagnosis of dengue disease and critically reviews some of the most relevant biosensors and rapid diagnostic tests developed, implemented and reported so far for point-of-care testing of dengue infections. The invaluable contributions of microfluidics and nanotechnology encompass the whole paper, while evaluation concerns of rapid diagnostic tests and foreseen technological improvements in this field are also overviewed for the diagnosis of dengue and other infectious and tropical diseases as well.     

Self‐assembled supramolecular microgels: Fractal structure and aggregation mechanism

Multifunctional molecules were designed to produce microgels with specific structures. Both static light scattering and dynamic light scattering were employed to determine the fractal dimension of the microgels. The protein, avidin, was strongly bound to four biotin moieties. Biotin was attached covalently to specifically engineered peptide nucleic acid (PNA) oligomers. Three designed DNA oligomers self‐assembled to produce a trifunctional three‐way junction (TWJ) with single‐stranded ends that were complementary to the PNA sequence. The sizes of the supramolecular aggregates were characterized by dynamic light scattering. The fractal dimension was obtained from the angular dependence of the scattered intensity when the microgels were large enough. When the microgels were formed via cooling from a temperature above the melting point of the PNA–DNA helices, reversible structures with a fractal dimension of approximately 1.86 were formed, which is consistent with a cluster–cluster aggregation mechanism. When the microgels were formed by the slow addition of biotinylated PNA bound to the TWJ to a solution of avidin at room temperature, the observed fractal dimension approached 2.6, which is consistent with a point–cluster aggregation mechanism. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 3037–3046, 2003     

The ‘fully protected backbone’ approach as a versatile tool for a new solid-phase PNA synthesis strategy

The ‘fully protected backbone’ (FPB) strategy has been efficiently adapted to the solid-phase synthesis of homothymine, homocytosine and ‘mixed’ pyrimidine PNAs. This versatile and simple method avoids the preparation of PNA monomers and relies on easy available starting materials, highly efficient backbone elongations and effective nucleobase units condensations.