DyNAs: constitutional dynamic nucleic acid analogues

Dynamic cationic polymers were generated in aqueous media from functionally complementary monomers bearing nucleobase groups. (1)H NMR spectroscopy was used to follow the polycondensation reaction of the nucleobase-appended dihydrazides 1 and 2 with the dialdehydes B and C. The reversibility of these polymers was established by proton NMR spectroscopy through exchange of the dihydrazide 2 with polymer 1 B. The polymers 1 B, 2 B, 1 C, and 2 C represent dynamic biopolymers of nucleic acid type, DyNAs. Electrostatic interaction of these polymers with polyanionic entities, such as polyphosphates, polynucleotides, and polyaspartic acid, was shown to take place. It induces a change in size of the dynamic polymer, as it responds by an increase in degree of polymerization to an increase of the overall anionic charge introduced, that is, to the total electrostatic interaction.     

BNAs: novel nucleic acid analogs with a bridged sugar moiety

This article deals with our recent studies on the synthesis of BNAs (Bridged Nucleic Acids), novel nucleic acid analogs bearing a preorganized sugar conformation by a bridged structure. Duplex- and triplex-forming abilities of the BNA modified oligonucleotides are also described.     

Synthesis of bridged aza-rebeccamycin analogues

The syntheses of rebeccamycin analogues possessing a 7-azaindole moiety instead of an indole unit, and with both indole and azaindole moieties linked to the carbohydrate are described. In these bridged aza compounds, the oxygen of the pyranose heterocycle is oriented towards either the indole, or the azaindole unit. In these series, compounds bearing a free imide nitrogen were synthesized by coupling the corresponding aglycones with a sugar pre-tosylated in 2-position via a Mitsunobu reaction. To obtain a precursor for bridged aza-rebeccamycin analogues substituted in 6-position on the sugar moiety, a 2,6-ditosylated sugar was used.     

High-affinity peptide nucleic acid oligomers containing tricyclic cytosine analogues

[structure: see text] Peptide nucleic acid (PNA) monomers containing the tricyclic cytosine analogues phenoxazine, 9-(2-aminoethoxy)phenoxazine (G-clamp), and 9-(3-aminopropoxy)phenoxazine (propyl-G-clamp) have been synthesized. The modified nucleobases were incorporated into PNA oligomers using Boc-chemistry for solid-phase synthesis. PNAs containing single G-clamp modifications exhibit significantly enhanced affinity toward RNA and DNA targets relative to unmodified PNA while maintaining mismatch discrimination. These PNA G-clamp modifications exhibit the highest increase in affinity toward nucleic acid targets reported so far for PNA modifications.     

Utility of lab-on-a-chip technology for high-throughput nucleic acid and protein analysis

On-chip electrophoresis can provide size separations of nucleic acids and proteins similar to more traditional slab gel electrophoresis. Lab-on-a-chip (LoaC) systems utilize on-chip electrophoresis in conjunction with sizing calibration, sensitive detection schemes, and sophisticated data analysis to achieve rapid analysis times (<120 s). This work describes the utility of LoaC systems to enable and augment systems biology investigations. RNA quality, as assessed by an RNA integrity number score, is compared to existing quality control (QC) measurements. High-throughput DNA analysis of multiplex PCR samples is used to stratify gene sets for disease discovery. Finally, the applicability of a high-throughput LoaC system for assessing protein purification is demonstrated. The improvements in workflow processes, speed of analysis, data accuracy and reproducibility, and automated data analysis are illustrated.     

Synthesis and properties of nucleic acid analogues consisting of a benzene-phosphate backbone

[Chemical reaction: See text] The synthesis and properties of a nucleic acid analogue consisting of a benzene-phosphate backbone are described. The building blocks of the nucleic acid analogue are composed of bis(hydroxymethyl)benzene residues connected to nucleobases via the biaryl-like axis. Stabilities of the duplexes were studied by thermal denaturation. It was found that the thermal stabilities of the duplexes composed of the benzene-phosphate backbone are highly dependent on their sequences. The duplexes with the benzene-phosphate backbone comprised of the mixed sequences were thermally less stable than the natural DNA duplexes, whereas that composed of the homopyrimidine and homopurine sequences was thermally and thermodynamically more stable than the corresponding natural DNA duplex. It was suggested that the analogues more efficiently stabilize the duplexes in a B-form duplex rather than in an A-form duplex. Thus, the duplexes consisting of the benzene-phosphate backbone, especially composed of the homopyrimidine and homopurine sequences, may offer a novel structural motif useful for developing novel materials applicable in the fields of bio- and nanotechnologies.     

Peptide nucleic acid stabilized perovskite nanoparticles for nucleic acid sensing

Nanostructural hybrid organic-inorganic metal halide perovskites offer a wide range of potential applications including photovoltaics, solar cells, and light emitting diodes. Up to now the surface stabilizing ligands were used solely to obtain the optimal properties of nanoparticles in terms of dimensionality and stability, however their possible additional functionality was rarely considered. In the present work, hybrid lead bromide perovskite nanoparticles (PNP) were prepared using a unique approach where a peptide nucleic acid is used as a surface ligand. Methylammonium lead bromide perovskite colloidal nanoparticles stabilized by thymine-based peptide nucleic acid monomer (PNA-M) and relevant trimer (PNA-T) were prepared exhibiting the size below 10 nm. Perovskite structure and crystallinity were verified by X-ray powder diffraction spectroscopy and high resolution transmission electron microscopy. PNP-PNA-M and PNP-PNA-T colloidal dispersions in chloroform and toluene possessed green-blue fluorescence, while Fourier-transform infrared spectroscopy (FT-IR) and quantum chemical calculations showed that the PNA coordinates to the PNP surface through the primary amine group. Additionally, the sensing ability of the PNA ligand for adenine nucleic acid was demonstrated by photoluminescence quenching via charge transfer. Furthermore, PNP thin films were effectively produced by the centrifugal casting. We envision that combining the unique, tailored structure of peptide nucleic acids and the prospective optical features of lead halide perovskite nanoparticles could expand the field of applications of such hybrids exploiting analogous ligand chemistry.     

Synthesis and properties of a bridged nucleic acid with a perhydro-1,2-oxazin-3-one ring

A novel derivative of 2',4'-bridged nucleic acid, named hydroxamate-bridged nucleic acid (HxNA), containing a six-membered perhydro-1,2-oxazin-3-one ring, was designed and synthesized. The introduction of a carbonyl function along with an N-O linkage in the six-membered bridged structure is the unique structural feature of the novel 2',4'-bridged nucleic acid analogue. The design was carried out to restrict the flexibility of the sugar moiety through the trigonal planarity of carbonyl function, which would improve the properties of the modification. The synthesized monomer was incorporated into oligonucleotides, and their properties were examined. The HxNA-modified oligonucleotides exhibited selectively high affinity toward complementary ssRNA. Furthermore, the nuclease resistance of the HxNA-modified oligonucleotide was found to be higher than that of the corresponding natural and 2',4'-BNA/LNA-modified oligonucleotides. Interestingly, exposure of HxNA modified oligonucleotide to 3'-exonuclease resulted in gradual opening of the bridge, which stopped further digestion. Moreover, ring-opening of only one modification at the 3'-end of the oligonucleotides was observed, even if two or three HxNA modifications were present in the sequence. The results demonstrate the strong potential of the HxNA modification as a switch for the generation of highly nuclease-resistant RNA selective oligonucleotide in situ, which could have potential applications in antisense technology.     

A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology

In the development of orthogonal extra base pairs for expanding the genetic alphabet, we created novel, unnatural base pairs between fluorophore and quencher nucleobase analogues. We found that the nucleobase analogue, 2-nitropyrrole (denoted by Pn), and its 4-substitutions, such as 2-nitro-4-propynylpyrrole (Px) and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (NH(2)-hx-Px), act as fluorescence quenchers. The Pn and Px bases specifically pair with their pairing partner, 7-(2,2'-bithien-5-yl)imidazo[4,5-b]pyridine (Dss), which is strongly fluorescent. Thus, these unnatural Dss-Pn and Dss-Px base pairs function as reporter-quencher base pairs, and are complementarily incorporated into DNA by polymerase reactions as a third base pair in combination with the natural A-T and G-C pairs. Due to the static contact quenching, the Pn and Px quencher bases significantly decreased the fluorescence intensity of Dss by the unnatural base pairings in DNA duplexes. In addition, the Dss-Px pair exhibited high efficiency and selectivity in PCR amplification. Thus, this new unnatural base pair system would be suitable for detection methods of target nucleic acid sequences, and here we demonstrated the applications of the Dss-Pn and Dss-Px pairs as molecular beacons and in real-time PCR. The genetic alphabet expansion system with the replicable, unnatural fluorophore-quencher base pair will be a useful tool for sensing and diagnostic applications, as well as an imaging tool for basic research.     

Photochromic nucleic base units suitable for nucleic acid labelling

New molecules incorporating a uracil nucleic base and a dihydroindolizine (DHI) unit linked via spacer arms, i.e., uracil-spyrodihydroindolizine (4), were synthesised as models for light sensitive systems for nucleic acid labelling. The uracil-DHI (4) undergoes easy photocoloration to the uracil-betaine (5) generating the UV-detectable species. Preliminary results show rather weak binding of uracil-DHI (4) to calf thymus-DNA.     

Azidopeptide nucleic acid. An alternative strategy for solid-phase peptide nucleic acid (PNA) synthesis

[reaction: see text] A practical and efficient method for PNA synthesis using an azide group to mask the N-terminus is reported. The deprotection was carried out in 5 min, while couplings were complete within 60 min. The near neutral conditions of the phosphine deprotection combined with the base-free coupling using hydroxybenzotriazole-activated monomers make this approach very mild.     

Synthesis and conformation of a novel bridged nucleic acid having a trans-fused 3,5,8-trioxabicyclo[5.3.0]decane structure

A novel bridged nucleic acid analogue, 2′-deoxy-trans-3′,4′-BNA thymine monomer, was successfully synthesized. An ab initio calculation and X-ray structure analysis revealed that the trans-fused bicyclo[5.3.0]decane structure of the 2′-deoxy-trans-3′,4′-BNA effectively constrained the sugar puckering in C_2^′-endo with appropriate γ, δ and χ angles.     

Fluorescent hybridization probes for nucleic acid detection

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.     

Standardisation and reporting for nucleic acid quantification

The real-time quantitative polymerase chain reaction (qPCR) is probably the most common molecular technique in use today, having become the method of choice for nucleic acid detection and quantification and underpinning applications ranging from basic research through biotechnology and forensic applications to clinical diagnostics. This key technology relies on fluorescence to detect and quantify nucleic acid amplification products, and its homogeneous assay format has transformed legacy polymerase chain reaction (PCR) from a low-throughput qualitative gel-based technique to a frequently automated, rapid, high-throughput quantitative technology. However, the enormous range of protocols together with frequently inappropriate pre-assay conditions, poor assay design and unsuitable data analysis methodologies are impeding its status as a mature, ??gold standard?? technology. This, combined with inconsistent and insufficient reporting procedures, has resulted in the widespread publication of data that can be misleading, in particular when this technology is used to quantify cellular mRNA or miRNA levels by RT-qPCR. This affects the integrity of the scientific literature, with consequences for not only basic research, but with potentially major implications for the potential development of molecular diagnostic and prognostic monitoring tools. These issues have been addressed by a set of guidelines that propose a minimum standard for the provision of information for qPCR experiments (??MIQE??). MIQE aims to systematise current variable qPCR methods into a more consistent format that will encourage detailed auditing of experimental detail, data analysis and reporting principles. General implementation of these guidelines is an important requisite for the maturing of qPCR into a robust, accurate and reliable nucleic acid quantification technology.     

Microfluidic chip for fast nucleic acid hybridization

The design and experimental verification of a fast nucleic acid hybridization microchip using the fluidic velocity and strain rate effects was conducted. This hybridization chip was able to increase the hybridization signal 6-fold, reduce non-specific target-probe binding and background noise within 30 min, as compared to conventional hybridization methods, which may take from 4 h to overnight. Excellent correlation between experimental results and simulation analysis was obtained in this study. A detailed study of a newly designed microfluidic chip for enhancing hybridization was conducted. Three different designs of devices were fabricated and tested. Two different lengths of targets, 25-mer oligonucleotide and 1.4 kb ssDNA, were tested in this study. The hybridization efficiency can be improved by introducing velocity and extensional strain rate to the sample. This study demonstrates that the signal in the proposed method exhibits intensities 6-fold higher than those in static conditions. The necessary time for the hybridization process can be reduced from overnight to 30 min using the methods developed in this study. Experimental results also show that the strain rate provides stronger effect on hybridization than that of velocity. Combining hybridization with microfluidic concepts of velocity and strain rate effects may provide additional specificity and efficiency in nucleic acid detection and genomic study. This microfluidic hybridization chip can provide potential application in genomic study.     

Design, synthesis, and properties of 2',4'-BNA(NC): a bridged nucleic acid analogue

The novel bridged nucleic-acid analogue 2',4'-BNA(NC) (2'-O,4'-C-aminomethylene bridged nucleic acid), containing a six-membered bridged structure with an N-O linkage, was designed and synthesized efficiently, demonstrating a one-pot intramolecular NC bond-forming key reaction to construct a perhydro-1,2-oxazine ring (11 and 12). Three monomers of 2',4'-BNA(NC) (2',4'-BNA(NC)[NH], [NMe], and [NBn]) were synthesized and incorporated into oligonucleotides, and their properties were investigated and compared with those of 2',4'-BNA (LNA)-modified oligonucleotides. Compared to 2',4'-BNA (LNA)-modified oligonucleotides, 2',4'-BNA(NC) congeners were found to possess: (i) equal or higher binding affinity against an RNA complement with excellent single-mismatch discriminating power, (ii) much better RNA selective binding, (iii) stronger and more sequence selective triplex-forming characters, and (iv) immensely higher nuclease resistance, even higher than the S(p)-phosphorthioate analogue. 2',4'-BNA(NC)-modified oligonucleotides with these excellent profiles show great promise for applications in antisense and antigene technologies.     

Miniaturised nucleic acid analysis

The application of micro total analysis systems has grown exponentially over the past few years, particularly diversifying in disciplines related to bioassays. The primary focus of this review is to detail recent new approaches to sample preparation, nucleic acid amplification and detection within microfluidic devices or at the microscale level. We also introduce some applications that have as yet to be explored in a miniaturised environment, but should benefit from improvements in analytical efficiency and functionality when transferred to planar-chip formats. The studies described in this review were published in commonly available journals as well as in the proceedings of three major conferences relevant to microfluidics (Micro Total Analysis Systems, Transducers and The Nanotechnology Conference and Trade Show). Although an emphasis has been placed on papers published since 2002, pertinent articles preceding this publication year have also been included.