Complementary Target Sequences Research Articles

Photochemical Grafting and Patterning of Biomolecular Layers onto TiO2 Thin Films

TiO2 thin films are highly stable and can be deposited onto a wide variety of substrate materials under moderate conditions. We demonstrate that organic alkenes will graft to the surface of TiO2 when illuminated with UV light at 254 nm and that the resulting layers provide a starting point for the preparation of DNA-modified TiO2 thin films exhibiting excellent stability and biomolecular selectivity. By using alkenes with a protected amino group at the distal end, the grafted layers can be deprotected to yield molecular layers with exposed primary amino groups that can then be used to covalently link DNA oligonucleotides to the TiO2 surface. We demonstrate that the resulting DNA-modified surfaces exhibit excellent selectivity toward complementary versus noncomplementary target sequences in solution and that the surfaces can withstand 25 cycles of hybridization and denaturation in 8.3 M urea with little or no degradation. Furthermore, the use of simple masking methods provides a way to directly control the spatial location of the grafted layers, thereby providing a way to photopattern the spatial distribution of biologically active molecules to the TiO2 surfaces. Using Ti films ranging from 10 to 100 nm in thickness allows the preparation of TiO2 films that range from highly reflective to almost completely transparent; in both cases, the photochemical grafting of alkenes can be used as a starting point for stable surfaces with good biomolecular recognition properties.

Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single‐step Format: Target‐Induced Configuration Transform

AbstractA new strategy for homogeneous detection of DNA hybridization in single‐step format was developed based on fluorescence quenching by gold nanoparticles. The gold nanoparticle is functionalized with 5′‐thiolated 48‐base oligonucleotide (probe sequence), whose 3′‐terminus is labeled with fluorescein (FAM), a negatively charged fluorescence dye. The oligonucleotide adopts an extended configuration due to the electrostatic repulsion between negatively charged gold nanoparticle and the FAM‐attached probe sequence. After addition of the complementary target sequence, specific DNA hybridization induces a conformation change of the probe from an extended structure to an arch‐like configuration, which brings the fluorophore and the gold nanoparticle in close proximity. The fluorescence is efficiently quenched by gold nanoparticles. The fluorescence quenching efficiency is related to the target concentration, which allows the quantitative detection for target sequence in a sample. A linear detection range from 1.6 to 209.4 nmol/L was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol/L. In the assay system, the gold nanoparticles act as both nanoscaffolds and nanoquenchers. Furthermore, the proposed strategy, in which only two DNA sequences are involved, is not only different from the traditional molecular beacons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods. In addition, the DNA hybridization detection was achieved in homogenous solution in a single‐step format, which allows real‐time detection and quantification with other advantages such as easy operation and elimination of washing steps.

In Vivo Imaging of miR-221 Biogenesis in Papillary Thyroid Carcinoma

To investigate the overexpression of miR-221 in papillary thyroid carcinoma (PTC), we developed a Gaussia luciferase (Gluc) system regulated by miR-221. Quantities of primary or mature miR-221 in normal thyroid cells (HT-ori3) and in PTC (NPA, TPC-1) were measured by quantitative real-time polymerase chain reaction. Cytomegalovirus (CMV)/Gluc-3xPT_miR221, which included three perfect complementary target sequences repeats of miR221 in the 3'-untranslated region of Gluc, was transfected into cells with pre-miR-221 or anti-miR-221 and Gluc activities were then compared in vitro and in vivo. Primary or mature miR-221 were overexpressed in PTC as compared with HT-ori3. In cells transfected with the Gaussia luciferase reporter system (CMV/Gluc-3xPT_miR221), Gluc activities were regulated according to miR-221 levels in vitro and in vivo. These results suggest that the devised CMV/Gluc-3xPT_miR221 system may be a useful tool for monitoring quantities of endogenous miR-221 in cells or living organisms.

Dual-Stage DNA Sensing: Recognition and Detection

Selective polynucleotide recognition and detection based on a dual-stage method are described. The method involves the development of a recognition surface based on gold nanoparticles modified with a thiolated capture probe able to hybridize with its complementary sequence (target). After hybridization, this sensing surface is removed from the solution and electrodeposited on an electrode surface. The detection of the hybridization event is achieved using the complex [Ru(NH(3))(5)L](2+), were L is [3-(2-phenanthren-9-yl-vinyl)-pyridine], as electrochemical indicator. This complex binds to double strand DNA more efficiently than to single stranded DNA. The advantage of this dual-stage DNA sensing method is the high selectivity derived from the separation of the hybridization event (occurring on one surface) from the detection step (on a different surface), enabling the analysis of long target DNAs, which is usually the case in real DNA sequence analysis. In addition, this approach not only quantifies pmol of a complementary target sequence but also is sensitive to the presence of a single mismatch and its position in the sequence.

Design and development of antisense drugs

Background: With the advent of nucleic acids as therapeutic molecules, the traditional drug discovery and development process has undergone a radical change. Because nucleic acids target complementary sequences and the recognition is on the basis of Watson–Crick base pair formation, the specificity of the whole process is high. The unwanted side reactions, which are a common phenomenon observed with small molecules, are thus cut down. Objectives: The objective of this review is to look at the concept of antisense oligonucleotides as nucleic acid medicines and trace the history of drug molecules based on this concept that are at various stages of advancement. The problems encountered in the development process and the possible delivery routes are critically analyzed. Conclusion: Although specificity and selectivity are the key features of antisense oligonucleotides, the need to target the right tissues and reach the nucleus remains a challenge to overcome.

Quantitative PCR measurements of the effects of introducing inosines into primers provides guidelines for improved degenerate primer design

Polymerase chain reaction (PCR) is used to detect groups of viruses with the use of group-specific degenerate primers. Inosine residues are sometimes used in the primers to match variable positions within the complementary target sequences, but there is little data on their effects on cDNA synthesis and amplification. A quantitative reverse-transcription PCR was used to measure the rate of amplification with primers containing inosine residues substituted at different positions and in increasing numbers. Experiments were conducted using standard quantities of cloned DNA copied from Potato virus Y genomic RNA and RNA (cRNA) transcribed from the cloned DNA. Single inosine residues had no affect on the amplification rate in the forward primer, except at one position close to the 3′ terminus. Conversely, single inosine residues significantly reduced the amplification rate when placed at three out of four positions in the reverse primer. Four or five inosine substitutions could be tolerated with some decline in rates, but amplification often failed from cRNA templates with primers containing larger numbers of inosines. Greater declines in the rate of amplification were observed with RNA templates, suggesting that reverse transcription suffers more than PCR amplification when inosine is included in the reverse primer.

Electrochemical DNA Biosensor for the Detection of Interaction between Di[azino-di(5,6-azafluorene)-κ2-NN′] Dibromicoppers and DNA

A new Cu(II) complex CuL(2)Br(2) (L = azino-di(5,6-azafluorene)-kappa(2)-NN') was synthesized, and a new method of electrochemical probe has been proposed for the determination of hepatitis B virus (HBV) based on its interaction with [CuL(2)](2+). This ligand, containing functional groups, as well as planar aromatic domains, is capable of binding to double-stranded DNA (dsDNA) more efficiently than to single-stranded DNA (ssDNA). Emphasis has been placed on the elucidation of the nature of the interaction by electrochemical techniques. The electroactive [CuL(2)](2+) could be employed as an electrochemical indicator to detect hybridization events in DNA biosensors. These biosensors have been constructed by immobilization of a probe DNA sequence from HBV onto glassy carbon electrode (GCE). After hybridization with the complementary target sequence, [CuL(2)](2+) was accumulated within the dsDNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range. Using this approach, complementary target sequences of HBV can be quantified over the range of 1.74 x 10(-9) to 3.45 x 10(-7) M, with a detection limit of 8.32 x 10(-10) M and a linear correlation coefficient of 0.9936.In addition, this approach is capable of detecting hybridization of complementary sequences containing one or three mismatched bases.

Synergistic effects of nano-ZnO/multi-walled carbon nanotubes/chitosan nanocomposite membrane for the sensitive detection of sequence-specific of PAT gene and PCR amplification of NOS gene

The remarkable synergistic effects of the zinc oxide (ZnO) nanoparticles and multi-walled carbon nanotubes (MWNTs) were developed for the ssDNA probe immobilization and fabrication of the electrochemical DNA biosensor. The ZnO/MWNTs/chitosan nanocomposite membrane-modified glassy carbon electrode (ZnO/MWNTs/CHIT/GCE) was fabricated and the ssDNA probes were immobilized on the modified electrode surface. The preparation method is quite simple and inexpensive. The hybridization events were monitored by differential pulse voltammetry (DPV) using methylene blue (MB) as an indicator. As compared with previous MWNTs-based DNA biosensors, this composite matrix combined the attractive biocompatibility of ZnO nanoparticles with the excellent electron-transfer ability of MWNTs and fine membrane-forming ability of CHIT increased the DNA attachment quantity and complementary DNA detection sensitivity. The approach described here can effectively discriminate complementary DNA sequence, noncomplementary sequence, single-base mismatched sequence and double-base mismatched sequence related to phosphinothricin acetyltransferase (PAT) gene in transgenic corn. Under optimal conditions, the dynamic detection range of the sensor to PAT gene complementary target sequence was from 1.0 × 10 −11 to 1.0 × 10 −6 mol/L with the detection limit of 2.8 × 10 −12 mol/L. The polymerase chain reaction (PCR) amplification of nopaline synthase (NOS) gene from the real sample of one kind of transgenic soybeans was also satisfactorily detected with this electrochemical DNA biosensor, suggesting that the ZnO/MWNTs/CHIT nanocomposite hold great promises for sensitive electrochemical biosensor applications.

Nano-ZnO/Chitosan Composite Film Modified Electrode for Voltammetric Detection of DNA Hybridization

A sensitive electrochemical DNA biosensor based on nano-ZnO/chitosan composite matrix for DNA hybridization detection was developed. The Nano-ZnO was synthesized by the hydrothermal method and dispersed in chitosan, which was used to fabricate the modification of the glassy carbon electrode (GCE) surface. The ZnO/chitosan-modified electrode exhibited good biocompatibility and excellent electrochemical conductivity. The hybridization detection was monitored with differential pulse voltammetry (DPV) measurement using methylene blue (MB) as an indicator. The established biosensor can effectively discriminate complementary target sequence and two-base-mismatched sequence, with a detection limit of 1.09 × 10−11 mol L−1 of complementary target.

Architectures based on the use of gold nanoparticles and ruthenium complexes as a new route to improve genosensor sensitivity

The preparation of DNA-sensing architectures based on gold nanoparticles (Au-NPs) in conjunction with an “in situ” prepared ruthenium complex as a new route to improve the analytical properties of genosensors is described. In the development of these architectures several strategies to obtain Au-NPs modified gold electrodes (Au-NP/Au) have been essayed, in particular covalent binding and electrochemical deposition from a solution containing Au-NPs previously synthesized. UV–vis absorption measurements in conjunction with transmission electron microscope (TEM) images reveal that the synthesized Au-NPs are stable for at least 4 weeks and have a narrow size distribution. Atomic force microscopy (AFM) was employed to characterize the morphology and to estimate the Au-NPs surface coverage of the modified gold electrodes obtained following the different modification strategies. In order to assess the utility of these architectures as DNA-sensing devices, a thiolated capture probe sequence from Helicobacter pylori was immobilized onto the as-prepared surface. This sequence was chosen as a case of study within the framework of developing approaches of wide applicability. The hybridization event is detected using a water-soluble pentaamin ruthenium [3-(2-phenanthren-9-yl-vinyl)-pyridine] complex (Ru(NH3)5L) prepared “in situ”. This complex, due to its intercalative character, is able to bind to double stranded DNA more efficiently than to single stranded DNA. In addition, the metal provides with a redox center that can be used as an electrochemical indicator. On the basis of this strategy, complementary target sequences of H. pylori have been detected over the range of 40–800pmol with a detection limit of 25±2pmol.

Multiplexed Detection of Fungal Nucleic Acid Signatures

Diagnoses of opportunistic mycotic infections constitute an increasing clinical problem. Conventional diagnostic tests are time consuming and lack specificity and sensitivity for accurate and timely prognoses. This unit provides a comprehensive description of a fungal detection method that combines nucleic acid signatures with flow cytometry. The multiplexed assay, which uses xMAP technology, consists of unique fluorescent microspheres covalently bound to species-specific fungal oligonucleotide probes. In the presence of the complementary target sequence, the probe hybridizes to its biotinylated target. Quantification of the reaction is based on the fluorescence signal of the reporter molecule that binds to the biotin moieties of the target. The assay can be expanded to include other microorganisms and has the capability to simultaneously test 100 different fungal probes per tube/well. The speed, flexibility in design, and high-throughput capability makes this assay an attractive diagnostic tool for fungal infections and other related maladies.

Multilevel Regulation of Gene Expression by MicroRNAs

MicroRNAs (miRNAs) are approximately 22-nucleotide-long noncoding RNAs that normally function by suppressing translation and destabilizing messenger RNAs bearing complementary target sequences. Some miRNAs are expressed in a cell- or tissue-specific manner and may contribute to the establishment and/or maintenance of cellular identity. Recent studies indicate that tissue-specific miRNAs may function at multiple hierarchical levels of gene regulatory networks, from targeting hundreds of effector genes incompatible with the differentiated state to controlling the levels of global regulators of transcription and alternative pre-mRNA splicing. This multilevel regulation may allow individual miRNAs to profoundly affect the gene expression program of differentiated cells.

Nucleic acid sensor for M. tuberculosis detection based on surface plasmon resonance

Cysteine modified NH(2)-end peptide nucleic acid (PNA) (24-mer) probe and 5'-thiol end labeled deoxyribonucleic acid (DNA) probes specific to Mycobacterium tuberculosis have been immobilized onto BK-7 gold coated glass plates for the detection of complementary, one-base mismatch, non-complementary targets and complementary target sequence in genomic DNA of Mycobacterium tuberculosis using a surface plasmon resonance (SPR) technique. The DNA/Au and PNA/Au bio-electrodes have been characterized using contact angle, atomic force microscopy (AFM), electrochemical impedance spectroscopy (EIS) and cyclic voltammetric (CV) techniques, respectively. It is revealed that there is a 252 millidegrees SPR angle change in the case of PNA immobilization and 205 millidegrees for DNA immobilization, indicating increased amount of immobilized PNA molecules. Hybridization studies reveal that there is no binding of the non-complementary target to DNA/Au and PNA/Au electrode. Compared to the DNA/Au bioelectrode, PNA/Au electrode has been found to be more efficient for detection of one-base mismatch sequence. The PNA/Au bioelectrode shows better detection limit (1.0 ng ml(-1)) over the DNA-Au bioelectrode (3.0 ng ml(-1)). The values of the association (k(a)) and dissociation rate constant (k(d)) for the complementary sequence in case of the PNA/Au bioelectrode have been estimated as 8.5 x 10(4) m(-1) s(-1) and 3.6 x 10(-3) s(-1), respectively.

Lentivirus-mediated antagomir expression for specific inhibition of miRNA function

Micro RNAs (miRNA) regulate gene expression by hybridization and recruitment of multi-protein complexes to complementary mRNA target sequences. miRNA function can transiently be antagonized by antagomirs—chemically modified oligonucleotides complementary to individual miRNAs. Here, we describe the induction of stable loss-of-function phenotypes for specific miRNAs by lentivirus-mediated antagomir expression. Lentivirally expressed antagomirs are transcribed from a H1-promoter located within the lentiviral 3′LTR and were directed against miRNAs encoded on the polycistronic miR17-92 transcript. Functional silencing of miR-18a, miR-19b and miR-20a by the corresponding antagomirs specifically relieves miRNA-mediated reporter gene repression. Inhibition of miRNA function correlates to reduction of ‘miRNA’ amplification by miRNA-specific quantitative RT-PCR. Furthermore, protein expression of E2F-1, a known miR-20 target, is enhanced by lentivirally expressed anti-miR-20 antagomirs in a dose-dependent manner, whereas over-expression of miR-20a reduces E2F-1 levels. Finally, combined over-expression of specific miRNAs and antagomirs reveals individual and complementary functions of miR-18a and miR-20a and demonstrates specific miRNA impact on cell proliferation in a cell culture model.

Single-Mismatch Position-Sensitive Detection of DNA Based on a Bifunctional Ruthenium Complex

A ruthenium complex, pentaamine ruthenium [3-(2-phenanthren-9-yl-vinyl)-pyridine] (which we refer to as RuL in the text) generated in situ has been used as a sensitive and selective electrochemical indicator in DNA sensing. The complex incorporates dual functionalities with the Ru center providing a redox probe and the ligand (L) providing a fluorescent tag. The presence of the aromatic groups in the ligand endows the complex with an intercalative character and makes it capable of binding to double-stranded DNA (dsDNA) more efficiently than to single-stranded DNA (ssDNA). Combining spectroscopic and electrochemical techniques, we have elucidated the nature of the interactions. From these data we conclude that the binding mode is fundamentally intercalative. The ligand-based fluorescence allows characterization of the complex formation as well as for melting experiments to be carried out. The metal-based redox center is employed as an electrochemical indicator to detect the hybridization event in a DNA biosensor. The biosensor has been developed by immobilization of a thiolated capture probe sequence from Helicobacter pylori onto gold electrodes. With the use of this approach, complementary target sequences of Helicobacter can be quantified over the range of 106 to 708 pmol with a detection limit of 92+/-0.4 pmol and a linear correlation coefficient of 0.995. In addition, this approach allows the detection, without the need for a hybridization suppressor in solution, such as formamide, of not only a single mismatch but also its position in a specific sequence of H. pylori, due to the selective interaction of this bifunctional ruthenium complex with dsDNA.

MicroRNAs and regeneration: Let-7 members as potential regulators of dedifferentiation in lens and inner ear hair cell regeneration of the adult newt

MicroRNAs are known to regulate the expression of many mRNAs by binding to complementary target sequences at the 3′UTRs. Because of such properties, miRNAs may regulate tissue-specific mRNAs as a cell undergoes transdifferentiation during regeneration. We have tested this hypothesis during lens and hair cell regeneration in newts using microarray analysis. We found that distinct sets of miRNAs are associated with lens and hair cell regeneration. Members of the let-7 family are expressed in both events and they are regulated in a similar fashion. All the let-7 members are down regulated during the initiation of regeneration, which is characterized by dedifferentiation of terminally differentiated cells. This is the first report to correlate expression of miRNAs as novel regulators of vertebrate regeneration, alluding to a novel mechanism whereby transdifferentiation occurs.

Piezoelectric Sensor for Determination of Genetically Modified Soybean Roundup Ready (R) in Samples not Amplified by PCR

The chemically modified piezoelectrodes were utilized to develop relativelycheap and easy to use biosensor for determination of genetically modified Roundup Readysoybean (RR soybean). The biosensor relies on the immobilization onto goldpiezoelectrodes of the 21-mer single stranded oligonucleotide (probes) related to5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, which is an active componentof an insert integrated into RR soybean genome. The hybridization reaction between theprobe and the target complementary sequence in solution was monitored. The system wasoptimized using synthetic oligonucleotides, which were applied for EPSPS gene detectionin DNA samples extracted from animal feed containing 30% RR soybean amplified by thePCR and nonamplified by PCR. The detection limit for genomic DNA was in the range of4.7·105 numbers of genom copies contained EPSPS gene in the QCM cell. The propertiessuch as sensitivity and selectivity of piezoelectric senor presented here indicated that it could be applied for the direct determination of genetically modified RR soybean in the samples non-amplified by PCR.

Triplex Molecular Beacons as Modular Probes for DNA Detection

Detecting nucleic acid sequences is of central importance in modern life sciences. Given the rapid growth of the available sequence data, the diagnosis of DNA and RNA is likely to increase in significance over the next decade. The most useful methods employ probes that allow quantitative measurements in homogeneous solution, thereby omitting the need to separate bound from unbound probes. Molecular beacons (MBs) have become a class of widely used probes for nucleic acid analysis. These probes carry a fluorophore and a quencher at their termini. In the absence of a complementary target sequence, MBs form a stem–loop structure (Figure 1A), which results in quenching of the fluorescence.

Immobilization of single stranded DNA probe onto polypyrrole-polyvinyl sulfonate for application to DNA hybridization biosensor

Electrochemical DNA biosensor based on polypyrrole-polyvinyl sulfonate (PPy-PVS) coated onto Pt disc electrode (∼0.03 cm 2) has been fabricated by immobilizing 25 bases long single stranded probe polydeoxycytidine (dC) using both biotin–avidin binding (indirect immobilization) and carbodiimide coupling (direct immobilization), to detect 25 bases long complementary target sequence polydeoxyguanosine (dG). These DNA immobilized electrodes have been characterized using differential pulse voltammetry (DPV), Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM) techniques, respectively. Compared to the indirect method of immobilization, direct immobilization of dC probe results in enhanced detection limit by 2200 times (upto 0.01 fmol) and improved sensitivity by about six times. These DNA electrodes have response time of 30 s and are stable for about 4 months when stored at 4 °C.

Dual-labeled oligonucleotide probe for sensing adenosine via FRET: A novel alternative to SNPs genotyping

A novel FRET based strategy for DNA sequence analysis utilising base-discriminating fluorescence (BDF) nucleoside, (Py)U/(2-Ant)U, as donor in the dual-labelled oligonucleotide probe is reported; a selective/specific emission from acceptor, was observed upon excitation at the donor, only when the opposite base of the "smart" fluorescently labeled BDF nucleoside, (Py)U/(2-Ant)U, is adenine on the complementary target sequence.