In vitro evolution of functional DNA using capillary electrophoresis

Electrophoretic selection with capillary electrophoresis (CE) is used, for the first time, to isolate functional nucleic acid sequences using SELEX (systematic evolution of ligands by exponential enrichment). SELEX uses molecular evolution to select functional sequences (aptamers) from random RNA or DNA libraries. Conventional SELEX is usually performed with affinity chromatography, which may introduce significant bias into the selection step. Important biases include the slow kinetics involved in the elution of strongly bound sequences and performing the selection with the target molecule tethered to the stationary support, not in free solution. In this novel CE-SELEX approach, selection occurs in free solution. The nucleic acid sequences that bind the target undergo a mobility shift, migrating at a different rate, allowing them to be separated from the inactive sequences. Thus, there is no need to wash the active sequences off a column as in conventional SELEX, eliminating any kinetic bias. In this work, the viability of CE-SELEX was demonstrated by performing selections against immunoglobulin E (IgE). Anti-IgE aptamers with dissociation constants as low as 40 nM were obtained in only two rounds of selection.     

Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets

Molecular beacons are sensitive fluorescent probes hybridizing selectively to designated DNA and RNA targets. They have recently become practical tools for quantitative real-time monitoring of single-stranded nucleic acids. Here, we comparatively study the performance of a variety of such probes, stemless and stem-containing DNA and PNA (peptide nucleic acid) beacons, in Tris-buffer solutions containing various concentrations of NaCl and MgCl(2). We demonstrate that different molecular beacons respond differently to the change of salt concentration, which could be attributed to the differences in their backbones and constructions. We have found that the stemless PNA beacon hybridizes rapidly to the complementary oligodeoxynucleotide and is less sensitive than the DNA beacons to the change of salt thus allowing effective detection of nucleic acid targets under various conditions. Though we found stemless DNA beacons improper for diagnostic purposes due to high background fluorescence, we believe that use of these DNA and similar RNA constructs in molecular-biophysical studies may be helpful for analysis of conformational flexibility of single-stranded nucleic acids. With the aid of PNA "openers", molecular beacons were employed for the detection of a chosen target sequence directly in double-stranded DNA (dsDNA). Conditions are found where the stemless PNA beacon strongly discriminates the complementary versus mismatched dsDNA targets. Together with the insensitivity of PNA beacons to the presence of salt and DNA-binding/processing proteins, the latter results demonstrate the potential of these probes as robust tools for recognition of specific sequences within dsDNA without denaturation and deproteinization of duplex DNA.     

Ion‐Tagged Oligonucleotides Coupled with a Magnetic Liquid Support for the Sequence‐Specific Capture of DNA

The isolation of specific nucleic acid sequences is a major bottleneck in molecular diagnostics. Magnetic beads/particles are typically used as solid supports for the capture of DNA targets to improve sample throughput but aggregate over time resulting in lower capture efficiency and obstruction of liquid handling devices. Herein, we describe a particle‐free approach to sequence‐specific DNA extraction using a magnetic liquid support and ion‐tagged oligonucleotide (ITO) probes. ITO conjugates were synthesized with the highest yields ever achieved for the radical thiol‐ene coupling of a substrate and oligonucleotide. In addition to distinguishing nucleotide mismatches, the ITO and magnetic liquid‐based approach was more sensitive than a commercial magnetic bead‐based method for the capture of target DNA from a pool of interfering genomic DNA.     

Signal amplification by rolling circle amplification on universal flaps yielded from target-specific invasive reaction

Detection of nucleic acids with signal amplification is preferable in clinical diagnosis. A novel approach was developed for signal amplification by coupling invasive reaction with hyperbranched rolling circle amplification (HRCA). Invasive reaction, which does not rely on specific recognition sequences in a target but a specific structure formed by the specific binding of an upstream probe and a downstream probe to a target DNA, can generate thousands of flaps from one target DNA; then the flaps are ligated with padlock probes to form circles, which are the templates of HRCA. As HRCA amplicon sequence is free of target DNA sequence, signal amplification is achieved. Because flap sequence is the same to any target of interest, HRCA is universal; the detection cost is hence greatly reduced. The sensitivity of the proposed method is less than 1 fM artificial DNA targets; and the specificity of the method is high enough to discriminate one base difference in the target sequence. The feasibility was verified by detecting real biological samples from HBV carriers, indicating that the method is highly sensitive, cost-effective, and has a low risk of cross-contamination from amplicons. These properties should give great potential in clinical diagnosis.     

Use of 6‐Methylisoxanthopterin,a Fluorescent Guanine Analog,to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences

Fluorescent nucleic acid base mimics serve as excellent site‐specific and real‐time reporters of the local and global dynamics. In this work, using the fluorescent guanine mimic 6‐methylisoxanthopterin (6‐MI), we unravel the differential dynamics of replication fork barrier/terminator sequences (RFB1 and RFB3) mediated by fork blocking protein (Fob1). By strategic and site‐specific incorporation of this probe, we show that 6‐MI is able to capture the changes in global dynamics exhibited by Fob1 and aids in distinguishing between varied architectural forms like double‐stranded DNA versus Holliday junctions (HJs). This is important as these barriers are hotspots for recombination. Fluorescence lifetime and anisotropy decay studies further revealed that Fob1 strongly dampens the dynamics in double‐stranded RFB1, and the sequence inherently possesses lesser flexibility in comparison to RFB3. We show that 6‐MI can probe the differential oligomeric status of Fob1 in response to various architectures, that is, double‐stranded versus HJs. This work highlights the unique advantages of 6‐MI as a probe when incorporated in nucleic acid frameworks.     

A generic sandwich-type biosensor with nanomolar detection limits

A quantitative and highly sensitive, yet simple and rapid, biosensor system was developed for the detection of nucleic acid sequences that can also be adapted to the detection of antigens. A dipstick-type biosensor with liposome amplification, based on a sandwich assay format with optical detection, was combined with a simple coupling reaction that allows the transformation of the generic biosensor components to target specific ones by a mere incubation step. This biosensor platform system was developed and optimized, and its principle was proven using DNA oligonucleotides that provided a nucleic acid biosensor for the specific detection of RNA and DNA sequences. However, the coupling reaction principle chosen can also be used for the immobilization of antibodies or receptor molecules, and therefore for the development of immunosensors and receptor-based biosensors. The generic biosensor consists of liposomes entrapping sulforhodamine B that are coated with streptavidin on the outside, and polyethersulfone membranes with anti-fluorescein antibodies immobilized in the detection zone. In order to transform the generic biosensor into a specific DNA/RNA biosensor, two oligonucleotides that are able to hybridize to the target sequence were labeled with a biotin and a fluorescein molecule, respectively. By simultaneously incubating the liposomes, both oligonucleotides, and the target sequence in a hybridization buffer for 20–30 min at 42 ^°C, a sandwich complex was formed. The mixture was applied to the polyethersulfone membrane. The complex was captured in the detection zone and quantified using a handheld reflectometer. The system was tested using RNA sequences from B. anthracis, C. parvum and E. coli. Quantitation of concentrations between 10 fmol and 1000 fmol (10–1000 nM) was possible without altering any biosensor assay conditions. In addition, no changes to hybridization conditions were required when using authentic nucleic acid sequence-based amplified RNA sequences, and the generic biosensor compared favorably with those previously developed specifically for the RNA sequences. Therefore, the universal biosensor described is an excellent tool, for use in laboratories or at test sites, for rapidly investigating and quantifying any nucleic acid sequence of interest, as well as potentially any antigen of interest that can be bound by two antibodies simultaneously.     

Sensing Picomolar Concentrations of RNA Using Switchable Plasmonic Chirality

Detecting small sequences of RNA in biological samples such as microRNA or viral RNA demands highly sensitive and specific methods. Here, a reconfigurable DNA origami template has been used where a chiral arrangement of gold nanorods on the structure can lead to the generation of strong circular dichroism (CD). Switching of the cross‐like DNA structure is achieved by the addition of nucleic acid sequences, which arrests the structure in one of the possible chiral states by specific molecular recognition. A specific sequence can thus be detected through the resulting changes in the plasmonic CD spectrum. We show the sensitive and selective detection of a target RNA sequence from the hepatitis C virus genome. The RNA binds to a complementary sequence that is part of the lock mechanism, which leads to the formation of a defined state of the plasmonic system with a distinct optical response. With this approach, we were able to detect this specific RNA sequence at concentrations as low as 100 pm .     

Sequence‐Specific DNA Alkylation by Tandem Py–Im Polyamide Conjugates

Tandem N‐methylpyrrole? N‐methylimidazole (Py? Im) polyamides with good sequence‐specific DNA‐alkylating activities have been designed and synthesized. Three alkylating tandem Py? Im polyamides with different linkers, which each contained the same moiety for the recognition of a 10 bp DNA sequence, were evaluated for their reactivity and selectivity by DNA alkylation, using high‐resolution denaturing gel electrophoresis. All three conjugates displayed high reactivities for the target sequence. In particular, polyamide 1 , which contained a β‐alanine linker, displayed the most‐selective sequence‐specific alkylation towards the target 10 bp DNA sequence. The tandem Py? Im polyamide conjugates displayed greater sequence‐specific DNA alkylation than conventional hairpin Py? Im polyamide conjugates ( 4 and 5 ). For further research, the design of tandem Py? Im polyamide conjugates could play an important role in targeting specific gene sequences.     

Polyvalent Spherical Nucleic Acids for Universal Display of Functional DNA with Ultrahigh Stability

For nanomaterials that are difficult to functionalize by covalent attachment of DNA, we herein communicate a general method taking advantage of the high avidity of polyvalent binding and the 3D structure of densely functionalized spherical nucleic acids (SNAs). Using DNA‐functionalized gold nanoparticles, simple mixing leads to the formation of highly stable conjugates on 11 different materials including metals, metal oxides, metal–organic frameworks, transition‐metal dichalcogenides, nanocarbons, and polymers. The adsorption affinity of SNAs can be over thousand‐fold higher than that of free DNA of the same sequence, and practically irreversible conjugates are formed withstanding various denaturing agents. The surface attachment and molecular recognition functions of DNA are spatially separated, showing a key advantage of SNAs. The functionalized materials possess the properties of both the substrate and the SNA, allowing specific DNA hybridization in buffer and in serum.     

Label-free selective DNA detection with high mismatch recognition by PNA beacons and ion exchange HPLC

Two 11mer peptide nucleic acid (PNA) beacons were synthesized and tested for the detection of full-matched or single mismatched DNA. Fluorescent measurements carried out in solution showed only partial discrimination of the mismatched sequence, while using anion-exchange HPLC, in combination with fluorimetric detection, allowed DNA analysis to be performed with high sensitivity and extremely high sequence selectivity. Up to >90 : 1 signal discrimination in the presence of one single mismatched base was observed. The analysis was tested on both short and long DNA oligomers. Detection of DNA obtained from PCR amplification was also performed allowing the selective detection of the target sequence in complex mixtures. Label free detection of the DNA with high sequence selectivity is therefore possible using the present approach.     

A Cell‐Penetrating Foldamer with a Bioreducible Linkage for Intracellular Delivery of DNA

Despite significant advances in foldamer chemistry, tailored delivery systems based on foldamer architectures, which provide a high level of control over secondary structure, are curiously rare among non‐viral technologies for transporting nucleic acids into cells. A potent pH‐responsive, bioreducible cell‐penetrating foldamer (CPF) was developed through covalent dimerization of a short (8‐mer) amphipathic oligourea sequence bearing histidine‐type units. This CPF exhibits a high capacity to assemble with pDNA and mediates efficient delivery of nucleic acids into the cell. Furthermore, it does not adversely affect cellular viability and was shown to compare favorably with a cognate peptide transfection agent based on His‐rich sequences.     

5‐(Pyren‐1‐yl)uracil as a Base‐Discriminating Fluorescent Nucleobase in Pyrrolidinyl Peptide Nucleic Acids

A pyrene‐labeled uridine (U^Py) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2‐aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U^Py base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T_m) experiments. The fluorescence of the U^Py‐containing single‐stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7–41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U^Py and dA, making the U^Py‐modified acpcPNA useful as a hybridization‐responsive fluorescence probe for DNA‐sequence determination.     

新型超支状液晶核酸传感器用于p53突变基因的检测

基于核酸杂交链式反应影响液晶取向的原理, 构建了一种新型的超支状液晶核酸传感器用于检测p53突变基因. 本文突破传统构建超支状分子的方式, 采用杂交链式反应方法, 以目标序列p53突变基因作为引发剂, 3种不同的发卡探针Hairpin A, Hairpin B和Hairpin C为单体, 在温和的条件下, 通过改变单体的浓度和反应时间自发杂交组装形成尺寸和分子量可控的超支状DNA(branched-like DNA, bDNA). 借助捕获探针将该超支状DNA连接到液晶传感基底表面, 观察液晶分子取向改变前后的光学信号, 实现了p53基因含249密码子突变序列的快速检测. 本方法有望为核酸诊断的发展提供一种新的方法和思路.     

Discovering protein-binding RNA motifs with a generative model of RNA sequences

Recent advances in high-throughput experimental technologies have generated a huge amount of data on interactions between proteins and nucleic acids. Motivated by the big experimental data, several computational methods have been developed either to predict binding sites in a sequence or to determine if an interaction exists between protein and nucleic acid sequences. However, most of the methods cannot be used to discover new nucleic acid sequences that bind to a target protein because they are classifiers rather than generators. In this paper we propose a generative model for constructing protein-binding RNA sequences and motifs using a long short-term memory (LSTM) neural network. Testing the model for several target proteins showed that RNA sequences generated by the model have high binding affinity and specificity for their target proteins and that the protein-binding motifs derived from the generated RNA sequences are comparable to the motifs from experimentally validated protein-binding RNA sequences. The results are promising and we believe this approach will help design more efficient in vitro or in vivo experiments by suggesting potential RNA aptamers for a target protein.     

Next‐Generation Sequencing as Input for Chemometrics in Differential Sensing Routines

Differential sensing (DS) methods traditionally use spatially arrayed receptors and optical signals to create score plots from multivariate data which classify individual analytes or complex mixtures. Herein, a new approach is described, in which nucleic acid sequences and sequence counts are used as the multivariate data without the necessity of a spatial array. To demonstrate this approach to DS, previously selected aptamers, identified from the literature, were used as semi‐specific receptors, Next‐Gen DNA sequencing was used to generate data, and cell line differentiation was the test‐bed application. The study of a principal component analysis loading plot revealed cross‐reactivity between the aptamers. The technique generates high‐dimensionality score plots, and should be applicable to any mixture of complex and subtly different analytes for which nucleic acid‐based receptors exist.     

Sequence Specific Electrochemical DNA Detection Based on Solution‐Phase Competitive Hybridization

We report a novel electrochemical method for detecting sequence‐specific DNA based on competitive hybridization that occurs in a homogeneous solution phase instead of on a solution‐electrode interface as in previously reported competition‐based electrochemical DNA detection schemes. The method utilizes the competition between the target DNA (t‐DNA) and a ferrocene‐labeled peptide nucleic acid probe (Fc‐PNA) to hybridize with a probe DNA (p‐DNA) in solution. The neutral PNA backbone and the electrostatic repulsion between the negatively‐charged DNA backbone and the negatively‐charged electrode surface are then exploited to determine the result of the competition through measurement of the electrochemical signal of Fc. Upon the introduction of the t‐DNA, the stronger hybridization affinity between the t‐DNA and p‐DNA releases the Fc‐PNA from the Fc‐PNA/p‐DNA hybrid, allowing it to freely diffuse to the negatively charged electrode to produce a significantly enhanced electrochemical signal of Fc. Therefore, the presence of the t‐DNA is indicated by the appearance or enhancement of the electrochemical signal, rendering a signal‐on DNA detection, which is less susceptible to false positive and can produce more reliable results than signal‐off detection methods. All the competitive hybridizations occur in a homogeneous solution phase, resulting in very high hybridization efficiency and therefore extremely short assay time. This simple and fast signal‐on solution‐competition‐based electrochemical DNA detection strategy has promising potential to find application in fields such as nucleic acid‐based point‐of‐care testing.     

Toward a solid-phase nucleic acid hybridization assay within microfluidic channels using immobilized quantum dots as donors in fluorescence resonance energy transfer

The optical properties and surface area of quantum dots (QDs) have made them an attractive platform for the development of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Solid-phase assays based on FRET using mixtures of immobilized QD–oligonucleotide conjugates (QD biosensors) have been developed. The typical challenges associated with solid-phase detection strategies include non-specific adsorption, slow kinetics of hybridization, and sample manipulation. The new work herein has considered the immobilization of QD biosensors onto the surfaces of microfluidic channels in order to address these challenges. Microfluidic flow can be used to dynamically control stringency by adjustment of the potential in an electrokinetic-based microfluidics environment. The shearing force, Joule heating, and the competition between electroosmotic and electrophoretic mobilities allow the optimization of hybridization conditions, convective delivery of target to the channel surface to speed hybridization, amelioration of adsorption, and regeneration of the sensing surface. Microfluidic flow can also be used to deliver (for immobilization) and remove QD biosensors. QDs that were conjugated with two different oligonucleotide sequences were used to demonstrate feasibility. One oligonucleotide sequence on the QD was available as a linker for immobilization via hybridization with complementary oligonucleotides located on a glass surface within a microfluidic channel. A second oligonucleotide sequence on the QD served as a probe to transduce hybridization with target nucleic acid in a sample solution. A Cy3 label on the target was excited by FRET using green-emitting CdSe/ZnS QD donors and provided an analytical signal to explore this detection strategy. The immobilized QDs could be removed under denaturing conditions by disrupting the duplex that was used as the surface linker and thus allowed a new layer of QD biosensors to be re-coated within the channel for re-use of the microfluidic chip.     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Senosr

A piezoelectric nucleic acid sensor was constructed ofr detection of tumor necrosis factor gene.Two methods were employed for immobilization of nucleic acid probe on gold electrode of piezoelectric crystal.The results show that polyethyleneimine adbesion and glutaraldehyde cross-linking method has higher sensitivity,stability and selectivity than protein A method.The solid-phase nucleic acid hybridization of oligo unclecotides and tumor necrosis factor target gene sequence were monitorde using this sensor.Tumor necrosis factor gene sequence(580bp) was detected by this nucleic acid sensor for the first time.     

Label‐Free Bioelectronic Detection of Point Mutation by Using Peptide Nucleic Acid Probes

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probes with a label‐free protocol is described. The detection of PNA‐DNA and DNA‐DNA hybridizations were accomplished based on the oxidation signal of guanine by using differential pulse voltammetry (DPV) at carbon paste electrode (CPE). It was observed that the oxidation signals of guanine obtained from the PNA and DNA probe modified CPEs were higher than those obtained from the PNA‐DNA and DNA‐DNA hybrid modified CPEs due to the accessible unbound guanine bases. The detection of hybridization between PNA probe and point mutation containing DNA target sequences was clearly observed due to the difference of the oxidation signals of guanine bases, because the point mutation was guanine nearly at the middle of the sequence. The effect of the DNA target concentration on the hybridization signal was also observed. The PNA probe was also challenged with excessive and equal amount of noncomplementary DNA and also mixtures of point mutation and target DNA.     

Sequence‐Dependent dsDNA‐Templated Formation of Fluorescent Copper Nanoparticles

There are only a few systematic rules about how to selectively control the formation of DNA‐templated metal nanoparticles (NPs) by varying sequence combinations of double‐stranded DNA (dsDNA), although many attempts have been made. Herein, we develop a facile method for sequence‐dependent formation of fluorescent CuNPs by using dsDNA as templates. Compared with random sequences, AT sequences are better templates for highly fluorescent CuNPs. Other specific sequences, for example, GC sequences, do not induce the formation of CuNPs. These results shed light on directed DNA metallization in a sequence‐specific manner. Significantly, both the fluorescence intensity and the fluorescence lifetime of CuNPs can be tuned by the length or the sequence of dsDNA. In order to demonstrate the promising practicality of our findings, a sensitive and label‐free fluorescence nuclease assay is proposed.