Templated Chemistry for Sequence‐Specific Fluorogenic Detection of Duplex DNA

We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple‐helix formation at adjacent positions on a specific purine‐rich target sequence of duplex DNA. One fluorescein‐labeled probe contains an α‐azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine group that is designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of about 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably; this demonstrated high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and could allow detection of double‐stranded DNA, at least for homopurine–homopyrimidine target sites, under native and nondenaturing conditions.     

Single Labeled DNA FIT Probes for Avoiding False‐Positive Signaling in the Detection of DNA/RNA in qPCR or Cell Media

Oligonucleotide hybridization probes that fluoresce upon binding to complementary nucleic acid targets allow the real‐time detection of DNA or RNA in homogeneous solution. The most commonly used probes rely on the distance‐dependent interaction between a fluorophore and another label. Such duallabeled oligonucleotides signal the change of the global conformation that accompanies duplex formation. However, undesired nonspecific binding events and/or probe degradation also lead to changes in the label–label distance and, thus, to ambiguities in fluorescence signaling. Herein, we introduce singly labeled DNA probes, “DNA FIT probes”, that are designed to avoid false‐positive signals. A thiazole orange (TO) intercalator dye serves as an artificial base in the DNA probe. The probes show little background because the attachment mode hinders 1) interactions of the “TO base” in cis with the disordered nucleobases of the single strand, and 2) intercalation of the “TO nucleotide” with double strands in trans. However, formation of the probe–target duplex enforces stacking and increases the fluorescence of the TO base. We explored open‐chain and carbocyclic nucleotides. We show that the incorporation of the TO nucleotides has no effect on the thermal stability of the probe–target complexes. DNA and RNA targets provided up to 12‐fold enhancements of the TO emission upon hybridization of DNA FIT probes. Experiments in cell media demonstrated that false‐positive signaling was prevented when DNA FIT probes were used. Of note, DNA FIT probes tolerate a wide range of hybridization temperature; this enabled their application in quantitative polymerase chain reactions.     

Split Spinach Aptamer for Highly Selective Recognition of DNA and RNA at Ambient Temperatures

Split spinach aptamer (SSA) probes for fluorescent analysis of nucleic acids were designed and tested. In SSA design, two RNA or RNA/DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for low‐fluorescent 3,5‐difluoro‐4‐hydroxybenzylidene imidazolinone (DFHBI) dye, which resulted in up to a 270‐fold increase in fluorescence. The major advantage of the SSA over state‐of‐the art fluorescent probes is high selectivity: it produces only background fluorescence in the presence of a single‐base‐mismatched analyte, even at room temperature. SSA is therefore a promising tool for label‐free analysis of nucleic acids at ambient temperatures.     

A Single‐Electrode,Dual‐Potential Ferrocene–PNA Biosensor for the Detection of DNA

A Fc–PNA biosensor (Fc: ferrocenyl, C₁₀H₉Fe) was designed by using two electrochemically distinguishable recognition elements with different molecular information at a single electrode. Two Fc–PNA capture probes were therefore synthesized by N‐terminal labeling different dodecamer PNA sequences with different ferrocene derivatives by click chemistry. Each of the two strands was thereby tethered with one specific ferrocene derivative. The two capture probes revealed quasi‐reversible redox processes of the Fc^0/+ redox couple with a significant difference in their electrochemical half‐wave potentials of ΔE_1/2=160 mV. A carefully designed biosensor interface, consisting of a ternary self‐assembled monolayer (SAM) of the two C‐terminal cysteine‐tethered Fc–PNA capture probes and 6‐mercaptohexanol, was electrochemically investigated by square wave (SWV) and cyclic voltammetry (CV). The biosensor properties of this interface were analyzed by studying the interaction with DNA sequences that were complementary to either of the two capture probes by SWV. Based on distinct changes in both peak current and potential, a parallel identification of these two DNA sequences was successful with one interface design. Moreover, the primary electrochemical response could be converted by a simple mathematical analysis into a clear‐cut electrochemical signal about the hybridization event. The discrimination of single‐nucleotide polymorphism (SNP) was proven with a chosen single‐mismatch DNA sequence. Furthermore, experiments with crude bacterial RNA confirm the principal suitability of this dual‐potential sensor under real‐life conditions.     

Highly Efficient Fluorescent Interstrand Photo‐crosslinking of DNA Duplexes Labeled with 5‐Fluoro‐4‐thio‐2′‐O‐methyluridine

The formation of a fluorescent photoadduct between 5‐fluoro‐4‐thiouridine ( ^FS U ), in the sequence context 5′‐A ^FS U A‐3′ and incorporated into a synthetic oligonucleotide either at its 3′‐ or 5′‐end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo‐crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo‐crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo‐crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.     

A Differential Fluorescent Receptor for Nucleic Acid Analysis

Differential receptors use an array of sensors to recognize analytes. Each sensor in the array can recognize not one, but several analytes with different rates, so a single analyte triggers a response of several sensors in the array. The receptor thus produces a pattern of signals that is unique for each analyte, thereby enabling identification of a specific analyte by producing a “fingerprint” pattern. We applied this approach for the analysis of DNA sequences of Mycobacterium tuberculosis strains that differ by single nucleotide substitutions in the 81‐bp hot‐spot region that imparts rifampin resistance. The technology takes advantage of the new multicomponent, selfassembling sensor, which produces a fluorescent signal in the presence of specific DNA sequences. A differential fluorescent receptor (DFR) contained an array of three such sensors and differentiated at least eight DNA sequences. The approach requires only one molecular‐beacon‐like fluorescent reporter, which can be used by all three sensors. The DFR developed in this study represents a cost‐efficient alternative to molecular diagnostic technologies that use fluorescent hybridization probes.     

Enhancement of target-DNA hybridization efficiency by pre-hybridization on sequence-orientated micro-arrayed probes

The enhancement of hybridization efficiency of deoxyribonucleic acid (DNA) targets using oligonucleotide pre-hybridization is studied on two sequence-inversed micro-arrayed probes. The sequences for pre-hybridizing both oligo and target DNA are designed to be fully complementary with their shared DNA probe in a coaxial stacking configuration; i.e. they hybridize immediately alongside each other along the continuous complement probe strand. The pre-hybridizing oligo and target DNA are differentiated by being labeled with two distinct fluorescent dyes, and the cooperative effect on hybridization efficiency is investigated through the comparison of the stacking and individual hybridization configurations based on the detection signals of the labeling dyes. The results show that the pre-hybridization of a DNA oligo enhances the subsequent hybridization efficiency of the target-DNA coupling onto the same probe. The efficiency is enhanced if the hybridization position occurs at a site close to the substrate surface.     

纳米粒子三明治型传感器的组装及其在BRCA-1检测中的应用

采用纳米磁、DNA、纳米金组装三明治型生物传感器。其中,纳米磁粒子(PMPS)用于捕获并分离目标DNA,而被基因探针序列修饰过的纳米金(Au-NPs)则扮演识别序列及产生信号的角色,从而使目标DNA序列量转化为光信号,继而通过紫外分光光度计进行定量分析。这种基于纳米金修饰的DNA探针的新型基因诊断技术,可以用来定量检测分析目标DNA。结果显示,这是一种非常简单经济且实用的检测单个突变基因序列的新方法。     

以亚甲基蓝为杂交指示剂的DNA电化学传感器

构建了一个以亚甲基蓝(MB)为杂交指示剂的电化学DNA传感体系:通过自组装的方式将巯基改性的单链DNA5′端(HS-ssDNA)连接到金电极表面形成Au-ssDNA,当检测体系中加入和Au-ssDNA互补的目标单链DNA(cssDNA)时,会形成一个双链DNA系统(Au-dsDNA),加入MB并通过循环伏安法检测了杂交过程中的信号变化,验证了Au-ssDNA及Au-dsDNA的形成。在4.0×10-6～1.0×10-5mol/L内,检测灵敏度随MB浓度的增加而升高,当浓度达到2.0×10-5mol/L时接近最大值。示差脉冲伏安法检测结果表明,该检测体系对目标DNA的选择性识别能力高,可区分具有单碱基错配的目标DNA序列。检测体系对目标DNA的检测灵敏度随着目标DNA浓度的增加而增加,在5.0×10-10～1.8×10-9mol/L内呈线性关系,计算所得对目标DNA的检测限为5.0×10-10mol/L。使用寿命检测表明,经过5次变性/杂交循环后,检测信号降低并接近于检测限。     

A “four-ferrocene” modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA

We report the use of a four-ferrocene modified oligonucleotide as a probe for DNA detection with a gold electrode microsystem. This oligonucleotide is synthesized by automated solid-phase synthesis with four successive ferrocene moieties at the 5′-end and a C6-thiol modifier group at the 3′-end. The grafting of this 4Fc-DNA probe on a gold electrode microsystem results in the appearance of the ferrocene redox couple in cyclic voltammetry. The probe sequence is a stem-loop structure that folds efficiently on the electrode, thus optimizing electron transfer. Such architecture serves as sensor for DNA detection which is based on hybridization. The resulting disposable voltammetric sensor allowed direct, reagentless DNA detection in a small volume (20 μL). Electrochemical response upon hybridization with complementary short sequence (30-base length) and long sequence (50-base length) strands was observed by differential pulse voltammetry. Current variations were compared. The longer the sequence, the greater the decrease in current. The system's detection limit was estimated at 3.5 pM (0.07 fmol in 20 μL) with the 50-base length target and provided a dynamic detection range between 3.5 pM and 5 nM. Single mismatch detection showed a good level of sensitivity. The system was regenerated twice with no significant loss of Fc signal. Finally, 1 pM sensitivity was reached with a long chain analog of DNA PCR products of Influenza virus.     

Ultrasensitive Molecular Beacon Designed with Totally Serinol Nucleic Acid (SNA) for Monitoring mRNA in Cells

An artificial nucleic acid based on acyclic serinol building blocks and termed “serinol nucleic acid” (SNA) was used to construct a fluorescent probe for RNA visualization in cells. The molecular beacon (MB) composed of only SNA with a fluorophore at one terminus and a quencher at the other was resistant to enzymatic digestion, due to its unnatural acyclic scaffold. The SNA‐MB could detect its complementary RNA with extremely high sensitivity; the signal‐to‐background (S/B) ratio was as high as 930 when perylene and anthraquinone were used as the fluorophore and quencher pair. A high S/B ratio was also achieved with SNA‐MB tethering the conventional Cy3 fluorophore, and this probe enabled selective visualization of target mRNA in fixed cells. Thus, SNA‐MB has potential for use as a biological tool capable of visualizing RNA in living cells.     

Bifunctional DNA Duplexes Permit Efficient Incorporation of pH Probes into Liposomes

Enzyme-mediated proton transport across biological membranes is critical for many vital cellular processes. pH-sensitive fluorescent dyes are an indispensable tool for investigating the molecular mechanism of proton-translocating enzymes. Here, we present a novel strategy to entrap pH-sensitive probes in the lumen of liposomes that has several advantages over the use of soluble or lipid-coupled probes. In our approach, the pH sensor is linked to a DNA oligomer with a sequence complementary to a second oligomer modified with a lipophilic moiety that anchors the DNA conjugate to the inner and outer leaflets of the lipid bilayer. The use of DNA as a scaffold allows subsequent selective enzymatic removal of the probe in the outer bilayer leaflet. The method shows a high yield of insertion and is compatible with reconstitution of membrane proteins by different methods. The usefulness of the conjugate for time-resolved proton pumping measurements was demonstrated by using two large membrane protein complexes.     

A Disassembly Strategy for Imaging Endogenous Pyrophosphate in Mitochondria by Using an FeIII–salen Complex

Inorganic pyrophosphate (PPi) is produced from nucleoside triphosphates in important biosynthetic reactions and is considered a diagnostic marker for various diseases, such as cancer, crystal deposition disease, and arthritis. Traditional methods for biological PPi detection rely on off‐line analytics after sample destruction. Molecular probes for imaging this biologically important analyte with temporal and spatial control in living cells are currently in demand. Herein, we report an Fe^III–salen complex as the first small reaction‐based probe for endogenous mitochondrial PPi following a disassembly approach. Significantly, we successfully applied this complex for the detection of increased cellular PPi levels, and its performance was not affected by the presence of mitochondrial ATP in living cells.     

Peptide Nucleic Acid Conjugated with Ruthenium‐Complex Stabilizing Double‐Duplex Invasion Complex Even under Physiological Conditions

Peptide nucleic acid (PNA) can form a stable duplex with DNA, and, accordingly, directly recognize double‐stranded DNA through the formation of a double‐duplex invasion complex, wherein a pair of complementary PNA strands form two PNA/DNA duplexes. Because invasion does not require prior denaturation of DNA, PNA holds great potential for in cellulo or in vivo applications. To broaden the applicability of PNA invasion, we developed a new conjugate of PNA with a ruthenium complex. This Ru–PNA conjugate exhibits higher DNA‐binding affinity, which results in enhanced invasion efficiency, even under physiological conditions.     

A highly selective electrochemical biosensor for Hg using hemin as a redox indicator

A highly selective electrochemical biosensor for the detection of Hg²⁺ in aqueous solution has been developed. This sensor is based on the strong and specific binding of Hg²⁺ by two DNA thymine bases (T–Hg²⁺–T). The hemin worked as a redox indicator to generate a readable electrochemical signal. Short oligonucleotide strands containing 5 thymine (T₅) were used as probe. Thiolated T₅ strands were self-assembled through Au–S bonding on gold electrode. In the presence of Hg²⁺, the specific coordination between Hg²⁺ and thymine bases resulted in more stable and porous arrangement of oligonucleotide strands, so hemin could be adsorbed on the surface of gold electrode and produced an electrochemical signal, which was monitored by differential pulse voltammetry (DPV). The DPV showed a linear correlation between the signal and the concentration of Hg²⁺ over the range 0–2 μM (R² = 0.9983) with a detection limit of 50 nM. The length of probe DNA had no significant impact on the sensor performance. This electrochemical biosensor could be widely used for selective detection of Hg²⁺.     

Peptide Synthesis on a Next‐Generation DNA Sequencing Platform

Methods for displaying large numbers of peptides on solid surfaces are essential for high‐throughput characterization of peptide function and binding properties. Here we describe a method for converting the >10⁷ flow cell‐bound clusters of identical DNA strands generated by the Illumina DNA sequencing technology into clusters of complementary RNA, and subsequently peptide clusters. We modified the flow‐cell‐bound primers with ribonucleotides thus enabling them to be used by poliovirus polymerase 3D^pol. The primers hybridize to the clustered DNA thus leading to RNA clusters. The RNAs fold into functional protein‐ or small molecule‐binding aptamers. We used the mRNA‐display approach to synthesize flow‐cell‐tethered peptides from these RNA clusters. The peptides showed selective binding to cognate antibodies. The methods described here provide an approach for using DNA clusters to template peptide synthesis on an Illumina flow cell, thus providing new opportunities for massively parallel peptide‐based assays.