Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics

DNA and Nanomaterials: A Functional Combination for DNA Sensing

Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.

CRISPR-Based Split Luciferase as a Biosensor for Unique DNA Sequences In Situ

To date, CRISPR-based DNA targeting approaches have typically used fusion proteins between full fluorescent reporters and catalytically inactive Cas9 (dCas9) for imaging rather than detection of endogenous genomic DNA sequences. A promising alternative strategy for DNA targeting is the direct biosensing of user-defined sequences at single copy with single-cell resolution. Our recently described DNA biosensing approach using a dual fusion protein biosensor comprised of two independently optimized fragments of NanoLuc luciferase (NLuc) directionally fused to dCas9 paired with user-defined single-guide RNAs (sgRNAs) could allow users to sensitively detect unique copies of a target sequence in individual living cells using common laboratory equipment such as a microscope or a luminescence-equipped microplate reader. Here we describe a protocol for using such a DNA biosensor noninvasively in situ.

HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham

A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule-molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom-atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA.

Preparation of electrochemical sensor based on glassy carbon electrode and its specificity and sensitivity for directional detection of antibiotic resistance genes spreading in the water environment

Antibiotic-resistant bacteria/resistance genes (ARB/ARGs) have been paid much attention due to the environmental risks they might bring. They were demonstrated to be widespread in surface water and wastewater. Determining the concentrations of ARGs is the first step to evaluate the degree of pollution. In this study, electrochemical detection technology was studied due to its advantages of low cost, fast response, and satisfactory selectivity. Additionally, the electrochemical sensor technology was used to determine the concentration of a ubiquitous ARG (ampicillin gene bla_TEM) in the water environment. A kind of electrochemical sensor was prepared on a glassy carbon electrode (GCE). The results of X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry (CV) curves indicated that the single-stranded DNA (ssDNA) probe can be successfully immobilized on the surface of the GCE. In addition, the performance of hybridization between the ssDNA probe and the target DNA at diverse temperatures was compared, of which 35 °C was the optimum. Moreover, the change of charge transfer resistance (ΔRct) for the GCE sensor hybridizing with complementary DNA was much higher than that of DNA with the mismatched base, which indicated that the electrochemical sensor prepared in this study was specific. The sensitivity of the sensor was also proved by the strong correlation between the concentrations of ARGs and ΔRct (with the correlation coefficient (R²) of 0.9905). All in all, this study is meaningful for the comprehend on the detection of ARGs through the electrochemical method.

Applications of triplex DNA nanostructures in sensor development

Triplex DNA nanostructures are one of the most emerging and fascinating self-assembled nanostructures due to their unique nanoparticle-like organization and inherit characteristics. They have attracted numerous interests recently because of their versatile and powerful utility in diverse areas of science and technology, such as clinical or disease diagnosis and stimuli-based drug delivery. This review addresses particularly the utilization of DNA triplexes in the development of biosensors for detecting nucleic acid; strategies in sensing pH, protein activity, ions, or molecules. Finally, an outlook for potential applications of triplex DNA nanoswitches is provided.

Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor

An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.

Spectroscopic, thermodynamic and kinetic analysis of selective triplex formation by peptide nucleic acid with double-stranded RNA over its DNA counterpart

Unlike conventional triplex-forming oligonucleotide (TFO), triplex-forming peptide nucleic acid (PNA) can tightly bind with double-stranded RNA (dsRNA) than double-stranded DNA (dsDNA). Here, we performed spectroscopic, thermodynamic and kinetic experiments for triplex formation by PNA to examine different binding behaviors between PNA - dsRNA and PNA - dsDNA triplexes. We found 9-mer PNA (cytosine content of 66%) formed the thermally stable triplex with dsRNA compared to dsDNA over a wide range of pH (5.5-8.0), salt concentration (50-500 mM NaCl). Both the calorimetric binding constant and the association rate constant for dsRNA were larger than those for dsDNA, indicating the favorable association process for the PNA - dsRNA triplex formation. Comparison with the DNA/RNA heteroduplexes revealed that the DNA strand was detrimental to the triplex stability for PNA, a contrasting result for conventional TFO. The keys underlying the difference in the triplex formation of PNA with different duplexes appear to be the conformational adoptability and the geometric compatibility of PNA to fit the deep, narrow major groove of dsRNA and the helical rigidity difference of the duplexes. Our results emphasize the importance of both the sugar puckering of the duplex and the appropriate conformational flexibility of PNA for the triplex formation.

Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide

We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py-Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py-Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py-Im polyamide as a molecular tool to modulate the formation of DNA assemblies.

A triplex-forming linear probe for sequence-specific detection of duplex DNA with high sensitivity and affinity

A triplex-forming oligonucleotide (TFO) linear probe containing perylene derivatives was synthesized. The TFO linear probe formed a remarkably stable triplex with a target DNA duplex, resulting in the light-up of fluorescence emission. The sensitivity was extremely high even at pH 7. Detection of PCR-amplified target DNA was demonstrated.

Synthesis of 2'-Deoxyuridine Modified with a 3,5-Difluoro-4-Methoxybenzylidene Imidazolinone Derivative for Incorporation into Oligonucleotide Probes for Detection of HER2 Breast Cancer Marker

Nucleoside intercalator conjugates (NICs) describe an innovative methodology developed in our research group for preparation of fluorescence turn-on DNA hybridization probes targeting specific mRNA sequences (e.g., breast cancer markers). In this methodology, we conjugate a non-fluorescent intercalator to the base of a nucleic acid (e.g., uracil) via a flexible spacer. This modified monomer can be incorporated into oligonucleotides by solid-phase synthesis and a large fluorescence enhancement is observed when the modified oligonucleotide is hybridized with its complementary strand due to intercalation of the fluorophore between the two strands. 5-(6-p-Methoxybenzylidene imidazolinone-1-hexene)-2'-deoxyuridine (dU^MBI ) is a synthetic monomer to which 4-methoxybenzylidene imidazolinone (MBI), the fluorescent chromophore of green fluorescent protein (GFP), has been conjugated via a flexible spacer. The detection of human epidermal growth factor receptor 2 (HER2) mRNA by this probe has already been established by our group. The fluorescent intensity of the single-strand DNA can be considered as negligible due to the free rotation of the fluorophore. Upon hybridization, however, the flexible spacer allows for the intercalation of the fluorophore between the hybridized strands, giving rise to enhanced fluorescence and indicating the presence of target mRNA. 3,5-Difluoro-4-methoxybenzylidene (DFMBI) has enhanced photophysical properties compared to MBI fluorophore. This protocol describes a simple, reliable, efficient, and general method for the synthesis of improved derivative dU^DFMBI as a monomer of fluorescent turn-on DNA hybridization probe with application for detection of HER2 mRNA. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Synthesis of 5-[(6)-3,5-difluoro-4-methoxybenzylidene imidazolinone-1-hexene]-2'-deoxyuridine.

Carbon dot-based fluorometric optical sensors: an overview

Fluorescent carbon dots (CDs) are a new class of carbon nanomaterials and have demonstrated excellent optical properties, good biocompatibility, great aqueous solubility, low cost, and simple synthesis. Since their discovery, various synthesis methods using different precursors were developed, which were mainly classified as top-down and bottom-up approaches. CDs have presented many applications, and this review article mainly focuses on the development of CD-based fluorescent sensors. The sensing mechanisms, sensor design, and sensing properties to various targets are summarized. Broad ranges of detection, including temperature, pH, DNA, antibiotics, cations, cancer cells, and antibiotics, have been discussed. In addition, the challenges and future directions for CDs as sensing materials are also presented.

Exploration of intramolecular split G-quadruplex and its analytical applications

Distinct from intermolecular split G-quadruplex (Inter-SG), intramolecular split G-quadruplex (Intra-SG) which could be generated in a DNA spacer-inserted G-quadruplex strand has not been systematically explored. Not only is it essential for the purpose of simplicity of DNA-based bioanalytical applications, but also it will give us hints how to design split G-quadruplex-based system. Herein, comprehensive information is provided about influences of spacer length and split mode on the formation of Intra-SG, how to adjust its thermodynamic stability, and selection of optimal Intra-SG for bioanalysis. For instances, non-classical Intra-SG (e.g. 2:10, 4:8 and 5:7) displays lower stability than classical split strands (3:9, 6:6 and 9:3), which is closely related to integrity of consecutive guanine tract; as compared to regular Intra-SG structures, single-thymine capped ones have reduced melting temperature, providing an effective approach to adjustment of stability. It is believed that the disclosed rules in this study will contribute to the effective application of split G-quadruplex in the field of DNA technology in the future.

Pathogen-specific DNA sensing with engineered zinc finger proteins immobilized on a polymer chip

A specific double-stranded DNA sensing system is of great interest for diagnostic and other biomedical applications. Zinc finger domains, which recognize double-stranded DNA, can be engineered to form custom DNA-binding proteins for the recognition of specific DNA sequences. As a proof of concept, a sequence-enabled reassembly of a TEM-1 β-lactamase system (SEER-LAC) was previously demonstrated to develop zinc finger protein (ZFP) arrays for the detection of a double-stranded bacterial DNA sequence. Here, we implemented the SEER-LAC system to demonstrate the direct detection of pathogen-specific DNA sequences present in E. coli O157:H7 on a lab-on-a-chip. ZFPs custom-designed to detect Shiga toxin in E. coli O157:H7 were immobilized on a cyclic olefin copolymer (COC) chip, which can function as a non-PCR based molecular diagnostic device. Pathogen-specific double-stranded DNA was directly detected by using engineered ZFPs immobilized on the COC chip with high specificity, providing a detection limit of 10 fmol of target DNA in a colorimetric assay. Therefore, in this study, we demonstrated the great potential of ZFP arrays on the COC chip for further development of a simple and novel lab-on-a-chip technology for the detection of pathogens.

Stem–loop clutch probes for sequence-specific dsDNA analysis with improved single-mismatch selectivity

A stem–loop clutch probe based strategy has been proposed to guide sequence-specific dsDNA analysis with enhanced single-base mismatch selectivity.

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research

Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.

A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids

A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.

Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes

Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson–Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson–Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2′-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.

Invader probes: Harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications

Development of probes capable of recognizing specific regions of chromosomal DNA has been a long-standing goal for chemical biologists. Current strategies such as PNA, triplex-forming oligonucleotides, and polyamides are subject to target choice limitations and/or necessitate non-physiological conditions, leaving a need for alternative approaches. Toward this end, we have recently introduced double-stranded oligonucleotide probes that are energetically activated for DNA recognition through modification with +1 interstrand zippers of intercalator-functionalized nucleotide monomers. Here, probes with different chemistries and architectures - varying in the position, number, and distance between the intercalator zippers - are studied with respect to hybridization energetics and DNA-targeting properties. Experiments with model DNA targets demonstrate that optimized probes enable efficient (C50 < 1 μM), fast (t50 < 3h), kinetically stable (> 24h), and single nucleotide specific recognition of DNA targets at physiologically relevant ionic strengths. Optimized probes were used in non-denaturing fluorescence in situ hybridization experiments for detection of gender-specific mixed-sequence chromosomal DNA target regions. These probes present themselves as a promising strategy for recognition of chromosomal DNA, which will enable development of new tools for applications in molecular biology, genomic engineering and nanotechnology.

Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine and 2'-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms.

Recognition of Double-Stranded DNA Using Energetically Activated Duplexes Modified with N2'-Pyrene-, Perylene-, or Coronene-Functionalized 2'-N-Methyl-2'-amino-DNA Monomers

Invader probes have been proposed as alternatives to polyamides, triplex-forming oligonucleotides, and peptide nucleic acids for recognition of chromosomal DNA targets. These double-stranded probes are activated for DNA recognition by +1 interstrand zippers of pyrene-functionalized nucleotides. This particular motif forces the intercalating pyrene moieties into the same region, resulting in perturbation and destabilization of the probe duplex. In contrast, the two probe strands display very high affinity toward complementary DNA. The energy difference between the probe duplexes and recognition complexes provides the driving force for DNA recognition. In the present study, we explore the properties of Invader probes based on larger intercalators, i.e., perylene and coronene, expecting that the larger π-surface area will result in additional destabilization of the probe duplex and further stabilization of probe-target duplexes, in effect increasing the thermodynamic driving force for DNA recognition. Toward this end, we developed protocols for 2'-N-methyl-2'-amino-2'-deoxyuridine phosphoramidites that are functionalized at the N2'-position with pyrene, perylene, or coronene moieties and incorporated these monomers into oligodeoxyribonucleotides (ONs). The resulting ONs and Invader probes are characterized by thermal denaturation experiments, analysis of thermodynamic parameters, absorption and fluorescence spectroscopy, and DNA recognition experiments. Invader probes based on large intercalators efficiently recognize model targets.

Sensitive and direct electrochemical detection of double-stranded DNA utilizing alkaline phosphatase-labelled zinc finger proteins

Direct detection of double-stranded DNA (dsDNA) using zinc finger proteins (ZFPs) is of great importance in biomedical applications such as identifying pathogens and circulating DNAs. However, its sensitivity is still not sufficiently high because limited signalling labels can be conjugated or fused. Herein, we report sensitive and direct detection of dsDNA using (i) alkaline phosphatase (ALP) as a fast catalytic label conjugated to ZFPs along with (ii) electrochemical measurement of an ALP product (l-ascorbic acid) at the indium-tin oxide electrode with a high signal-to-background ratio. ALP is simply conjugated to a ZFP through lysine residues in a ZFP purification tag, a maltose binding protein (MBP). Sandwich-type electrochemical detection of dsDNA allows a detection limit of ca. 100 fM without using DNA amplification.

Field effect sensors for nucleic Acid detection: recent advances and future perspectives

In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs’ greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab.

Polyamide fluorescent probes for visualization of repeated DNA sequences in living cells

DNA imaging in living cells usually requires transgenic approaches that modify the genome. Synthetic pyrrole-imidazole polyamides that bind specifically to the minor groove of double-stranded DNA (dsDNA) represent an attractive approach for in-cell imaging that does not necessitate changes to the genome. Nine hairpin polyamides that target mouse major satellite DNA were synthesized. Their interactions with synthetic target dsDNA fragments were studied by thermal denaturation, gel-shift electrophoresis, circular dichroism, and fluorescence spectroscopy. The polyamides had different affinities for the target DNA, and fluorescent labeling of the polyamides affected their affinity for their targets. We validated the specificity of the probes in fixed cells and provide evidence that two of the probes detect target sequences in mouse living cell lines. This study demonstrates for the first time that synthetic compounds can be used for the visualization of the nuclear substructures formed by repeated DNA sequences in living cells.

Sequence specificity at targeting double-stranded DNA with a γ-PNA oligomer modified with guanidinium G-clamp nucleobases

γ-PNA, a new class of peptide nucleic acids, promises to overcome previous sequence limitations of double-stranded DNA (dsDNA) targeting with PNA. To check the potential of γ-PNA, we have synthesized a biotinylated, pentadecameric γ-PNA of mixed sequence carrying three guanidinium G-clamp nucleobases. We have found that strand invasion reactions of the γ-PNA oligomer to its fully complementary target within dsDNA occurs with significantly higher binding rates than to targets containing single mismatches. Association of the PNA oligomer to mismatched targets does not go to completion but instead reaches a stationary level at or below 60%, even at conditions of very low ionic strength. Initial binding rates to both matched and mismatched targets experience a steep decrease with increasing salt concentration. We demonstrate that a linear DNA target fragment with the correct target sequence can be purified from DNA mixtures containing mismatched target or unrelated genomic DNA by affinity capture with streptavidin-coated magnetic beads. Similarly, supercoiled plasmid DNA is obtained with high purity from an initial sample mixture that included a linear DNA fragment with the fully complementary sequence. Based on the results obtained in this study we believe that γ-PNA has a great potential for specific targeting of chosen duplex DNA sites in a sequence-unrestricted fashion.

Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers

Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.

Distinguishing cytosine methylation using electrochemical, label-free detection of DNA hybridization and ds-targets

In this communication we report on two important effects related to the detection of DNAs. Firstly, we investigate the sensor response to target DNA when the target is in a double stranded (ds) form and compare the response to single stranded (ss) target DNA. The importance in evaluating such an effect lies in the fact that most biological DNA targets are found in ds form. Secondly, we use synthetic ds targets to investigate the effect of DNA methylation on the sensor response. DNA methylation is known to affect functional properties of DNA and is related to a number of diseases, including various cancers. In these studies, we utilize our previously developed sensor platform, which is based on the use of a glassy carbon electrode-confined conducting polymer that is covalently modified with DNA probe sequences. The signal detection methodology we use is measuring a change in the reaction kinetics of ferro-ferricyanide redox couple at the electrode upon hybridization by means of electrical impedance spectroscopy (EIS). Additionally, EIS is utilized to study the kinetics of the hybridization of the conducting polymer-bound probe with methylated vs. non-methylated ds-DNA. Preliminary results are proving valuable as a guide to the future design of sensors for gene methylation.

Specific enrichment of prokaryotic DNA using a recombinant DNA-binding protein

Targeted enrichment of DNA is often necessary for its detection and characterization in complex samples. We describe the development and application of the novel molecular tool for the specific enrichment of prokaryotic DNA. A fused protein comprising the DNA-binding subunit of the bacterial topoisomerase II, gyrase, was expressed, purified, and immobilized on magnetic particles. We demonstrated the specific affinity of the immobilized protein towards bacterial DNA and investigated its efficiency in the samples with high background of eukaryotic DNA. The reported approach allowed for the selective isolation and further detection of as few as 5 pg Staphylococcus aureus DNA from the sample with 4 × 10(6)-fold surplus of human DNA. This method is a promising approach for the preparation of such type of samples, for example in molecular diagnostics of sepsis.

Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences

Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.

Fluorescent probes for nucleic Acid visualization in fixed and live cells

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.

Recognition of mixed-sequence DNA duplexes: design guidelines for invaders based on 2'-O-(pyren-1-yl)methyl-RNA monomers

The development of agents that recognize mixed-sequence double-stranded DNA (dsDNA) is desirable because of their potential as tools for detection, regulation, and modification of genes. Despite progress with triplex-forming oligonucleotides, peptide nucleic acids, polyamides, and other approaches, recognition of mixed-sequence dsDNA targets remains challenging. Our laboratory studies Invaders as an alternative approach toward this end. These double-stranded oligonucleotide probes are activated for recognition of mixed-sequence dsDNA through modification with +1 interstrand zippers of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl-RNA monomers and have recently been shown to recognize linear dsDNA, DNA hairpins, and chromosomal DNA. In the present work, we systematically studied the influence that the nucleobase moieties of the 2'-O-(pyren-1-yl)methyl-RNA monomers have on the recognition efficiency of Invader duplexes. Results from thermal denaturation, binding energy, and recognition experiments using Invader duplexes with different +1 interstrand zippers of the four canonical 2'-O-(pyren-1-yl)methyl-RNA A/C/G/U monomers show that incorporation of these motifs is a general strategy for activation of probes for recognition of dsDNA. Probe duplexes with interstrand zippers comprising C and/or U monomers result in the most efficient recognition of dsDNA. The insight gained from this study will drive the design of efficient Invaders for applications in molecular biology, nucleic acid diagnostics, and biotechnology.

Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA

In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (Φ_F ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (Φ_F =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.

Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA

The development of synthetic agents that recognize double-stranded DNA (dsDNA) is a long-standing goal that is inspired by the promise for tools that detect, regulate, and modify genes. Progress has been made with triplex-forming oligonucleotides, peptide nucleic acids, and polyamides, but substantial efforts are currently devoted to the development of alternative strategies that overcome the limitations observed with the classic approaches. In 2005, we introduced Invader locked nucleic acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through modification with "+1 interstrand zippers" of 2'-N-(pyren-1-yl)methyl-2'-amino-α-l-LNA monomers. Despite promising preliminary results, progress has been slow because of the synthetic complexity of the building blocks. Here we describe a study that led to the identification of two simpler classes of Invader monomers. We compare the thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2'-amino-α-l-LNA, 2'-N-methyl-2'-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling, and NMR spectroscopy are used to elucidate the structural factors that govern probe activation. We demonstrate that probes with +1 zippers of 2'-O-(pyren-1-yl)methyl-RNA or 2'-N-methyl-2'-N-(pyren-1-yl)methyl-2'-amino-DNA monomers recognize DNA hairpins with similar efficiency as original Invader LNAs. Access to synthetically simple monomers will accelerate the use of Invader-mediated dsDNA recognition for applications in molecular biology and nucleic acid diagnostics.

Invaders: Recognition of Double-Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2'-O-(Pyren-1-yl)methyl-ribonucleotides

The invasion has begun: Invaders are shown to recognize DNA hairpins in cell-free assays and chromosomal DNA during non-denaturing fluorescence in situ hybridization (nd-FISH) experiments. As Invaders are devoid of inherent sequence limitations, many previously inaccessible DNA targets could become accessible to exogenous control with important ramifications for karyotyping, in vivo imaging, and gene regulation.

Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn

Fluorophores that are conjugated with N-methylpyrrole-N-methylimidazole (Py-Im) polyamides postulates versatile applications in biological and physicochemical studies. Here, we show the design and synthesis of new types of pyrene-conjugated hairpin Py-Im polyamides (1-5). We evaluated the steady state fluorescence of the synthesized conjugates (1-5) in the presence and absence of oligodeoxynucleotides 5'-CGTATGGACTCGG-3' (ODN 1) and 5'-CCGAGTCCATACG-3' (ODN 2) and observed a distinct increase in emission at 386nm with conjugates 4 and 5. Notably, conjugate 5 that contains a β-alanine linker had a stronger binding affinity (K(D)=1.73×10(-8)M) than that of conjugate 4 (K(D)=1.74×10(-6)M). Our data suggests that Py-Im polyamides containing pyrene fluorophore with a β-alanine linker at the γ-turn NH(2) position can be developed as the competent fluorescent DNA-binding probes.

Spectroscopic and calorimetric studies on the binding of an indoloquinoline drug to parallel and antiparallel DNA triplexes

11-Phenyl-substituted indoloquinolines have been found to exhibit significant antiproliferative potency in cancer cells but to show only moderate affinity toward genomic double-helical DNA. In this study, parallel as well as antiparallel triple-helical DNA targets are employed to evaluate the triplex binding of these ligands. UV melting experiments with parallel triplexes indicate considerable interactions with the drug and a strong preference for TAT-rich triplexes in line with an increasing number of potential intercalation sites of similar binding strength between two TAT base triads. Via substitution of a singly charged aminoethylamine side chain by a longer and doubly charged bis(aminopropyl)amine substituent at the ligand, binding affinities increase and also start to exhibit long-range effects as indicated by a strong correlation between the binding affinity and the overall length of the TAT tract within the triplex stem. Compared to parallel triplexes, an antiparallel triplex with a GT-containing third strand constitutes a preferred target for the indoloquinoline drug. On the basis of pH-dependent titration experiments and corroborated by a Job analysis of continuous variation, binding of the drug to the GT triplex not only is strongly enhanced when the solution pH is lowered from 7 to 5 but also reveals a pH-dependent stoichiometry upon formation of the complex. Calorimetric data demonstrate that stronger binding of a protonated drug at acidic pH is associated with a more exothermic binding process. However, at pH 7 and 5, binding is enthalpically driven with additional favorable entropic contributions.

Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing

Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10¹²-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing β/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5′-WCGCGW-3′ from 5′-WGCGCW-3′. Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications.