Use of immobilized PCR primers to generate covalently immobilized DNAs for in vitro transcription/translation reactions

Biosensing with Polymerase Chain Reaction-Stable DNA-Functionalized Magnetically Susceptible Carbon-Iron Microparticles

We demonstrate a rapid and sensitive method for DNA detection without the need for fluorescence. This is based on carbon-coated magnetic iron (Fe) microparticles with a covalent surface attachment of DNA. We show that these magnetic microparticles can capture complementary DNA. Significantly, the DNA covalent surface bonds are robust to high temperatures and can be included in a sample during polymerase chain reaction (PCR). This method is employed for the detection of targeted DNA sequences (40-50 bp). Hybridization probes on the surface of the magnetically susceptible Fe microparticle recognize the target DNA sequence-specifically. The double-stranded DNA (dsDNA) microparticles are then quickly captured with a magnet from the sample matrix. This foregoes postpurification processes, such as electrophoresis, which make our technique time- and cost-effective. Captured dsDNA can be detected with intercalating dyes such as ethidium bromide through a loss in the UV absorption signal with a limit of detection (LOD) of 24 nM within 15 min. Likewise, surface-bound DNA can act as a primer in PCR to decrease the LOD to 5 pM within 2 h. This is the first instance of a nucleotide-modified magnetically susceptible carbon substrate that is PCR-compatible. Besides DNA capture, this strategy can eventually be applied to sequence-specific nucleic acid purification and enrichment, PCR cleanup, and single-strand generation. The DNA-coated particles are stable under PCR conditions (unlike commonly used polystyrene or gold particles).

DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging

DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.

Covalent Biosensing Polymer Chain Reaction Enabling Periphery Blood Testing to Predict Tumor Invasiveness with a Platelet Procancerous Protein

Periphery blood testing is an attractive and relatively less invasive way of early cancer screening. In this work, based on the latest understanding of the pivotal role of platelets in promoting cancer invasion, a method for detecting a procancerous protein overexpressed both on platelets and in cancer cells is developed. As a kinase, the enzymatic activity, abundance, and self-phosphorylation of this protein are all important factors influencing its procancerous activity. To simultaneously determine these three important biochemical parameters, electrochemical control is called upon to connect or disconnect a polymer chain reaction (PCR) primer with a small-molecule synthetic probe, and with the target protein, in a target-specific manner. The resulting PCR signal amplification greatly improves the sensitivity of the design and also enables direct detection of the protein and its catalytic activity as well as its self-phosphorylation in clinical periphery blood samples from hepatocellular carcinoma (HCC) patients. This may point to future application of the proposed method in the early screening of HCC to assist its diagnosis and treatment.

How Surfaces Affect Hybridization Kinetics

Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.

Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction

Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10⁶ primers/2.8-μm-diameter bead) via either azide-alkyne click chemistry or Michael addition. The primers are viable polymerase substrates (4-7% bead-immobilized enzymatic extension product yield from one thermal cycle). Carbodiimide-activated carboxylic acid beads only react with oligonucleotides under conditions that promote nonspecific interactions (low salt, low pH, no detergent), comparably immobilizing primers on beads, but yielding no detectable enzymatic extension product. Click-functionalized beads perform satisfactorily in emPCR of a site-saturation mutagenesis library, generating monoclonal templated beads (10⁴-10⁵ copies/bead, 1.4-kb amplicons). This simpler, chemical approach to primer immobilization may spur more economical library preparation for high-throughput sequencing and enable more complex surface elaboration for in vitro evolution.

Development of repeatable arrays of proteins using immobilized DNA microplate (RAPID-M) technology

Background

Protein microarrays have enormous potential as in vitro diagnostic tools stemming from the ability to miniaturize whilst generating maximum evaluation of diagnostically relevant information from minute amounts of sample. In this report, we present a method known as repeatable arrays of proteins using immobilized DNA microplates (RAPID-M) for high-throughput in situ protein microarray fabrication. The RAPID-M technology comprises of cell-free expression using immobilized DNA templates and in situ protein purification onto standard microarray slides.

Results

To demonstrate proof-of-concept, the repeatable protein arrays developed using our RAPID-M technology utilized green fluorescent protein (GFP) and a bacterial outer membrane protein (OmpA) as the proteins of interest for microarray fabrication. Cell-free expression of OmpA and GFP proteins using beads-immobilized DNA yielded protein bands with the expected molecular sizes of 27 and 30 kDa, respectively. We demonstrate that the beads-immobilized DNA remained stable for at least four cycles of cell-free expression. The OmpA and GFP proteins were still functional after in situ purification on the Ni–NTA microarray slide.

Conclusion

The RAPID-M platform for protein microarray fabrication of two different representative proteins was successfully developed.

DNA nano-carrier for repeatable capture and release of biomolecules

DNA can be manipulated to design nano-machines through specific sequence recognition. We report a switchable DNA carrier for repeatable capture and release of a single stranded DNA. The activity of the carrier was regulated by the interactions among a double-stranded actuator, single stranded target, fuel, and anti-fuel DNA strands. Inosine was used to maintain a stable triple-stranded complex when the actuator's conformation was switched between open (capture) and closed (release) configurations. Time lapse fluorescence measurements show repeatable capture and release of target strands. TEM images also show visible capture of target DNA strands when gold nanoparticles were attached to the DNA carrier and the target DNA strand. The carrier activity was controlled by length of toeholds, number of mismatches, and inosine substitutions. Significantly, unlike in previously published work that reported the devices functioned only when there is a perfect match between the interacting DNA strands, the present device works only when there are mismatches in the fuel strand and the best performance is achieved for 1-3 mismatches. The device was used to successfully capture and release gold nanoparticles when linked to the target single-stranded DNA. In general, this type of devices can be used for transport and delivery of theranostic molecules.

Cell-free protein synthesis using multiply-primed rolling circle amplification products

Utilizing in vitro transcription and translation (IVTT) to produce small quantities of proteins is convenient but requires a significant supply of pure template DNA. This can be cumbersome, particularly when the method is used for many different templates in a high-throughput manner. Multiply-primed rolling circle amplification (RCA) with ϕ29 DNA polymerase is a simple way to generate large amounts of DNA; however, the products of this amplification method have interruptions in both strands and branched structures. In this study, we tested whether RCA-generated DNA can serve as the template for in vitro transcription. We found that RCA DNA–generated transcripts work in coupled in vitro translation with nearly the same efficiency (per nanogram of DNA) as those obtained from purified plasmid. We propose a convenient, single-tube format for template amplification, transcription, and translation.

Steric effects and mass-transfer limitations surrounding amplification reactions on immobilized long and clinically relevant DNA templates

DNA and RNA are commonly captured on solid substrates during purification and isolation, where they can be transferred to downstream amplification and transcription reactions. When compared to the solution phase, however, immobilized DNA- and RNA-directed reactions are less efficient because of a variety of complex factors. Steric inhibition because of the bead surface and neighboring biological polymers, a change in solution chemistry because of the high local concentration of template molecules, and mass transfer to the bead surface could all affect the overall reaction kinetics. Furthermore, these effects may be particularly evident when working with long clinically relevant molecules, such as mRNA, viral RNA, and cDNA. In this paper, we focus on the in vitro transcription reaction (IVT) of both a long and short strand of H5 influenza A RNA (1777 and 465 nt) on both free and immobilized DNA templates to study these phenomena. We found that transcription was less efficient on immobilized beads than in solution, but that it can be dramatically increased with optimal solution chemistry. Using high ribonucleotide concentrations (>6 mM total rNTP), the RNA yield from long immobilized cDNA templates was boosted to 60% of solution control. Surprisingly, we found that steric effects because of surrounding immobilized molecules were only significant when the DNA molecules were short enough to achieve a high density (9x10(-4) microm2/molecule) on the silica substrate, such that the gap between molecules is on the order of the polymerase diameter. Eventually, these findings can be exploited in an automated microreactor, where isolation, purification, amplification, and detection of nucleic acids can be unified into one portable device.

Silica-coated, Au/Ag striped nanowires for bioanalysis

Striped metallic nanowires (NW) have been coated with a silica shell of controllable thickness (6-150 nm), and the assay performance of coated vs uncoated NW has been compared. The silica coating does not interfere with identification of the metal striping pattern and protects Ag segments from oxidation, extending the range of assay conditions under which barcoded NW can be used. Much higher and more uniform fluorescence intensities were observed for dye-labeled ssDNA bound to SiO2-coated as compared to intensities for uncoated NW. Simultaneous, multiplexed DNA hybridization assays for three pathogen-specific target sequences on SiO2-coated NW showed good discrimination of complementary from noncomplementary targets. Application of SiO2-coated NW in discrimination of single base mismatches corresponding to a mutation of the p53 gene was also demonstrated. Finally, we have shown that thiolated probe DNA resists desorption under thermocycling conditions if attached via siloxane chemistry to SiO2-coated NW, but not if it is attached via direct adsorption to bare Au/Ag NW.

Metallic barcodes for multiplexed bioassays

Both detection and postdiagnosis monitoring are critical for cancer isolation and treatment. Particle-based sensing strategies could help to address these medical needs. This review describes barcoded metallic nanowires as particle scaffolds for multiplexed detection of antigens or nucleic acids. Barcode patterns are compositionally encoded as stripes of gold and silver metal along the nanowire length during fabrication by templated electrodeposition. Particle identification is accomplished using reflectance optical microscopy and can be coupled with fluorescence readout of antigen- or nucleic acid-binding events. Several approaches to multiplexed biodetection based on barcoded nanowires will be described and the potential for these particles in cancer detection will be discussed.

Detection and identification of IHN and ISA viruses by isothermal DNA amplification in microcapillary tubes

Unique base sequences derived from RNA of both infectious hematopoietic necrosis virus (IHNV) and infectious salmon anemia virus (ISAV) were detected and identified using a combination of surface-associated molecular padlock DNA probes (MPPs) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV or ISAV were recognized by MPPs. Circularized MPPs were then captured on the inner surfaces of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA produced DNA concatamers, which were labeled with fluorescent SYBR Green II nucleic acid stain, and measured by microfluorimetry. Molecular padlock probes, combined with this method of surface-associated isothermal RCA, exhibited high selectivity without the need for thermal cycling. This method is applicable to the design of low-power field sensors capable of multiplex detection of viral, bacterial, and protozoan pathogens within localized regions of microcapillary tubes.

Solid-phase translation and RNA-protein fusion: a novel approach for folding quality control and direct immobilization of proteins using anchored mRNA

A novel cell-free translation system is described in which template-mRNA molecules were captured onto solid surfaces to simultaneously synthesize and immobilize proteins in a more native-state form. This technology comprises a novel solid-phase approach to cell-free translation and RNA–protein fusion techniques. A newly constructed biotinylated linker-DNA which enables puromycin-assisted RNA–protein fusion is ligated to the 3′ ends of the mRNA molecules to attach the mRNA-template on a streptavidin-coated surface and further to enable the subsequent reactions of translation and RNA–protein fusion on surface. The protein products are therefore directly immobilized onto solid surfaces and furthermore were discovered to adopt a more native state with proper protein folding and superior biological activity compared with conventional liquid-phase approaches. We further validate this approach via the production of immobilized green fluorescent protein (GFP) on microbeads and by the production and assay of aldehyde reductase (ALR) enzyme with 4-fold or more activity. The approach developed in this study may enable to embrace the concept of the transformation of ‘RNA chip-to-protein chip’ using a solid-phase cell-free translation system and thus to the development of high-throughput microarray platform in the field of functional genomics and in vitro evolution.

Highly parallel genomic assays

Recent developments in highly parallel genome-wide assays are transforming the study of human health and disease. High-resolution whole-genome association studies of complex diseases are finally being undertaken after much hypothesizing about their merit for finding disease loci. The availability of inexpensive high-density SNP-genotyping arrays has made this feasible. Cancer biology will also be transformed by high-resolution genomic and epigenomic analysis. In the future, most cancers might be staged by high-resolution molecular profiling rather than by gross cytological analysis. Here, we describe the key developments that enable highly parallel genomic assays.

Polyelectrolyte functionalized magnetic emulsion for specific isolation of nucleic acids

A magnetic oil in water (o/w) emulsion was cationized by adsorption of poly(ethyleneimine) (PEI). In a subsequent step, the cationic particles were derivatized with partially hydrolyzed poly(maleic anhydride-alt-methyl vinyl ether) copolymer (PMAMVE) to lead negatively charged colloids. The experimental conditions for the covalent grafting of the PMAMVE were selected on the basis of colloidal stability, charge inversion and absence of inhibition of the enzymatic DNA/RNA amplification reactions. Once the experimental conditions were selected, oligonucleotides (ODN) bearing particles were obtained according to the sequential process: (i) grafting of single stranded ODNs onto PMAMVE; (ii) grafting of the PMAMVE-ODN conjugates onto the cationic particles according to the conditions defined above. In this strategy, both steps could be independently controlled. The ODN-PMAMVE-particles conjugates were very stable with time, did not inhibit RT-PCR and were capable of hybridizing specifically with the complementary target.

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5′-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability towards thermocycling, functionalization reproducibility and storage stability. The derivatization process, first developed for glass slides, was then adapted to microfabricated glass channels containing integrated fluidic connections. This implementation resulted in an important reduction of reaction times, consumption of reagents and process automation. Innovative analytical methods for the characterization of attached DNA were developed for assessing the surface immobilized DNA content after amplification. The results obtained showed that the BTA chemistry is compatible and suitable for forming highly dense arrays of DNA colonies with optimal surface coverage of about 10 million colonies/cm² from the amplification of initial single-template DNA molecules immobilized. We also demonstrate that the dsDNA colonies generated can be quantitatively processed in situ by restriction enzymes digestion. DNA colonies generated using the BTA reagent can be used for further sequence analysis in an unprecedented parallel fashion for low-cost genomic studies.

Magnetic colloids for the generic capture of viruses

In molecular biology or in the diagnostic field, a strong interest has been devoted to the use of magnetic nanoparticles as an efficient tool for a fast and easy biomolecule extraction. Various methods allow the synthesis of numerous types of magnetic particles, but very few of them can be adapted to biological protocols. For biological tests based on the final detection of nucleic acids, the major difficulties in the choice of these magnetic beads are their fast magnetic separation, requiring a high magnetic oxide content and overall a good compatibility with enzymes used for nucleic acid amplification. In this study, magnetic colloids were obtained from oil in water (o/w) magnetic emulsion by a two-step polymer immobilization procedure. First, a polycation, poly(ethyleneimine), was adsorbed to ensure charge inversion of the emulsion droplets. Then poly(maleic anhydride-co-methyl vinyl ether) was either chemically grafted or adsorbed if under its hydrolyzed form. The obtained colloids were characterized in terms of colloidal stability, surface charge density, and morphology and were evaluated in a reverse transcription-PCR (RT-PCR) inhibition test. Selected colloids were used for the nonspecific capture of viruses, with RT-PCR being used as a means of detection. Particle size and charge studies allowed us to follow each step of their synthesis, showing the relevance of these methods. The prepared magnetic particles exhibit a good RT-PCR compatibility when used in the range of 5-40 microg in the 50 microl amplification mix. Finally, virus capture tests revealed a capture efficiency of 90% with an average detection sensitivity of 10(3)pfu/ml.

Epistatic interactions among herbicide resistances in Arabidopsis thaliana: the fitness cost of multiresistance

The type of interactions among deleterious mutations is considered to be crucial in numerous areas of evolutionary biology, including the evolution of sex and recombination, the evolution of ploidy, the evolution of selfing, and the conservation of small populations. Because the herbicide resistance genes could be viewed as slightly deleterious mutations in the absence of the pesticide selection pressure, the epistatic interactions among three herbicide resistance genes (acetolactate synthase CSR, cellulose synthase IXR1, and auxin-induced AXR1 target genes) were estimated in both the homozygous and the heterozygous states, giving 27 genotype combinations in the model plant Arabidopsis thaliana. By analyzing eight quantitative traits in a segregating population for the three herbicide resistances in the absence of herbicide, we found that most interactions in both the homozygous and the heterozygous states were best explained by multiplicative effects (each additional resistance gene causes a comparable reduction in fitness) rather than by synergistic effects (each additional resistance gene causes a disproportionate fitness reduction). Dominance coefficients of the herbicide resistance cost ranged from partial dominance to underdominance, with a mean dominance coefficient of 0.07. It was suggested that the csr1-1, ixr1-2, and axr1-3 resistance alleles are nearly fully recessive for the fitness cost. More interestingly, the dominance of a specific resistance gene in the absence of herbicide varied according to, first, the presence of the other resistance genes and, second, the quantitative trait analyzed. These results and their implications for multiresistance evolution are discussed in relation to the maintenance of polymorphism at resistance loci in a heterogeneous environment.

In vitro transcription of a whole gene on a surface-coupled template

An artificial gene was constructed combining the T7 promoter and terminator with the EGFP-gene from the plasmid pEGFP. The functionality of the construct was shown by in vitro translation. The gene-construct was immobilised on a planar glass surface. The transcription was performed on the immobilised gene and mRNA was determined by RT-PCR. Multiple use of the immobilised gene was demonstrated.

High-throughput method for detecting DNA methylation

Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Detection of promoter hypermethylation of cancer-related gene may be useful for cancer diagnosis or the detection of recurrence. However, most of the studies have focused on a single gene only and gave little information about the concurrent methylation status of multiple genes. In this study, we attempted to develop a microarray method coupled with linker-PCR for detecting methylation status of multiple genes in the tumor tissue. A series of synthesized oligonucleotides were synthesised and purified to completely match with 16 investigated targets. Then they were immobilized on the aldehyde-coated glass slide to fabricate a DNA microarray for detecting methylation status of these genes. The results indicated that these genes were all methylated in the positive control. However, no methylated was found in these genes for the negative control. Only p16 and p15 genes were methylated in investigated genes for the gastric tumor tissue, whereas others were not methylated. The above results were validated by bisulfite DNA sequencing. Our experiments successfully demonstrated that the DNA microarray could be applied as a high-throughput tool to determine methylation status of the investigated genes.

DNA analysis with multiplex microarray-enhanced PCR

We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are carried out simultaneously in the reaction chamber: on or within gel elements, and in bulk solution over the gel element array. MME-PCR is initiated by multiple complex primers containing gene-specific, forward and reverse, sequences appended to the 3′ end of a universal amplification primer. The complex primer pair is covalently tethered through its 5′ end to the polyacryl- amide backbone. In the bulk solution above the gel element array, a single pair of unattached universal primers simultaneously directs pseudo-monoplex PCR of all targets according to normal solution-phase PCR. The presence of a single universal PCR primer pair in solution accelerates amplification within gel elements and eliminates the problem of primer interference that is common to conventional multiplex PCR. We show 10⁶-fold amplification of targeted DNA after 50 cycles with average amplification efficiency 1.34 per cycle, and demonstrate specific on-chip amplification of six genes in Bacillus subtilis. All six genes were detected at 4.5 pg of bacterial genomic DNA (equivalent to 10³ genomes) in 60 independent amplification reactions performed simultaneously in single reaction chamber.

Polymer-anchored DNA gene monolayers

Monolayers of DNA chains of polymeric dimensions, considered here to be longer than approximately 100 nucleotides, are widely encountered in biomolecular diagnostics as well as present for a model system for investigating behavior of polyelectrolytes at interfaces. A major challenge in advancing such applications is assembling the DNA on the surface in a controlled way. Although covalent immobilization is expected to produce optimal stability, the multitude of potential reactive sites along the contour of long DNA molecules requires that any chemical transformations be strictly site-specific to preserve control over attachment geometry and function. A synthetic approach to fabricating monolayers of DNA genes on gold using polymeric anchor (adhesion) films is presented that (i) possesses stringent site-specificity of surface-attachment, (ii) exhibits excellent stability to elevated temperatures, allowing denaturation of duplex chains at 90 degrees C without loss of surface-linked strands, and (iii) achieves surface coverages suitable for investigating multichain polyelectrolyte behavior in regimes of strong interchain interactions.

Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences

Large DNA constructs of arbitrary sequences can currently be assembled with relative ease by joining short synthetic oligodeoxynucleotides (oligonucleotides). The ability to mass produce these synthetic genes readily will have a significant impact on research in biology and medicine. Presently, high-throughput gene synthesis is unlikely, due to the limits of oligonucleotide synthesis. We describe a microfluidic PicoArray method for the simultaneous synthesis and purification of oligonucleotides that are designed for multiplex gene synthesis. Given the demand for highly pure oligonucleotides in gene synthesis processes, we used a model to improve key reaction steps in DNA synthesis. The oligonucleotides obtained were successfully used in ligation under thermal cycling conditions to generate DNA constructs of several hundreds of base pairs. Protein expression using the gene thus synthesized was demonstrated. We used a DNA assembly strategy, i.e. ligation followed by fusion PCR, and achieved effective assembling of up to 10 kb DNA constructs. These results illustrate the potential of microfluidics-based ultra-fast oligonucleotide parallel synthesis as an enabling tool for modern synthetic biology applications, such as the construction of genome-scale molecular clones and cell-free large scale protein expression.

Monitoring Molecular Beacon/DNA Interactions Using Atomic Force Microscopy

The molecular beacon (MB) is a new fluorescence probe containing a single-stranded oligonucleotide with a probe sequence embedded in complementary sequences that form a hairpin stem. Due to the inherent fluorescent signal transduction mechanism, an MB functions as a sensitive probe with a high signal-to-background ratio for real-time monitoring and provides a variety of exciting opportunities in DNA, RNA, and protein studies. To better understand the properties of MBs, the specific interactions between MB and target DNA (complementary and one-base mismatch) have been directly investigated by atomic force microscopy. The interaction force between a linear DNA probe and the target DNA was also detected and compared to that between MB and target DNA. The results demonstrate the high specificity of the MB/target DNA compared to the linear DNA/target DNA interaction.

Microbead display of proteins by cell-free expression of anchored DNA

Gene expression technologies where nucleic acid sequences remain physically linked to their corresponding gene products are important tools for selection and identification of rare variants in large protein libraries. Here, we describe a gene expression system, which combines the potential of bead-based suspension array technology (SAT) with gene expression and clonal identification. Using streptavidin-coated polystyrene micrometer-sized beads as solid supports for anchored PCR products, we have investigated conditions for cell-free expression and bioaffinity technology to provide clonal co-anchoring of corresponding gene products. Experiments showed that coupled transcription and translation of PCR product expression cassettes resulted in display of affinity-anchored proteins whose binding characteristics could be analyzed via direct and selective interaction with a fluorescently labeled target protein. Interestingly, experiments performed with differently biotinylated PCR products showed that the efficiency of display was dependent on the directionality of the expression cassette relative to the bead surface. In spiked systems, using small immunoglobulin binding proteins as models, we demonstrate efficient flow cytometric sorting of beads corresponding to the target interacting clones, verified by post-sorting analysis and clonal identification at DNA level. The use of this technology, including alternative formats, for different proteomics applications is discussed.

On filtering false positive transmembrane protein predictions

While helical transmembrane (TM) region prediction tools achieve high (>90%) success rates for real integral membrane proteins, they produce a considerable number of false positive hits in sequences of known nontransmembrane queries. We propose a modification of the dense alignment surface (DAS) method that achieves a substantial decrease in the false positive error rate. Essentially, a sequence that includes possible transmembrane regions is compared in a second step with TM segments in a sequence library of documented transmembrane proteins. If the performance of the query sequence against the library of documented TM segment-containing sequences in this test is lower than an empirical threshold, it is classified as a non-transmembrane protein. The probability of false positive prediction for trusted TM region hits is expressed in terms of E-values. The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments ( approximately 95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is approximately 99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.

Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides

We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.

Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method)

We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.

Multifunctional DNA conjugates for the in vitro selection of new catalysts

DNA-substrate conjugates are required for the direct in vitro selection of novel DNA catalysts for reactions between two small reactants. Here we describe the introduction of all necessary features into ssDNA by a novel, multifunctional primer containing a flexible PEG spacer, an o-nitrobenzyl moiety allowing for selective photocleavage, and anthracene as a reactant, a fluorescence label and/or an immobilization tag. These components were checked individually and by a mock selection.