Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly.

Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.

Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference.

8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N6-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca2+-mediated reaction and the greater preference for Ca2+ over Mg2+ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg2+ and Ca2+. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.

Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets.

A new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.

Novel enzymatic single-nucleotide modification of DNA oligomer: prevention of incessant incorporation of nucleotidyl transferase by ribonucleotide-borate complex.

Terminal deoxynucleotidyl transferase (TdT), which mediates template-independent polymerization with low specificity for nucleotides, has been used for nucleotide extension of DNA oligomers. One concern is that it is difficult to control the number of incorporated nucleotides, which is a limitation on the use of TdT for single-nucleotide incorporation of DNA oligomers. Herein, we uncovered an interesting inhibitory effect on TdT when ribonucleotide substrates (rNTPs) were employed in a borate buffer. On the basis of unique inhibitory effects of the ribonucleotide-borate complex, we developed a novel enzymatic method for single-nucleotide incorporation of a DNA oligomer with a modified rNTP by TdT. Single-nucleotide incorporation of a DNA oligomer with various modified rNTPs containing an oxanine, biotin, aminoallyl or N6-propargyl group was achieved with a high yield. The 'TdT in rNTP-borate' method is quite simple and efficient for preparing a single-nucleotide modified DNA oligomer, which is useful for the design of functional DNA-based systems.

"In-House" Production of Single Stranded Oligodeoxyribonucleotides.

The most widely used technique for the production of DNA aptamers/oligonucleotides is chemical synthesis. Despite its effectiveness, this technique cannot be performed "in house", making the user fully dependent on a supplier. In this work, we present a simplified method by which it is possible to enzymatically produce DNA aptamers "in house". This new method uses the rolling circle replication followed by a unique cleavage step using the SchI endonuclease. Potentially, any oligonucleotide can be produced by the enzymatic method proposed in this study. To illustrate, we present the production of three variations of the 31-TBA aptamer, a single stranded DNA which has anticoagulant action.

Chemical synthesis of RNA with site-specific methylphosphonate modifications.

Methylphosphonate(mP)-modified RNA serves as valuable probe to evaluate biomolecular interactions between the nucleic acid backbone and binding partners, such as proteins or small molecules. Here, we describe an efficient workflow for the synthesis of RNA with a single mP modification in diastereomerically pure form. While the automated assembly of mP-modified RNA is straightforward, its deprotection under basic conditions is challenging; a carefully optimized step-by-step procedure is provided. In addition, we demonstrate purification and separation strategies for the RP and SP-configurated RNA diastereomers using a combination of anion-exchange and reversed-phase HPLC, and comment on troubleshooting if their separation appears difficult. Furthermore, we demonstrate the stereochemical assignment of short RP and SP mP-modified RNA diastereomers based on 2D ROESY NMR spectroscopy and we report on the impact of the mP modification on thermal and thermodynamic stabilities of RNA-DNA hybrid and RNA-RNA duplexes.

Oligodeoxynucleotides expressing polyguanosine motifs promote antitumor activity through the upregulation of IL-2.

The primary goal of cancer immunotherapy is to elicit an immune response capable of eliminating the tumor. One approach toward accomplishing that goal uses general (rather than tumor-specific) immunomodulatory agents to boost the number and activity of pre-existing CTLs. We find that the intratumoral injection of polyguanosine (poly-G) oligonucleotides (ODN) has such an effect, boosting antitumor immunity and promoting tumor regression. The antitumor activity of poly-G ODN was mediated through CD8 T cells in a TLR9-independent manner. Mechanistically, poly-G ODN directly induced the phosphorylation of Lck (an essential element of the T cell-signaling pathway), thereby enhancing the production of IL-2 and CD8 T cell proliferation. These findings establish poly-G ODN as a novel type of cancer immunotherapy.

Transfection of nuclear factor-kappaB decoy oligodeoxynucleotide protects against ischemia/reperfusion injury in a rat epigastric flap model.

BACKGROUND: Nuclear factor-kappaB (NF-κB) is considered to play an important role in the response to ischemia/reperfusion (I/R) injury in flap surgery. To inhibit NF-κB, synthetic double-stranded oligodeoxynucleotide (ODN) was used as a decoy. The present study aimed to evaluate the suppressive effects of NF-κB against I/R injury of experimental rat flap model. METHODS: An extended epigastric island flap was raised and ischemia was induced for 3 h. NF-κB decoy ODN (group D) or single-strand ODN (control; group S) was injected via the contralateral artery when the pedicle was clamped. Transfection efficiency was evaluated with fluorescein isothiocyanate (FITC)-labeled ODN. The effects of NF-κB decoy ODN were analyzed in groups D and S, and an untreated group (group N). RESULTS: FITC-labeled ODN was distributed over the entire flap. Mean survival rate of the flap was significantly higher in group D than in the other groups (group D: 57.9%; group S: 31.1%; group N 31.7%; p < 0.005). Injured muscle fibers, neutrophils and the expression of inducible nitric oxide synthase were significantly lower in group D. A real-time polymerase chain reaction also demonstrated a tendency for suppression of tumor necrosis factor-α, interleukin (IL)-1ß and IL-6. CONCLUSIONS: We show that NF-κB decoy ODN protected against flap necrosis as a result of I/R injury in rats. We also indicate that intra-arterial injection of naked NF-κB decoy ODN is effective for transfection into target organs. Therefore, transfection of NF-κB decoy ODN represents a novel therapeutic strategy for the treatment of flap surgery in I/R injury.

In vivo transfection of nuclear factor κB decoy protects pulmonary function against acute lung contusion in rabbits.

BACKGROUND: The transcription factor nuclear factor κB (NF-κB) regulates the expression of numerous proinflammatory factors that may exacerbate the response to acute injury. We investigated the effect of an inhibitory NF-κB decoy oligodeoxynucleotide on proinflammatory factor expression and pulmonary function after acute lung contusion in rabbits. METHODS: Thirty-minutes after acute lung contusion, the NF-κB decoy or a scrambled control oligodeoxynucleotide was injected via the jugular vein. Blood samples were collected for blood gas analysis and plasma tumor necrosis factor α, interleukin 1ß (IL-1ß), IL-13, and IL-10 were measured by enzyme-linked immunosorbent assay at 1, 2, 3, and 4 hours after contusion. In addition, NF-κB protein expression in lung tissue was detected by Western blot analysis. RESULTS: The blood PO2 decreased immediately after lung contusion, whereas PAO2 increased significantly, indicative of disrupted respiratory function. Respiratory function improved after sense NF-κB decoy injection but not after injection of the inactive scrambled form. Injection of NF-κB decoy resulted in significant inhibition of NF-κB protein expression in lung tissue and a reduction in the serum concentrations of proinflammatory cytokines tumor necrosis factor α and IL-1ß compared with those of control rabbits injected with the scrambled decoy. In contrast, serum levels of the anti-inflammatory cytokines IL-10 and IL-13 increased after decoy injection compared with those of control animals and rabbits injected with the scrambled decoy. CONCLUSION: The sense NF-κB decoy protected respiratory function and reduced serum proinflammatory factor secretion after acute lung contusion. Inhibition of NF-κB may allow for preservation of pulmonary function for patients with acute lung injury.

Synthesis of oligodeoxyribonucleotides containing a conformationally-locked anti analogue of O6-methyl-2'-deoxyguanosine and their recognition by MGMT and Atl1.

We show that DNA containing a conformationally-locked anti analogue of O(6)-alkylguanine is a poor substrate for human O(6)-methylguanine-DNA methyltransferase (MGMT) and the alkyltransferase-like protein, Atl1. This highlights the requirement for the syn conformation and rationalises why certain O(6)-alkylguanines are poor MGMT substrates.

Quantitative measurement of translesion DNA synthesis in mammalian cells.

Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism, in which specialized low-fidelity DNA polymerases bypass lesions that interfere with replication. This process is inherently mutagenic due to the miscoding nature of DNA lesions, but it prevents double strand breaks, genome instability, and cancer. We describe here a quantitative method for measuring TLS in mammalian cells, based on non-replicating plasmids that carry a defined and site-specific DNA lesion in a single-stranded DNA region opposite a gap. The assay is responsive to the cellular composition of TLS DNA polymerases, and TLS regulators. It can be used with a broad variety of cultured mammalian cells, and is amenable to RNAi gene silencing, making it a useful tool in the study of TLS in mammalian cells.

A rapid, cost-effective method of assembly and purification of synthetic DNA probes >100 bp.

Here we introduce a rapid, cost-effective method of generating molecular DNA probes in just under 15 minutes without the need for expensive, time-consuming gel-extraction steps. As an example, we enzymatically concatenated six variable strands (50 bp) with a common strand sequence (51 bp) in a single pool using Fast-Link DNA ligase to produce 101 bp targets (10 min). Unincorporated species were then filtered out by passing the crude reaction through a size-exclusion column (<5 min). We then compared full-length product yield of crude and purified samples using HPLC analysis; the results of which clearly show our method yields three-quarters that of the crude sample (50% higher than by gel-extraction). And while we substantially reduced the amount of unligated product with our filtration process, higher purity and yield, with an increase in number of stands per reaction (>12) could be achieved with further optimization. Moreover, for large-scale assays, we envision this method to be fully automated with the use of robotics such as the Biomek FX; here, potentially thousands of samples could be pooled, ligated and purified in either a 96, 384 or 1536-well platform in just minutes.

Building block synthesis using the polymerase chain assembly method.

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

Oligonucleotide assembly in yeast to produce synthetic DNA fragments.

The yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp and can be as long as 200 nucleotides in length to produce kilobase-sized synthetic DNA molecules. A protocol for designing the oligonucleotides to be assembled, transforming them into yeast, and confirming their assembly is described here. This straightforward scheme for assembling chemically synthesized oligonucleotides can be a useful tool for building synthetic DNA molecules.

TopDown real-time gene synthesis.

This chapter introduces a simple, cost-effective TopDown one-step gene synthesis method, which is suitable for the sequence assembly of fairly long DNA. This method can be distinguished from conventional gene synthesis methods by two key features: (1) the melting temperature of the outer primers is designed to be ∼8°C lower than that of the assembly oligonucleotides, and (2) different annealing temperatures are utilized to selectively control the efficiencies of oligonucleotide assembly and full-length template amplification. This method eliminates the interference between polymerase chain reactions (PCR) assembly and amplification in one-step gene synthesis. Additionally, the TopDown gene synthesis has been combined with the LCGreen I DNA fluorescence dye in a real-time gene synthesis approach for investigating the stepwise efficiency and kinetics of PCR-based gene synthesis. The obtained real-time fluorescence signals are compared with gel electrophoresis results to optimize gene synthesis conditions.

Using DNAWorks in designing oligonucleotides for PCR-based gene synthesis.

The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than where they have been identified originally. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard for the parent genome. Yet design and construction of synthetic genes, especially those coding for large proteins, can be a slow, difficult, and confusing process. DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods.

De novo gene synthesis design using TmPrime software.

This chapter presents TmPrime, a computer program to design oligonucleotide for both ligase chain reaction (LCR)- and polymerase chain reaction (PCR)-based de novo gene synthesis. The program divides a long input DNA sequence based on user-specified melting temperatures and assembly conditions, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures in a PDF file, which will be sent to the user via e-mail. The program also provides functions on sequence pooling to separate long genes into smaller pieces for multipool assembly and codon optimization for expression based on the highest organism-specific codon frequency. This software has been successfully used in the design and synthesis of various genes with total length >20 kbp. This program is freely available at http://prime.ibn.a-star.edu.sg.

Evaluation of base recognition abilities of 2'-deoxynucleoside N-oxide derivatives by polymerase reactions.

The main products obtained by oxidation of cytosine and adenine bases with hydrogen peroxide are cytosine and adenine N-oxide derivatives. There is a possibility that these N-oxide derivatives are mutagenic in genomic DNA like 8-oxoguanine or thymine glycol. Although the chemical synthesis and properties of 2'-deoxynucleoside N-oxide derivatives have been well established, little has been reported about the chemical and biochemical behavior of oligodeoxynucleotides (ODNs) containing these modified 2'-deoxynucleoside. In this study, we examined their base recognition ability by DNA polymerase reactions. It was found that these modified derivatives were incorporated into the 3'-terminal site of an ODN by DNA polymerase selecting accurately the complementary G or T base on a template ODN. In the incorporation reaction using template ODNs containing 2'-deoxynucleoside N-oxide bases, their N-oxide bases were selectively recognized by the complementary 5'-triphosphate (dGTP or dTTP).

Enzymatic synthesis of perfluoroalkylated DNA.

Thymidine analogues 5-trifluoromethyl-, 5-pentafluoroethyl- and 5-(heptafluoro-n-propyl)-2'-deoxyuridines were synthesised and converted into the corresponding 5'-triphosphates 1a-c. Performing DNA polymerase-catalyzed primer extension reactions these modified nucleotides were incorporated into DNA to create perfluoroalkylated nucleic acids. Although single modified nucleotides were enzymatically incorporated and further elongated quite similar to the natural TTP, the enzymatic synthesis of multi-modified nucleic acids was initial only feasible with modifications at every fourth base. Nevertheless, as the effects of the modified dUTPs on DNA polymerases varied significantly with the used enzyme, Therminator DNA polymerase was proficient in incorporating 11 adjacent 5-trifluoromethyl-2'-deoxyuridine moieties.