Rapid Screening of Complex DNA Samples by Single-Molecule Amplification and Sequencing

Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample

Solvent strength of ionic liquid/CO2 mixtures

Previously we have shown that organic solutes can be extracted from ionic liquids (ILs) with supercritical CO2 and that ILs can be induced to separate from organic and aqueous mixtures by applying gaseous CO2 pressure. Thus, we are interested in the solvent strength of IL/CO2 mixtures. Here we use 4-nitroaniline, N,N-diethyl-4-nitroaniline and Reichardt's dye 33 to determine the Kamlet-Taft parameters for four different imidazolium based ILs and their mixtures with CO2 at 25 and 40degreesC. The effect of temperature and carbon dioxide concentration on these parameters was determined. The polarizability parameter depends weakly on the CO2 concentration. However, the hydrogen bond donating ability and the hydrogen bond accepting ability are virtually independent Of CO2 pressure. The results indicate that the strong interactions between ILs and probe molecules are not influenced by CO2.</p

Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides

<p>Abstract</p> <p>Background</p> <p>Sequencing-by-ligation (SBL) is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons). SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths.</p> <p>Results</p> <p>To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, <it>cyclic SBL </it>(cSBL), to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction.</p> <p>Conclusions</p> <p>Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.</p