Showing papers by "Matthias Meyer published in 2008"

Parallel tagged sequencing on the 454 platform

Abstract: Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.

Advanced aspects of electromagnetic SERS enhancement factors at a hot spot

Abstract: In this paper, we discuss some advanced theoretical aspects of electromagnetic enhancement factors (EFs) in surface-enhanced Raman scattering (SERS). We focus in particular on the influence of surface selection rules (SSRs) on SERS EFs at hot spots, and the determination of SERS depolarization ratios. Both aspects could be viewed as secondary (compared to the overall magnitude of the SERS EF), but are nevertheless observable experimentally and crucial for a fundamental understanding of SERS. They also share the property that they cannot be studied within the commonly used jEj 4 approximation to the SERS EFs, and appropriate tools are developed here to make predictions beyond this approximation in the case of a SERS hot spot. In addition, theoretical estimates of different types of (previously defined) EFs are provided, and their origins discussed for the typical example of a SERS substrate dominated by SERS hot spots. Finally, experimental measurements of SERS depolarization ratios are presented to support the theoretical predictions. Copyright  2008 John Wiley & Sons, Ltd.

From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing

Abstract: Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require microgram quantities of initial material. This is due to a lack of effective methods for quantifying 454 sequencing libraries, necessitating expensive and labour-intensive procedures when sequencing ancient DNA and other poor DNA samples. Here we report a 454 sequencing library quantification method based on quantitative PCR that effectively eliminates these limitations. We estimated both the molecule numbers and the fragment size distributions in sequencing libraries derived from Neandertal DNA extracts, SAGE ditags and bonobo genomic DNA, obtaining optimal sequencing yields without performing any titration runs. Using this method, 454 sequencing can routinely be performed from as little as 50pg of initial material without titration runs, thereby drastically reducing costs while increasing the scope of sample throughput and protocol development on the 454 platform. The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms.

Bi-analyte SERS with isotopically edited dyes.

Abstract: Isotopically substituted rhodamine dyes provide ideal probes for the study of single-molecule surface enhanced Raman scattering (SM-SERS) events through multiple-analyte techniques. Isotopic editing should, in principle, provide probes that have identical chemical properties (and surface chemistries); while exhibiting at the same time distinct Raman features which enable us to identify single-molecule SERS events. We present here a specific example of two-analyte SM-SERS based on the isotopic substitution of a methyl ester rhodamine dye. The dyes are carefully characterized (in both standard and SERS conditions) to confirm experimentally their similar chemical properties. We then demonstrate their utility for bi-analyte SERS (BiASERS) experiments and, as an example, highlight the transition from a single, to a few, to many molecules in the statistics of SM-SERS signals.

Evidence of natural isotopic distribution from single-molecule SERS

Abstract: We report on the observation of the natural isotopic spread of carbon from single-molecule Surface Enhanced Raman Spectroscopy (SM-SERS). By choosing a dye molecule with a very localized Raman active vibration in a cyano bond (C$\equiv$N triple bond), we observe (in a SERS colloidal liquid) a small fraction of SM-SERS events where the frequency of the cyano mode is softened and in agreement with the effect of substituting $^{12}$C by the next most abundant $^{13}$C isotope. This example adds another demonstration of single molecule sensitivity in SERS through isotopic editing which is done, in this case, not by artificial isotopic editing but rather by nature itself. It also highlights SERS as a unique spectroscopic tool, capable of detecting an isotopic change in one atom of a single molecule.