False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2’-bipyridine

• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 1434–1446, doi:10.3762/bjnano.7.135

• nucleobase; α-HL was also shown to discriminate between osmylated T and osmylated C. Experiments presented here confirm that the kinetics of osmylation are comparable for short oligos and long ssDNA and show that pyrimidine osmylation is practically complete in two hours at room temperature with less than 15

• ; osmylation; ssDNA; Introduction At the time the human genome was completed in 2001 [1][2], it was becoming clear that the relationships between genes, noncoding regions, epigenetic modifications, and the transcriptome were intertwined and led to health vs disease in complex patterns. A large effort in

• osmylation of the monomer, the deoxythymidylic acid triphosphate, 5’dTTP [30]. The across-the-board equal reactivity leads to predictable osmylation of any DNA without prior sequence knowledge. Conjugation of OsBp to a pyrimidine leads to a new chromophore that absorbs in the range of 300 to 320 nm, a range

Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore

• Yun Ding and
• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 91–101, doi:10.3762/bjnano.7.11

• surrogate for nanopore-based sequencing. Osmylation is the addition of osmium tetroxide 2,2’-bipyridine (OsBp) to the C5–C6 pyrimidine double bond. The process is simple, selective for deoxythymidine (dT) over deoxycytidine (dC), unreactive towards the purines, practically 100% effective, and strikingly

• above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA. Keywords: DNA sequencing; α-hemolysin; ion-channel measurements; nanopore; osmium tetroxide bipyridine; osmylated oligos; osmylation; single-stranded DNA (ssDNA); Introduction

• sequencing (see Figure 1 and [46][47]). The proposition was motivated by studies showing that the osmylation [48] is a remarkably clean reaction yielding the expected products in practically 100% yield with no detectable side-reactions. An example is provided in Figure 2 where the reaction between OsBp and