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

• properties of the degradation products via nanopore translocation can be evaluated to assure base calling quality in a DNA sequencing effort. Keywords: α-hemolysin; capillary electrophoresis; DNA sequencing; high-performance liquid chromatography; nanopores; osmium tetroxide bipyridine; osmylated oligos

• (OsBp). (b–d) confirm by spiking with increasing amounts of U-oligo that this minor product/degradant peak comigrates with the smaller of the two isomers of A10U(OsBp)A4, and its increase over time would have been clearly detectable. HPLC profiles of weeks-old-aged osmylated oligos. C* is an

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

• 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

• OsBp moiety that disrupts base stacking interactions [49]. This feature implies that any ssDNA of unknown sequence can be predictably osmylated. Additionally osmylated oligos and osmylated ssDNA are stable at room temperature for days as shown by CE analysis both in the presence of OsBp, or after

• native base, and led to a proposed sequencing strategy (Figure 1). Preliminary experiments to assess pore size suitability using solid-state silicon nitride nanopores [50] showed that 1.6 nm wide pores permit translocation of 80-mer long osmylated oligos, and exhibit dramatic translocation slowdown with