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

Title False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2'-bipyridine.
Authors A. Kanavarioti
Journal Beilstein J Nanotechnol
DOI 10.3762/bjnano.7.135
Abstract

Osmium tetroxide 2,2'-bipyridine (OsBp) is known to react with pyrimidines in ssDNA and preferentially label deoxythymine (T) over deoxycytosine (C). The product, osmylated DNA, was proposed as a surrogate for nanopore-based DNA sequencing due to OsBp's "perfect" label attributes. Osmylated deoxyoligos translocate unassisted and measurably slow via sub-2 nm SiN solid-state nanopores, as well as via the alpha-hemolysin (?-HL) pore. Both nanopores discriminate clearly between osmylated and intact nucleobase; ?-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 mM OsBp. Under the proposed labeling conditions: deoxyoligo backbone degradation measures less than 1/1,000,000; false positives such as osmylated deoxyadenine (A) and osmylated deoxyguanine (G) measure less than 1/100,000; false negatives, i.e., unosmylated C measure less than 1/10,000; and unosmylated T must measure substantially lower than 1/10,000 due to the 27-fold higher reactivity of T compared to C. However, osmylated C undergoes degradation that amounts to about 1-2% for the duration of the labeling protocol. This degradation may be further characterized, possibly suppressed, and the properties of the degradation products via nanopore translocation can be evaluated to assure base calling quality in a DNA sequencing effort.

Citation A. Kanavarioti.False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2'-bipyridine.. Beilstein J Nanotechnol. 2016;7:14341446. doi:10.3762/bjnano.7.135

Related Elements

Osmium

See more Osmium products. Osmium (atomic symbol: Os, atomic number: 76) is a Block D, Group 8, Period 6 element with an atomic weight of 190.23. Osmium Bohr ModelThe number of electrons in each of osmium's shells is [2, 8, 18, 32, 14, 2] and its electron configuration is [Xe] 4f14 5d6 6s2. The osmium atom has a radius of 135 pm and a Van der Waals radius of 216 pm. Osmium was discovered and first isolated by Smithson Tennant in 1803. Elemental OsmiumIn its elemental form, osmium has a silvery blue cast apperance. Osmium has the highest melting point and the lowest vapor pressure of any of the platinum group of metals it is also the densest naturally ocurring element. Osmium is the least abundant stable element in the earth's crust. It is found in the alloys osmiridium and iridiosmium and as a free element. The origin of the name Osmium comes from the Greek word osme, meaning a smell or odor.

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