RNA and DNA strands produce ionic current signatures when driven through an alpha-hemolysin channel by an applied voltage. Here we combine this nanopore detector with a support vector machine (SVM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length. This nanopore instrument can discriminate between individual DNA hairpins that differ by one base pair or by one nucleotide.

We introduce a computational method for classification of individual DNA molecules measured by an alpha-hemolysin channel detector. We show classification with better than 99% accuracy for DNA hairpin molecules that differ only in their terminal Watson-Crick basepairs. Signal classification was done in silico to establish performance metrics (i.e., where train and test data were of known type, via single-species data files). It was then performed in solution to assay real mixtures of DNA hairpins. Hidden Markov Models (HMMs) were used with Expectation/Maximization for denoising and for associating a feature vector with the ionic current blockade of the DNA molecule. Support Vector Machines (SVMs) were used as discriminators, and were the focus of off-line training. A multiclass SVM architecture was designed to place less discriminatory load on weaker discriminators, and novel SVM kernels were used to boost discrimination strength. The tuning on HMMs and SVMs enabled biophysical analysis of the captured molecule states and state transitions; structure revealed in the biophysical analysis was used for better feature selection.

We consider the Hamiltonian dynamics and thermodynamics of spherically symmetric Einstein-Maxwell spacetimes with a negative cosmological constant. We impose boundary conditions that enforce every classical solution to be an exterior region of a Reissner-Nordström-anti-de Sitter black hole with a nondegenerate Killing horizon, with the spacelike hypersurfaces extending from the horizon bifurcation two-sphere to the asymptotically anti-de Sitter infinity. The constraints are simplified by a canonical transformation, which generalizes that given by Kuchař in the spherically symmetric vacuum Einstein theory, and the theory is reduced to its true dynamical degrees of freedom. After quantization, the grand partition function of a thermodynamical grand canonical ensemble is obtained by analytically continuing the * Dedicated to Karel Kuchař on the occasion of his sixtieth birthday. (Physical Review D did not, alas, permit a dedication in the published version of this paper.) † On leave

Figure 4. Comparison of single-mismatch detection with gold-quenched beacons versus DABCYL-quenched beacons. Titration of 5 µM of random target mixed with 4.2 nM of gold-DNA-rhodamine 6G conjugate and 0.6 µM of gold (A), and 5 µM of random target mixed with 10 nM of molecular beacon (B), with the perfect target (target 2) and the mismatch one (target 3). Target concentrations vary from 67 pM to 13 µM. For both probes, the perfect target (solid line) produces a faster and sharper increase of fluorescence than the target containing the mismatch (dashed line). Fluorescence intensities due to the buffer and the gold have been subtracted. The inset graphs in (A) and (B) show the evolution of the fluorescence as a function of time when the probe is mixed with 5 µM of random targets. In both cases, the random targets do not induce any change of fluorescence of the probe during the time of the titration. The hybridization is thus very specific to the matched or the mismatched targets. (C) Ratio between the titration curve with the perfect target (target 2) and the titration curve with the mismatched one (target 3). (D) Resolution of a matched and a mismatched target, competing for hybridization. Molecular beacon (dashed line), gold-DNA-dye conjugate (solid line). α is the population ratio of match to mismatch targets. The concentration of perfect target is fixed at 0.2 µM. D