Estimating error rates for single molecule protein sequencing experiments.

The practical application of new single molecule protein sequencing (SMPS) technologies requires accurate estimates of their associated sequencing error rates. Here, we describe the development and application of two distinct parameter estimation methods for analyzing SMPS reads produced by fluorosequencing. A Hidden Markov Model (HMM) based approach, extends whatprot, where we previously used HMMs for SMPS peptide-read matching.

Robust and scalable single-molecule protein sequencing with fluorosequencing.

The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing.

Estimating error rates for single molecule protein sequencing experiments.

The practical application of new single molecule protein sequencing (SMPS) technologies requires accurate estimates of their associated sequencing error rates. Here, we describe the development and application of two distinct parameter estimation methods for analyzing SMPS reads produced by fluorosequencing. A Hidden Markov Model (HMM) based approach, extends , where we previously used HMMs for SMPS peptide-read matching.

Metal Coordination to Ligand-Modified Peptide Nucleic Acid Triplexes.

A challenging goal in nanotechnology is the precise and programmable arrangement of specific elements in nanosystems in the three-dimensional space. The use of ligand-modified nucleic acids represents an accurate and selective tool to achieve this goal when it comes to metal ion organization. The synthesis of peptide nucleic acid (PNA) monomers that contain ligands instead of nucleobases makes possible the creation of metal-mediated alternative base pairs and triplets at specific locations in PNA duplexes and triplexes, respectively.

Strong Ferromagnetic Exchange Coupling Mediated by a Bridging Tetrazine Radical in a Dinuclear Nickel Complex.

The radical bridged compound [(Ni(TPMA))-μ-bmtz](BF)·3CHCN (bmtz = 3,6-bis(2'-pyrimidyl)-1,2,4,5-tetrazine, TPMA = tris(2-pyridylmethyl)amine) exhibits strong ferromagnetic exchange between the S = 1 Ni centers and the bridging S = 1/2 bmtz radical with J = 96 ± 5 cm (-2JSS). DFT calculations support the existence of strong ferromagnetic exchange.

Spectroscopic and Theoretical Study of Spin-Dependent Electron Transfer in an Iron(III) Superoxo Complex.

It was shown previously (J. Am. Chem.

Spin crossover in tetranuclear Fe(II) complexes, {[(tpma)Fe(μ-CN)]4}X4 (X = ClO4(-), BF4(-)).

Two Fe(II) complexes, {[(tpma)Fe(μ-CN)]4}X4 (X = ClO4(-) (1a), BF4(-) (1b); tpma = tris(2-pyridylmethyl)amine), were prepared by reacting the {Fe(tpma)}(2+) building block with (Bu4N)CN. The crystal structures of 1a and 1b feature a tetranuclear cation composed of cyanide-bridged Fe(II) ions, each capped with a tetradentate tpma ligand. The Fe4(μ-CN)4 core of the complex is strongly distorted, assuming a butterfly-like geometry.

Characterization of a paramagnetic mononuclear nonheme iron-superoxo complex.

O2 bubbling into a THF solution of Fe(II)(BDPP) (1) at -80 °C generates a reversible bright yellow adduct 2. Characterization by resonance Raman and Mössbauer spectroscopy provides complementary insights into the nature of 2. The former shows a resonance-enhanced vibration at 1125 cm(-1), which can be assigned to the ν(O-O) of a bound superoxide, while the latter reveals the presence of a high-spin iron(III) center that is exchange-coupled to the superoxo ligand, like the Fe(III)-O2(-) pair found for the O2 adduct of 4-nitrocatechol-bound homoprotocatechuate 2,3-dioxygenase.