Abstract: This invention provides compounds and processes that allow enzymes to catalyze the copying of DNA and RNA molecules to make complements where individual nucleotides are replaced in a rule-based fashion by other nucleotides, using biversal nucleotides that pair with two different nucleotides.

Abstract: Disclosed here are compositions of matter that comprise DNA analogues that have been rectified by replacing the four standard components with alternative components that mitigate various problems frequently encountered during synthesis of these compounds, during the functioning of these compounds, and complex mixtures for information data storage.

Abstract: This invention covers methods for isothermal amplification of DNA, based on the unexpected discovery that primers having, at some positions, adenine substituted by 2-aminopurine or diaminopurine, guanine substituted by inosine, thymine substituted by 2-thiothymine, and cytosine substituted by N4-ethylcytosine are accepted by enzymes used in standard recombinase polymerase assays (RPA). Further unexpected was the discovery that target nucleotides are efficiently amplified in an RPA-like process (hereinafter abbreviated as simply RPA) using substituted primers. The invention also covers RPA-like processes that use substituted primers tagged with oligonucleotides incorporating nucleotides from artificially expanded genetic information systems (AEGIS).

Abstract: This invention relates to processes that amplify, in a polymerase chain reaction architecture, oligonucleotide analogs that incorporate non-standard nucleobase analogs from an artificially expanded genetic information system. These pair in DNA duplexes via patterns of hydrogen bonds that are different from patterns that join the thymine-adenine and guanine-cytosine nucleobase pairs.

Abstract: The invention concerns methods for applying evolutionary analyses to a set of aligned homologous protein sequences for the purpose of predicting a consensus model for the folded secondary structure of a protein family, identifying distant homologs and denying distant homology, assigning functional behavior to protein families, identifying protein pairs that interact as they function, identifying episodes of sequence evolution where functional behavior within a family is changing, and identifying specific chemical units of the protein that change in concert with changes in functional behavior. Accordingly, this invention is relevant to the use of genomic information to understand homology, fold, behavior and function in proteins.