Abstract: Disclosed herein is a method for generating a nucleic acid library, the method involving: (a) providing a population of single-stranded nucleic acid templates, each of the templates including a coding sequence and an operably linked promoter sequence; (b) hybridizing to the population of single-stranded nucleic acid templates a mixture of substantially complementary single-stranded nucleic acid fragments, the fragments being shorter in length than the nucleic acid template; (c) contacting each of the hybridization products of step (b) with both a DNA polymerase which lacks strand displacement activity and a DNA ligase under conditions in which the fragments act as primers for the completion of a second nucleic acid strand which is substantially complementary to the nucleic acid template; and (d) contacting the products of step (c) with RNA polymerase to generate an RNA library, the library being transcribed from the second nucleic acid strand.

Abstract: In general, the invention features proteins having covalently bonded C-terminal puromycin tags and methods for their production.

Abstract: Disclosed herein is a method for generating a 5′-nucleic acid-protein conjugate, the method involving: (a) providing a nucleic acid which carries a reactive group at its 5′ end; (b) providing a non-derivatized protein; and (c) contacting the nucleic acid and the protein under conditions which allow the reactive group to react with the N-terminus of the protein, thereby forming a 5′-nucleic acid-protein conjugate. Also disclosed herein are 5′-nucleic acid-protein conjugates and methods for their use.

Abstract: Disclosed herein is a method for detecting a compound-protein interaction, involving: (a) providing a compound library in which each member of the compound library is immobilized on a solid support; (b) contacting each member of the immobilized compound library in a single reaction chamber with each member of a protein-nucleic acid fusion library under conditions which allow the formation of compound-fusion complexes; (c) isolating the immobilized compound-fusion complexes; and (d) detecting a compound-fusion complex as an indication that the protein of the fusion interacts with the compound. In preferred embodiments, the protein is identified by reading the nucleic acid portion of the fusion, and the compound is identified by reading a detectable tag bound to either the compound or the solid support.

Abstract: Disclosed herein are arrays of nucleic acid-protein fusions which are immobilized to a solid surface through capture probes which include a non-nucleosidic spacer group and an oligonucleotide sequence to which the fusion (such as an RNA-protein fusion) is bound. Also disclosed herein are solid supports on which these arrays are immobilized as well as methods for their preparation and use (for example, for screening for protein-compound interactions such as protein-therapeutic compound interactions).

Abstract: Disclosed herein are methods for detecting multiple compounds in a sample, involving: (a) contacting the sample with a mixture of binding reagents, the binding reagents being nucleic acid-protein fusions, each having (i) a protein portion which is known to specifically bind to one of the compounds and (ii) a nucleic acid portion which encodes the protein portion and which includes a unique identification tag; (b) allowing the protein portions of the binding reagents and the compounds to form complexes; (c) capturing the binding reagent-compound complexes; (d) amplifying the nucleic acid portions of the complexed binding reagents; and (e) detecting the unique identification tag of each of the amplified nucleic acids, thereby detecting the corresponding compounds in the sample. Also disclosed herein are kits for carrying out such methods.

Abstract: Described herein are methods and reagents for encoding and sorting in vitro translated proteins.

Abstract: Described herein are methods and reagents for the ligation of a peptide acceptor to an RNA, as well as the RNA-peptide acceptor products.

Abstract: Disclosed herein are molecules that include a deoxyribonucleic acid (DNA) covalently bonded to a protein and uses thereof.

Abstract: Described herein are methods for removing the 3′-untranslated regions from cDNA or mRNA molecules, as well as methods for the use of such products for RNA-protein fusion formation.