Disclosed is a method of functional genomics determination including transducing a cell population with a set of nucleic acid molecules including a pooled library of genomic perturbagens to integrate multiple perturbagen cassettes into the genome. A phenotype of individual cells is determined and single cells of the population with targeted phenotypes are individually sorted into a set of compartments. Each compartment includes a forward primer with a nucleic acid sequence (NAS) that specifically binds a common nucleic acid sequence on the nucleic acid molecules and a compartment (cell)-specific nucleic acid barcode. Also included is a reverse primer with a NAS that specifically binds a common NAS on the nucleic acid molecules comprising a pooled library of genomic perturbagens. The genome-integrated perturbagen cassettes are create amplicons which are pooled and sequences determined. This method can be applied to other genome-level single-cell applications-immune receptor profiling, targeted DNA/RNA sequencing, and metagenomics.

Provided herein are methods for enriching a sample for nucleic acid sequences of interest, methods of serially depleting a sample of nucleic acids, and related kits. In some embodiments, the methods comprise a pre-depletion comprising phosphatase treatment of nucleic acids, cleavage with a plurality of nucleic acid-guided nuclease-guide nucleic acid (gNA) complexes, and exonuclease digestion of the nucleic acids.

The disclosure generally relates to compositions and methods for the production of nucleic acid molecules. In some aspects, the invention allows for the microscale generation of nucleic acid molecules, optionally followed by assembly of these nucleic acid molecules into larger molecules. In some aspects, the invention allows for efficient production of nucleic acid molecules (e.g., large nucleic acid molecules such as genomes).

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.

The present invention relates to innovative means of generating sequence-linked DNA fragments and subsequent uses of such linked DNA fragments for de novo haplotype-resolved whole genome mapping and massively parallel sequencing. In various embodiments described herein, the methods of the invention relate to methods of generating paired-end nucleic acid fragment sharing common linker nucleic acid sequences using a nicking endonuclease, a T7 endonuclease, a restriction enzyme, or a transposase, methods of analyzing the nucleotides sequences from the linked-paired-end sequenced fragments, and methods of de novo whole genome mapping. Thus, the methods of this invention allow establishing sequence contiguity across the whole genome, and achieving high-quality, low-cost de novo assembly of complex genomes.

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA.

Object of the present invention is to develop an artificial synthesis system of various peptides having an azole derivative structure and develop a library of such peptides. The present invention provides a method of producing a peptide having, in the backbone thereof, an azole derivative structure comprising the step of: synthesizing a substrate peptide of an azoline structure introducing enzyme having, in the modified region thereof, at least any one of the following amino acids, ##STR00001##
[in any of the compounds, X.sub.1 represents a group selected from the group consisting of SH, OH, NH.sub.2, SR.sup.1, OR.sup.1, NHR.sup.1, and N.sub.3 (R.sup.1 represents a protecting group), X.sub.2 represents an easily eliminable group; and X.sub.3 represents hydrogen or a substituted or unsubstituted alkyl or aryl group having from 1 to 10 carbon atoms]; reacting the substrate peptide with an azoline structure introducing enzyme to obtain a peptide having an azoline derivative structure; and converting the azoline derivative structure of the resulting peptide into an azole derivative structure by inducing an HX.sub.2 elimination reaction of X.sub.2 group.

The invention provides methods for generating a nucleic acid library. Target-specific primer-probes are hybridized to a target nucleic acid fragment to create a hybridization product. Each of the target-specific primer-probes comprises a target-specific sequence and a first adaptor sequence. The target nucleic acid fragment comprises a target genomic region of interest, wherein said target genomic region of interest comprises an exon of a gene and the target-specific primer-probes are tiled across the exon of the gene. The target nucleic acid fragment further comprises a second adaptor sequence different from said first adaptor sequence. Following hybridization, the target-specific primer-probes are extended to create double-stranded extension products and further amplified, thereby generating the nucleic acid library.