Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.

Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.

Provided are compositions, methods, and kits for improving CRISPR-based editing of DNA targets by a CRISPR-associated (Cas) enzyme. The improvement is made by combining the Cas enzyme and a CRISPR targeting RNA a heterologous DNA repair enzyme that is at least one of RecBCD, AddAB, or AdnAB. The heterologous DNA repair enzyme may have inactivated nuclease activity. The method can include using a DNA repair template to introduce one or more changes into the edited DNA. Cells that contain components of the improved CRISPR systems are included, as are kits for making such cells.

Provided are compositions, methods, and kits for improving CRISPR-based editing of DNA targets by a CRISPR-associated (Cas) enzyme. The improvement is made by combining the Cas enzyme and a CRISPR targeting RNA a heterologous DNA repair enzyme that is at least one of RecBCD, AddAB, or AdnAB. The heterologous DNA repair enzyme may have inactivated nuclease activity. The method can include using a DNA repair template to introduce one or more changes into the edited DNA. Cells that contain components of the improved CRISPR systems are included, as are kits for making such cells.

Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.

A method for preparing circular double stranded mitochondrial DNA (mtDNA) substantially free of genomic DNA (gDNA) comprising the steps of: providing a cellular lysate free of protein and RNA contaminants, precipitating cellular debris and proteins out of said lysate and obtaining a solution comprising purified circular double stranded mitochondrial DNA (mtDNA) and genomic DNA (gDNA), incubating said solution with an amount of Hind Exonuclease V for a time and at a temperature effective to cleave non-circular DNA and obtain circular double stranded mtDNA, incubating said circular double stranded mtDNA with an amount of Ampure beads effective to bind said circular double stranded mtDNA, washing said beads with ethanol, and eluting said mtDNA from said beads, wherein said method is free of ultra-centrifugation.

Methods and reagents for related kits are provided for assessing enrichment of extrachromosomal circular DNA (ec-cDNA) isolated from biological samples. The methods include spiking the biological samples with a known proportion of linearized and circular plasmid DNA molecules and measuring their relative amounts post-exonuclease treatment as a benchmark to validate enrichment of eccDNA in the isolation process. Alternatively, or in combination, the method includes measuring the relative amounts of endogenous mitochondrial DNA and chromosomal DNA post-exonuclease treatment to assess the enrichment of eccDNA in the isolation process.

A nucleotide production process comprises: decomposing an RNA by using a nuclease P1 so as to obtain nucleotides AMP, GMP, CMP and UMP, converting part or all of the nucleotide AMP into a nucleotide IMP by using adenosine deaminase, separating the obtained nucleotide by using an ion exchange resin, and then performing concentration and crystallization to obtain purified nucleotides AMP, GMP, CMP, UMP and IMP or obtain purified nucleotides GMP, CMP, UMP and IMP. The whole biocatalysis production of nucleotides is implemented by using a double-enzyme catalysis method, and high-purity nucleotides are obtained by using an ion resin separation technology and a solvent crystallization method; and the production process is simple and environmentally-friendly, and has low costs, high product safety and purity.

Sequencing adaptors and methods are provided for preparation of polynucleotides for sequencing. The sequencing adaptors contain a portion of a recognition sequence for a methyl-dependent endonuclease. Unwanted adaptor dimers that form during ligation of adaptors to target polynucleotides produce a complete restriction sequence and are cleaved by the endonuclease, followed by exonuclease digestion, thereby removing the dimers.