Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering recombination inside or outside of a cell using isolated and/or purified polypeptides and/or nucleic acid sequences from Alicyclobacillus acidocaldarius.

The invention provides methods of transforming photosynthetic organisms, such as green algae. The methods involve methylating one or more DNA fragments of a DNA construct and transforming the one or more fragments into the photosynthetic organism. The DNA fragments can be the product of a DNA amplification procedure, such as PCR or a PCR-like procedure. In one embodiment the one or more fragments of DNA that comprise a DNA construct are dam methylated prior to being transformed into the photosynthetic organism.

This disclosure provides CRISPR/Cas9 based fusion molecules and guide RNAs for use in in vivo targeted reduction or elimination of PCSK9 gene products. This disclosure also relates to formulations, methods of production and methods of use thereof.

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering recombination inside or outside of a cell using isolated and/or purified polypeptides and/or nucleic acid sequences from Alicyclobacillus acidocaldarius.

Disclosed herein are artificially synthesized nucleic acid constructs to guide an epigenetic modification for at least partially silencing or activating a target gene in an organism such as a plant or seed, and formulations thereof. Also disclosed are methods of applying such nucleic acid constructs to the plant or to the seed. Also disclosed are engineered seeds and plants obtained by the epigenetic modification.

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering recombination inside or outside of a cell using isolated and/or purified polypeptides and/or nucleic acid sequences from Alicyclobacillus acidocaldarius.

The invention relates to a novel enzyme composition comprising at least two different thermostable polypeptides having type II DNA methyltransferase activity as well as a restriction/modification system in particular for the transformation of microorganisms of the genus Caldicellulosiruptor, wherein said polypeptides methylate an adenine in a asymmetric DNA recognition site, where the adenine nucleotide is followed by a thymine nucleotide in the linear sequence of bases along its 5.fwdarw.3 direction, wherein the DNA recognition site is 5-GCATC-3 and/or wherein said polypeptide methylate the adenine in a complement DNA recognition site, where a thymine nucleotide is followed by a adenine nucleotide in the linear sequence of bases along its 3.fwdarw.5 direction, wherein the DNA recognition site is 3-CGTAG-5.

Provided herein is a method of detecting the presence or absence of a single naturally- or synthetically-modified nucleobase in a polynucleotide molecule, which is achieved by first contacting the polynucleotide molecule with one or more reagents capable of attaching a detectable moiety to at least one nucleobase of the polynucleotide molecule or to a nucleobase adjacent to the modified nucleobase, thereby forming a labeled nucleobase, while the presence or absence of the modified nucleobase is determined by the attachment. The polynucleotide molecule is then assayed using a nanopore device to detection the presence or absence of the labeled nucleobase, wherein the detectable moiety attached to at least one nucleobase in the polynucleotide molecule has a molecular weight that ranges from 40 to 1,000 Daltons, and the average pore diameter in the nanopore device is no more than 5 nanometers.

Provided herein are gene repressor systems comprising fusion proteins, such as fusion proteins comprising a DNA binding domain such as a TALE, zinc finger or catalytically-dead CRISPR protein and guide nucleic acid (gRNA), which are useful in the repression of a proprotein convertase subtilisin/kexin Type 9 (PCSK9) gene. Also provided are methods of using such systems to repress transcription of PCSK9.