title: A new class of genome rare cutters.
abstract: Although significant efforts have been directed at developing efficient techniques for rare and super rare genome cutting, only limited success has been achieved. Here we propose a new approach to solve this problem. We demonstrate that peptide nucleic acid 'clamps' (bis-PNAs) bind strongly and sequence specifically to short homopyrimidine sites on lambda and yeast genomic DNAs. Such binding efficiently shields methylation/restriction sites which overlap with the bis-PNA binding sites from enzymatic methylation. After removing the bis-PNA, the genomic DNAs are quantitatively cleaved by restriction enzymes into a limited number of pieces of lengths from several hundred kbp to several Mbp. By combining various bis-PNAs with different methylation/restriction enzyme pairs, a huge new class of genome rare cutters can be created. These cutters cover the range of recognition specificities where very few, if any, cutters are now available.
authors.affiliation: Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
authors.forename: A G
authors.initials: AG
authors.lastname: Veselkov
authors.forename: V V
authors.initials: VV
authors.lastname: Demidov
authors.forename: P E
authors.initials: PE
authors.lastname: Nielson
authors.forename: M D
authors.initials: MD
authors.lastname: Frank-Kamenetskii
mesh_terms: D001483:Base Sequence; D015825:Chromosomes, Fungal / Q000235:genetics; D015280:DNA Restriction-Modification Enzymes / Q000378:metabolism*; D004271:DNA, Fungal / Q000235:genetics* / Q000378:metabolism; D016681:Genome, Fungal; D008239:Lysine / Q000031:analogs & derivatives; D008967:Molecular Biology / Q000379:methods*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D015280:DNA Restriction-Modification Enzymes; D004271:DNA, Fungal; D009841:Oligonucleotides; D008239:Lysine