Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping.
DNA looping is one of the key factors allowing proteins bound to different DNA sites to signal one another via direct contacts. We demonstrate that DNA looping can be generated in an arbitrary chosen site by sequence-directed targeting of double-stranded DNA with pseudocomplementary peptide-nucleic acids (pcPNAs). We designed pcPNAs to mask the DNA from cleavage by type IIs restriction enzyme PleI while not preventing the enzyme from binding to its primary DNA recognition site. Direct interaction between two protein molecules (one bound to the original recognition site and the other to a sequence-degenerated site) results in a totally new activity of PleI: it produces a nick near the degenerate site. The PNA-induced nicking efficiency varies with the distance between the two protein-binding sites in a phase with the DNA helical periodicity. Our findings imply a general approach for the fine-tuning of proteins bound to DNA sites well separated along the DNA chain.
Protozanova
Ekaterina
E
Center for Advanced Biotechnology, Boston University, MA 02115, USA.
Demidov
Vadim V
VV
Soldatenkov
Viatcheslav
V
Chasovskikh
Sergey
S
Frank-Kamenetskii
Maxim D
MD
D001483:Base Sequence; D004247:DNA / Q000235:genetics* / Q000648:ultrastructure; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism* / Q000502:physiology; D019281:Dimerization; D018625:Microscopy, Atomic Force; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry; D017422:Sequence Analysis, DNA; D013997:Time Factors
D010455:Peptides; D004247:DNA; C075306:endodeoxyribonuclease PleI; D015252:Deoxyribonucleases, Type II Site-Specific