Developing a programmed restriction endonuclease for highly specific DNA cleavage

Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4–8 bp are not sufficiently specific for this purpose. In principle, the specificity of REases can be extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or triple-helix forming oligonucleotides (TFO). We have chosen to extend the specificity of REases using TFOs, given the combinatorial flexibility this fusion offers in addressing a short, yet precisely recognized restriction site next to a defined triple-helix forming site (TFS). We demonstrate here that the single chain variant of PvuII (scPvuII) covalently coupled via the bifunctional cross-linker N-(γ-maleimidobutryloxy) succinimide ester to a TFO (5′-NH(2)-[CH(2)](6 or 12)-MPMPMPMPMPPPPPPT-3′, with M being 5-methyl-2′-deoxycytidine and P being 5-[1-propynyl]-2′-deoxyuridine), cleaves DNA specifically at the recognition site of PvuII (CAGCTG) if located in a distance of approximately one helical turn to a TFS (underlined) complementary to the TFO (‘addressed’ site: 5′-TTTTTTTCTCTCTCTCN(∼10)CAGCTG-3′), leaving ‘unaddressed’ PvuII sites intact. The preference for cleavage of an ‘addressed’ compared to an ‘unaddressed’ site is >1000-fold, if the cleavage reaction is initiated by addition of Mg(2+) ions after preincubation of scPvuII-TFO and substrate in the absence of Mg(2+) ions to allow triple-helix formation before DNA cleavage. Single base pair substitutions in the TFS prevent addressed DNA cleavage by scPvuII-TFO

Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI

Hydrolytic deamination of cytosines in DNA creates uracil and, if unrepaired, these lesions result in C to T mutations. We have suggested previously that a possible way in which cells may prevent or reduce this chemical reaction is through the binding of proteins to DNA. We use a genetic reversion assay to show that a restriction enzyme, PspGI, protects cytosines within its cognate site, 5′-CCWGG (W is A or T), against deamination under conditions where no DNA cleavage can occur. It decreases the rate of cytosine deamination to uracil by 7-fold. However, the same protein dramatically increases the rate of deaminations within the site 5′-CCSGG (S is C or G) by ∼15-fold. Furthermore, a similar increase in cytosine deaminations is also seen with a catalytically inactive mutant of the enzyme showing that endonucleolytic ability of the protein is dispensable for its mutagenic action. The sequences of the mutants generated in the presence of PspGI show that only one of the cytosines in CCSGG is predominantly converted to thymine. Our results are consistent with PspGI ‘sensitizing’ the cytosine in the central base pair in CCSGG for deamination. Remarkably, PspGI sensitizes this base for damage despite its inability to form stable complexes at CCSGG sites. These results can be explained if the enzyme has a transient interaction with this sequence during which it flips the central cytosine out of the helix. This prediction was validated by modeling the structure of PspGI–DNA complex based on the structure of the related enzyme Ecl18kI which is known to cause base-flipping

Cucurbiturils as supramolecular inhibitors of DNA restriction by type II endonucleases

Cucurbiturils (CB6 and CB7) were shown to inhibit the enzymatically catalyzed restriction of plasmids and linear DNA. This effect can be inverted by supramolecular masking of the macrocycles through competitive complexation with polyamines. These experiments provide supramolecular control of biocatalytic processes.Spanish MINECO [CTQ2011-28390]; FEDER; COST [CM1005]; DFG [NA-686/5]; Portuguese FCT [SFRH/BD/81628/2011, PEst-OE/EQB/LA0023/2013

Two-chain structure of the interleukin 1 receptor

AbstractBy crosslinking radioiodinated recombinant human IL1 α to mouse EL4 thymoma cells we have identified in addition to the known IL1-binding proteins of 80 kDa, a second IL1-binding protein of about 40 kDa. This second binding protein could be demonstrated most easily when crosslinking to higher protein complexes was inhibited. This finding suggests that the IL1 receptor, similar to the receptor for other cytokines such as interleukin 2, is composed of a heterodimer, of which both polypeptides contribute to ligand binding