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A facilitated diffusion mechanism has been proposed to account for the kinetic efficiency with which restriction endonucleases are able to locate DNA recognition sites. Such a mechanism involves the initial formation of a nonspecific complex upon collision of the protein with the DNA, with the subsequent diffusion of the protein along the DNA helix until either a recognition site is located or the protein dissociates into solution. Protein translocation may be facilitated by either sliding along the DNA, hopping to nearby sites, or intersegment transfer over larger distances. Previous analyses of the manner in which restriction enzymes cleave DNA substrates did rule out the latter mechanism. To discriminate between protein sliding or scanning and protein hopping, we designed a unique DNA template with three overlapping, mutually exclusive recognition sites for the BssHII endonuclease. Analysis of the cleavage pattern demonstrated efficient usage of both external sites, whereas the centrally located site was not efficiently cleaved. These results confirm that linear diffusion of the BssHII enzyme occurs by scanning along the DNA. Furthermore, the scanning enzyme was found to stop and cleave at the first site encountered. Thus, a sliding restriction endonuclease recognizes cleavage sites with high fidelity, without skipping of potential sites.It is unlikely that site-specific DNA-binding proteins locate their target site by simple three-dimensional diffusion or trialand-error mechanism (reviewed in Ref. 1). In many cases, proteins use a nonspecific DNA binding affinity to remain attached to the DNA, where it moves freely and rapidly along the length of the DNA in search of specific target sequences. This mechanism will reduce the dimensionality of the search process and consequently speed up the rate of target location. Several mechanisms for the facilitated transfer of protein along a DNA ligand have been proposed (2). These include a sliding mechanism along the DNA and several types of dissociation-reassociation processes (e.g. hopping over short distances or intersegment transfer). This translocation reaction is interrupted either by location of and binding to the specific target site or by dissociation of the protein from the DNA molecule. The sliding or scanning mechanism has been observed for several DNAinteracting proteins like the Escherichia coli lac repressor (reviewed in Ref.3), RNA polymerase (4, 5), and Micrococcus luteus UV endonuclease (6).Despite their abundant use in molecular biology, only a few restriction endonucleases have been studied seriously as DNAbinding enzymes. The best understood of the type II restriction enzymes is the EcoRI endonuclease (7-10). Diffusion mechanisms along the DNA helix contour have been proposed to account for the kinetic efficiency with which this protein is able to locate its recognition and cleavage sites. Similar diffusion/ sliding/scanning mechanisms have been proposed for the HindIII and BamHI endonucleases, as well as for the BamHI methylase enzyme (10, 11).Kn...

Abstract. An extension of process algebra for modelling processes with backtracking is introduced. This extension is semantically based on processes that transform data because, in our view, backtracking is the undoing of the effects caused by a process in some initial data-state if this process fails. The data-states are given by a data environment, which is a structure that also defines in which data-states guards hold, and how (atomic) actions either transform these states or block and prevent subsequent processes from being executed. State operators are used to relate process terms to a given data environment. Backtracking is axiomatised in a few phases. First guarded commands (conditionals) and a standard ~ype of guards, expressing the enabledness of actions, are added to basic process algebra (process algebra without operators for parallelism) by involving a Boolean algebra. Then the set of actions is partitioned in order to distinguish between different types of behaviour of actions in the scope of a (binary) operator for backtracking. Also functions on actions are defined that change the 'type' of an action. Next an axiom system for modelling processes with backtracking is presented, and it is proved that backtracking is associative, provided that some semantic constraints are satisfied. Finally a method for recursively specifying processes is defined and an example of a recursively defined process with backtracking is provided. An operational semantics is defined relative to the Boolean algebra, describing transitions between process terms labelled with 'guarded actions'. The operational semantics is studied modulo strong bisimulation equivalence.