On the symmetries of multi-palindromic DNA sequences

There are several instances of multiple, overlapping palindromes in DNA sequences which have recently been reported. To ascertain the likelihood of specific biological function for these interdigitating symmetries it is necessary to calculate their probabilities of occurrence. While the probability of occurrence of a single palindrome in a random sequence is calculated in a straightforward fashion, the occurrence of overlapping palindromes is not so simply analyzed. In this paper a general method for handling multiple symmetries is presented. Several theorems concerning the constraints which overlapping symmetries place on each other are presented. A general result is that the probability of occurrence of a symmetry can be significantly enhanced by already existing symmetries. As examples of the theorems and methods developed, the lac operator, the lac CAP-binding site and a region of the λ left operator are examined. The occurrence of several overlapping symmetries appears to be fairly common in such sequences.     

β-1, 3-Glucanase from trichoderma viride. Purification and characterization

The extracellular complex of β-glucanases produced by the mould Trichoderma viride hydrolyzes β-1,3-; β-1,4- and β-1, 6-bonds of β-glucans, as well as mixed β-1,3- and β-1,4-glycosidic linkages. This complex contains also xylanase. The enzymes were isolated from liquid culture medium by centrifuge techniques, concentration and precipitation with acetone. Isolation and purification of β-1,3-glucanase was carried out according to a procedure involving filtration on Bio-Gel P-100, DEAE-Sephadex A 50 and CM-cellulose C-11 chromatography, ultrafiltration and selective adsorption on xylan. The homogeneity of the enzyme was determined by polyacrylamidegel electrophoresis. The purified homogeneous preparation of the isolated β-1,3-glucanase from Tr. riride was subjected to detailed characterization. Amino acid composition, molecular weight and optimum conditions for the enzymatic activity of the protein were determined. The isolated enzyme was shown to be highly specific to substrates with β-1,3-glycosidic linkages; the rate of degradation was found to be proportional to the degree of polymerization of the substrate.     

Escherichia coli integration host factor bends the DNA at the ends of IS1 and in an insertion hotspot with multiple IHF binding sites.

The integration host factor of Escherichia coli (IHF) is a small, histone-like protein which participates in the integration of bacteriophage lambda into the E. coli chromosome and in a number of regulatory processes. Our recent footprinting analysis has shown that IHF binds specifically to the ends of the transposable element IS1, as well as to several sites within a short segment of the plasmid pBR322. We have extended our studies of the binding of the IHF molecule to these sites in vitro using a gel retardation assay. We report here that IHF bends the DNA upon binding, as judged from the strong cyclic dependence of the protein-induced mobility shift on the position of the binding site. Using cloned, synthetic ends of IS1 as substrates, we have found that some mutations within the conserved bases of the IHF consensus binding sequence abolish binding, and that alterations of the flanking sequences can greatly reduce IHF binding. The presence of multiple IHF sites on a single DNA fragment increases binding very little, indicating that IHF does not bind cooperatively in this complex. We discuss the possibility that DNA bending is related to the role IHF plays in forming and stabilizing nucleoprotein complexes, and suggest that bending at the IHF sites may be important to its diverse effects in the cell.