Effect of supercoiling on formation of protein-mediated DNA loops.

DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic rod model of DNA to determine the free energy of forming short (50-100 basepair), protein mediated DNA loops. Superhelical stress in the DNA of living cells is a critical factor determining the energetics of loop formation, and we explicitly account for it in our calculations. The repressor protein itself is regarded as a rigid coupler; its geometry enters the problem through the boundary conditions it applies on the DNA. We show that a theory with these ingredients is sufficient to explain certain features observed in modulation of in vivo gene activity as a function of the distance between operator sites for the lac repressor. We also use our theory to make quantitative predictions for the dependence of looping on superhelical stress, which may be testable both in vivo and in single-molecule experiments such as the tethered particle assay and the magnetic bead assay.

Theory of high-force DNA stretching and overstretching.

Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.

Mapper: an intelligent restriction mapping tool.

MOTIVATION: To determine the most powerful artificial intelligence techniques for automated restriction mapping, and use them to create a powerful multiple-enzyme restriction mapping tool. RESULTS: The most effective search engine utilized model-driven exhaustive search and a form of binary logic pruning based on Pratt's separation theory. Additional experimentation led to the development of an input preprocessing module which significantly speeds up searches, and an output post-processing module which enables users to analyze large solution sets and reduce their apparent complexity. AVAILABILITY: An executable version of the resultant tool, Mapper, can be downloaded from our Web site (http://www.ai.eecs.uic.edu) by selecting the 'Software' option. CONTACT: nelson@eecs.uic.edu (http://www.ai.eecs.uic.edu/ñelson).

On the limitations of automated restriction mapping.

Eight important restriction mapping programs, developed between 1978 and 1993, are analyzed and their performance evaluated. The analyses concentrate on the practical value of the programs to molecular biologists who do restriction mapping on a daily basis, rather than on theoretical efficiency. Although all of the programs could find maps consistent with the data, none were able to discriminate reliably the true map from the other consistent maps, given realistic levels of error. To alleviate this problem, we propose an expert mapping system which utilizes the same inferences and mapping techniques used by expert human mappers to reduce the number of false maps found.

Design of custom hip stem prostheses using three-dimensional CT modeling.

Long life expectancy, demand for high activity levels, and bone loss at the time of revision motivate the search for reliable and successful noncemented hip stem designs. It is hypothesized that improved implant fit may increase the longevity of noncemented total joints. Quantitative X-ray CT has enabled the use of a computerized stem design program, which designs an optimal-fit hip stem for individual femurs. Computed tomography and interactive image processing methods are used to generate the individual three-dimensional femoral models, which are used by the stem design program. Optimal-fit design provides maximum stem-bone contact while satisfying the requirement of being surgically insertable. Previous methods of custom implant design, including those that use three-dimensional CT modeling, have not provided optimal stem-bone fit. Quantitative results of this new process are presented.

A compliant interface for total knee arthroplasty.

Low pressure sensitive Fujifilm was used to measure the load distribution between the resected tibial surface and a tibial component at axial loads up to 3,000 N for a rigid interface, a compliant interface of dacron double-sided velour, and a cemented interface. The pressure patterns consisted of a multitude of small red dots, generally reflecting the slight irregularities of the cut surface and the stiffness of the cancellous bone at the surface. The pressure patterns were photographed with high-contrast film and input into a computer using a photodiode matrix camera. The data were analyzed to yield the number of contact points for each sample. The velour was more effective in distribution of load to the proximal tibia than the rigid and cemented interfaces, while there was no significant difference between the cemented interface and the rigid interface. A second series of tests showed significant increases in contact points from rigid to one layer to two layers of velour. Cyclic axial loading tests were performed to study the characteristics of rigid and compliant interfaces in a model of in vitro subsidence. Static pressure patterns taken at regular intervals showed that subsidence occurred in vitro in up to 1/3 of the tibias, and that the regions of load transfer could change with time. A model of subsidence was proposed and it was suggested that a velour layer could inhibit the subsidence.