Propagation of melting cooperativity along the phosphodiester backbone of DNA

The role of the DNA phosphodiester backbone in the transfer of melting cooperativity between two helical domains was experimentally addressed with a helix-bulge-helix DNA model, in which the bulge consisted of a varying number of either conformationally flexible propanediol or conformationally constrained bicyclic anucleosidic phosphodiester backbone units. We found that structural communication between two double helical domains is transferred along the DNA backbone over the equivalent of ca. 12-20 backbone units, depending on whether there is a symmetric or asymmetric distribution of the anucleosidic units on both strands. We observed that extension of anucleosidic units on one strand only suffices to disrupt cooperativity transfer in a similar way as if extension occurs on both strands, indicating that the length of the longest anucleosidic inset determines cooperativity transfer. Furthermore, conformational rigidity of the sugar unit increases the distance of coopertivity transfer along the phosphodiester backbone. This is especially the case when the units are asymmetrically distributed in both strands

Propagation of Behavioral Variations with Delegation Proxies

Scoping behavioral variations to dynamic extents is useful to support non-functional concerns that otherwise result in cross-cutting code. Unfortunately, such forms of scoping are difficult to obtain with traditional reflection or aspects. We propose delegation proxies, a dynamic proxy model that supports behavioral intercession through the interception of various interpretation operations. Delegation proxies permit different behavioral variations to be easily composed together. We show how delegation proxies enable behavioral variations that can propagate to dynamic extents. We demonstrate our approach with examples of behavioral variations scoped to dynamic extents that help simplify code related to safety, reliability, and monitoring.