Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

The hybridization kinetics for a series of designed 25mer probe�target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments. Specifically, addition of three intramolecular base pairs in the probe and target structure slow hybridization by a factor of two. For individual strands containing four or more intramolecular base pairs, hybridization cannot be described by a traditional two-state model in solution-phase nor on the surface. Surface hybridization rates are also 20- to 40-fold slower than solution-phase rates for identical sequences and conditions. These quantitative findings may have implications for the design of better biosensors, particularly those using probes with deliberate secondary structure.

Optimal Scheduling of Secondary Content for Aggregation in Video-on-Demand Systems

Dynamic service aggregation techniques can exploit skewed access popularity patterns to reduce the costs of building interactive VoD systems. These schemes seek to cluster and merge users into single streams by bridging the temporal skew between them, thus improving server and network utilization. Rate adaptation and secondary content insertion are two such schemes. In this paper, we present and evaluate an optimal scheduling algorithm for inserting secondary content in this scenario. The algorithm runs in polynomial time, and is optimal with respect to the total bandwidth usage over the merging interval. We present constraints on content insertion which make the overall QoS of the delivered stream acceptable, and show how our algorithm can satisfy these constraints. We report simulation results which quantify the excellent gains due to content insertion. We discuss dynamic scenarios with user arrivals and interactions, and show that content insertion reduces the channel bandwidth requirement to almost half. We also discuss differentiated service techniques, such as N-VoD and premium no-advertisement service, and show how our algorithm can support these as well.