Microfluidics for Porous Systems: Fabrication,Microscopy and Applications

Transport in Porous Media - No matter how sophisticated the structures are and on what length scale the pore sizes are, fluid displacement in porous media can be visualized, captured, mimicked and...     

Solution Structure,Mechanism of Replication,and Optimization of an Unnatural Base Pair

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge‐on interactions, are replicated by means of a unique intercalative mechanism. Here, we report the synthesis and characterization of three novel derivatives of the nucleotide analogue d MMO2 , which forms an unnatural base pair with the nucleotide analogue d 5SICS . Replacing the para‐methyl substituent of d MMO2 with an annulated furan ring (yielding d FMO ) has a dramatically negative effect on replication, while replacing it with a methoxy (d DMO ) or with a thiomethyl group (d TMO ) improves replication in both steady‐state assays and during PCR amplification. Thus, d TMO –d 5SICS , and especially d DMO –d 5SICS , represent significant progress toward the expansion of the genetic alphabet. To elucidate the structure–activity relationships governing unnatural base pair replication, we determined the solution structure of duplex DNA containing the parental d MMO2 –d 5SICS pair, and also used this structure to generate models of the derivative base pairs. The results strongly support the intercalative mechanism of replication, reveal a surprisingly high level of specificity that may be achieved by optimizing packing interactions, and should prove invaluable for the further optimization of the unnatural base pair.     

Modeling of the structure of ribosomal protein L1 from the archaeon <Emphasis Type="Italic">Haloarcula marismortui</Emphasis>

The halophilic archaeon Haloarcula marismortui proliferates in the Dead Sea at extremely high salt concentrations (higher than 3 M). This is the only archaeon, for which the crystal structure of the ribosomal 50S subunit was determined. However, the structure of the functionally important side protuberance containing the abnormally negatively charged protein L1 (HmaL1) was not visualized. Attempts to crystallize HmaL1 in the isolated state or as its complex with RNA using normal salt concentrations (≤500 mM) failed. A theoretical model of HmaL1 was built based on the structural data for homologs of the protein L1 from other organisms, and this model was refined by molecular dynamics methods. Analysis of this model showed that the protein HmaL1 can undergo aggregation due to the presence of a cluster of positive charges unique for proteins L1. This cluster is located at the RNA–protein interface, which interferes with the crystallization of HmaL1 and the binding of the latter to RNA.     

On finite action solutions of the nonlinear σ-model

The instanton and anti-instanton solutions of the two-dimensional O(3) σ-model are special examples of harmonic maps, which have been studied extensively in the mathematical literature. We give an elementary and self-contained proof that these solutions are the only continuous maps for which the action is finite and stationary under variations, without assuming any additional boundary conditions at infinity. An element of the proof is the vanishing of the stress tensor for a finite action solution, which actually holds true for the general O(N) σ-model. For the two-dimensional O(2l + 1) σ-model we exhibit explicit finite action solutions that do not lie in any lower dimensional sphere; the existence of such solutions has been pointed out in the mathematical literature. We also present a rigorous proof, based on Derrick's scaling argument, that there are no nonconstant finite action solutions in more than two dimensions.