Measurement of the phase diagram of DNA unzipping in the temperature-force plane

We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15 to 50 degrees C, and measure the minimum force required to separate the two strands. The measurements also offer information on the free energy of double stranded DNA (dsDNA) at temperatures where dsDNA does not thermally denature in the absence of force. While parts of the phase diagram can be explained using existing models and free energy parameters, others deviate significantly. Possible reasons for the deviations between theory and experiment are considered.     

Dynamic viscoelastic properties of polymer melts

Summary An apparatus has been designed and constructed to measure the dynamic viscoelastic properties of polymer melts over the frequency range 10^–2–10³ Hz. The measurements made on two samples of polythene are discussed, the samples differing in their molecular weight distributions. Some fractions from these two parent polymers have also been studied. The results are compared with the modifiedRouse (3) theory for polymer melts, and with the liquid model proposed byBarlow,Erginsav andLamb (4).

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Zusammenfassung Mit Hilfe einer neuentwickelten Apparatur wurden Messungen der dynamischen viskoelastischen Eigenschaften von polymeren Schmelzen im Frequenzbereich 10^–2 bis 10^–3 Hz durchgeführt. Die Meßergebnisse, die an zwei Polyäthylenproben unterschiedlicher Molekulargewichtsverteilung erhalten wurden, werden diskutiert. Einige Fraktionen dieser beiden Polymeren wurden auch untersucht. Es wurden schließlich die Ergebnisse mit derRouseschen Theorie über polymere Schmelzen (3) und mit dem vonBarlow, Erginsav undLamb (4) vorgeschlagenen Flüssigkeitsmodell verglichen.

     

Deconstructing Classical Water Models at Interfaces and in Bulk

Using concepts from perturbation and local molecular field theories of liquids we divide the potential of the SPC/E water model into short and long ranged parts. The short ranged parts define a minimal reference network model that captures very well the structure of the local hydrogen bond network in bulk water while ignoring effects of the remaining long ranged interactions. This deconstruction can provide insight into the different roles that the local hydrogen bond network, dispersion forces, and long ranged dipolar interactions play in determining a variety of properties of SPC/E and related classical models of water. Here we focus on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. We further utilize these short ranged models along with local molecular field theory to quantify the influence of these interactions on the structure of hydrophobic interfaces and the crossover from small to large scale hydration behavior. The implications of our findings for theories of hydrophobicity and possible refinements of classical water models are also discussed.     

Simultaneous quantification of multiple nucleic acid targets using chemiluminescent probes

A novel method is described for simultaneous detection and quantification of attomoles or a few femtomoles of two (or potentially more) nucleic acid targets, without need for amplification. The technique depends on spectral-temporal resolution of chemiluminescence emitted from independent hybridization-induced chemiluminescent signal probes. The probes are internally quenched except in the presence of their specific targets, thereby allowing detection limits up to 10,000 times lower than with fluorescent probes. This is sufficient to obviate the need for amplification in many cases. The utility of the technique has been demonstrated by use of resolvable N-linked acridinium and 2,7-dimethoxyacridinium ester labeled probes in a homogeneous assay for sensitive and simultaneous independent quantification of pan-bacterial and pan-fungal target sequences in seawater.     

Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome

Higher-order structure influences critical functions in nearly all noncoding and coding RNAs. Most single-nucleotide resolution RNA structure determination technologies cannot be used to analyze RNA from scarce biological samples, like viral genomes. To make quantitative RNA structure analysis applicable to a much wider array of RNA structure-function problems, we developed and applied high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authentic genomic RNA of the xenotropic murine leukemia virus-related virus (XMRV). For analysis of fluorescently labeled cDNAs generated in high-sensitivity SHAPE experiments, we developed a two-color capillary electrophoresis approach with zeptomole molecular detection limits and subfemtomole sensitivity for complete SHAPE experiments involving hundreds of individual RNA structure measurements. High-sensitivity SHAPE data correlated closely (R = 0.89) with data obtained by conventional capillary electrophoresis. Using high-sensitivity SHAPE, we determined the dimeric structure of the XMRV packaging domain, examined dynamic interactions between the packaging domain RNA and viral nucleocapsid protein inside virion particles, and identified the packaging signal for this virus. Despite extensive sequence differences between XMRV and the intensively studied Moloney murine leukemia virus, architectures of the regulatory domains are similar and reveal common principles of gammaretrovirus RNA genome packaging.