The ionic effects on the dynamics and conformation of DNA in silt-like confinement are investigated. Confined λ-DNA is considered as a model polyelectrolyte, and its longest relaxation time, diffusivity, and size are measured at a physiological ionic strength between 1.7-170 mM. DNA properties change drastically in response to the varying ionic environment, and these changes can be explained by blob theory with an electrostatically mediated effective diameter and persistence length. In the ionic range we investigate, the effective diameter of DNA that represents the electrostatic repulsion between remote segments is found to be the main driving force for the observed change in DNA properties. Our results are useful for understanding the manipulation of biomolecules in nanofluidic devices.With the advance of nanotechnology, new devices have been created to manipulate biomolecules. Many such applications, including DNA separation 1 and gene mapping, 2 rely on the confinement-induced change in molecular properties. Several studies have been devoted to the investigation of those confinement effects on DNA and have had fruitful progress.3-6 On the other hand, the ionic environment is also known to have a strong influence on biomolecule properties and can be readily manipulated in experiments. However, the compound effects of confinement and ionic environment, critical for many applications, are yet to be fully understood.Several studies have investigated the ionic effects on confined DNA conformation in rectangular channels (height (h) ≈ width (d)).2,7,8 DNA extension was found to increase with decreasing ionic strength. This observation was explained either by de Gennes' blob theory (h and d > p (persistence length)) 9,10 or by Odijk's deflection chain theory (h and d < p). 11Although the finding is promising, we find that the buffer ionic strengths reported in these studies are somewhat inaccurate especially at low salt concentration due to neglect of the ionic contribution of antiphotobleaching agents. Furthermore, it is not clear how ionic environment will influence DNA dynamics and whether the above theories can be applied. In the current study, we investigate the ionic effects on both conformation and dynamics of DNA confined in nanoslits with better control on buffer ionic strength. We show that our analysis can be used to explain the ionic effects on both confined and unconfined DNA, providing a consistent picture for this highly debated issue of DNA/polyelectrolytes.To understand the physical origin of the ionic effects on polyelectrolytes, we first consider the conformation of neutral polymers. From the Flory theory, 12 the equilibrium size (R bulk ) of an unconfined, semiflexible polymer in good solvents can be expressed as:

The longest relaxation time (τ 1 ) of DNA confined in nanoslits is characterized, and its dependence on molecular weight (M) and channel height (h) is investigated. The relaxation time is extracted from the rotational autocorrelation function obtained from time-sequence images of confined DNA at equilibrium using fluorescence microscopy. We find that τ 1 ∼ M 2.45 h -0.92 , in partial agreement with the predictions of the blob theory (τ 1 ∼ M 5/2 h -7/6 ). The experimental results suggest that the assumptions of both a 2-dimensional self-avoiding walk of blobs and a 3-dimensional self-avoiding walk of polymer segments within blobs are valid, while the assumption of nondraining blobs is compromised. We also find (τ 1 /τ 1,bulk ) ∼ M 0.1 (R g,bulk /h) 0.92 , where τ 1,bulk is the bulk relaxation time and R g,bulk the bulk radius of gyration. Because of the very weak M dependence in above scalings, a master plot of (τ 1 /τ 1,bulk ) vs (R g,bulk /h) is constructed and is used to compare our results to other studies. The plot also provides a convenient way to estimate the relaxation time of DNA in varying degrees of confinement. Using the measured relaxation time and blob theory, we explain recent observations that a very large shear rate is required to deform DNA when it is confined to channels with a dimension comparable to or smaller than the bulk radius of gyration.

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.

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