Posted: Mar 15, 2010 7:41 am
Rainbow wrote:Please bear in mind that the starting concentrations used (60 μM 3H-labeled oleate) are 60 000 times higher than those expected in thermal vents. Even starting from these relatively high concentrations, they were only able to achieve a '5-fold accumulation'.
This is only related to the Linear capillaries, which, according to the "Extreme accumulation of nucleotides in simulated hydrothermal pore systems." - paper, differ markedly from concave or shaped capillaries.
They state:
Heat-driven molecular accumulation in hydrothermal pores. (a) Section through aragonite (CaCO3) from the submarine hydrothermal vent field at Lost City (kindly provided by D. Kelley; ref. 20). (b) Simulation of a part of the pore system. If subjected to a horizontal thermal gradient of 30 K, a 1,200-fold accumulation of single nucleotides is expected (logarithmic concentration color scale). A concatenation of three of these pore sections leads to a 10^9-fold accumulation. (c) The mechanism of accumulation is driven by heat in a twofold way. Thermal convection shuttles the molecules vertically up and down and thermophoresis pushes the molecules horizontally to the right. The result is a strong molecular accumulation from the top to the bottom (linear concentration color scale).
So the shape of the capillary is a highly deciding factor.
Also, the szostak paper's experiment consisted of simply adding the solution to the linear capillary in a setup with a simple temperature variance, then putting it in to rest for 24 hours. This obviously resulted in the heavier molecules coming to rest somewhat at the bottom.
In the environment, one would expect a continous flow of material in the system, providing the mechanism for extreme accumulation.
Further,the length-to-width ratio of the capillary and the size of the molecules also has a substantial impact on the concentration mechanism:
Predicted effects of the molecule size and pore length on the accumulation level. The simulation results are based on the experimentally measured Soret coefficients and diffusion coefficients for DNA and RNA (see Table 1). (a) The accumulation increases exponentially with the size of the molecule. Whereas single nucleotides are accumulated 7-fold in a short cleft of aspect ratio 10:1, double-stranded DNA comprising 1,000 base pairs accumulates 10^15-fold. The equilibration takes 9 min for single nucleotides and 14 min for single stranded RNA comprising 22 bases. For DNA polynucleotides of 100 and 1,000 bp it takes 18 or 33 min, respectively. (b) Elongation of the cleft exponentially increases the accumulation. For example, the accumulation of single nucleotides is raised to a 10^10-fold level in a pore with an aspect ratio of 125:1. A linear concentration scale is used in both plots, scaled to the respective maximal concentration. The time to reach steady state is 9 min for r = 10, 4 h for r = 50 and 23 h for r = 125.
Pertinent to our argument is the fact that accumulation grows exponentially both with the size of the molecule and the length of a concatenated pore system. In concatenated pores accumulation of molecules increases exponentially, a result of the considerable concentration independence of thermophoresis below molar concentrations (23–25). Thus, although single nucleotides accumulate merely 7-fold in the short pore of Fig. 2 a, concatenating 12 of these pores using a wide variety of orientation angles exponentiate the accumulation to an extreme 712 = 10^10-fold level. Elongation of the pore has exactly the same effect. As shown in Fig. 2 b, a pore system with a total aspect ratio of r = 125:1 accumulates single nucleotides 10^10-fold. Notably, the length of this pore system is only 18 mm, below the typical lengths of pore systems in hydrothermal settings.
Before you object to the fact that the above citation deals specifically with nucleotides, the paper goes on later to state:
Our approach has the advantage of offering an active concentration mechanism in an already existing, robust enclosure. Because thermophoretic drift is common for molecules, the accumulation scheme applies similarly to nucleic acids, amino acids, and lipids.
So, interestingly the shape and length of the capillary can help achieve concentrations in the ratios from millions to tens of billion fold.