Help with DNA extraction contamination [absorbance peak at 230 nm]?

[Emerick Larkin]

I recently extracted DNA from the roots of some lettuce plants. I used the MoBio PowerSoil kit for the extraction. The only way which I deviated from the standard protocol was bead beating the sample, in the initial steps, for twice the suggested time. I ran the sample on a DU800 spec to check some metrics: 

Sample C1-

260/280: 3.4
260/230: 0.51
Peak absorbance: 231 

Sample GL1-

260/280: 2.9
260/230: 0.43
Peak absorbance: 232

I have attached the spectral scans from 200-400 nm, of these samples, to this questions. 

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I do not think the contamination is phenolic. My best guess is that the strong 230 nm peak is indicative of Guanidine HCL or another chaotropic salt (I'm not sure what is used in the kit since it is proprietary). 

Would this level of contamination preclude the ability for amplification of 16s and ITS genes by PCR? 

If so, what is the best way to remove the salts and how can I better avoid this contamination in the future? 

I have also read that for an accurate measurement, A260 values should lie between 0.1 and 1. I diluted the samples 10-fold (5 ul + 45 ul) to save sample for downstream applications. My 260 absorbencies are in the 0.03 neighbourhood. Could this also be shifting the absorbance peak? 

[Nathan McCorkle]

If the absorbance is that low, then you don't seem to have much DNA... I can't however seem to find anything (quickly) on Guanidine HCL contamination on downstream effects. Here is something that describes briefly the spectral effects though:

http://www.genengnews.com/gen-articles/assuring-reliability-of-qpcr-rt-pcr-results/3808?page=2

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-Nathan

[Gordana Ostojic]

I am not familiar with the extraction kit but if you can check the absorbance of the kit solvents themselves (without DNA). Normally when we measured DNA content it was done by subtracting the absorbance of DNA+buffer and buffer only, you can do the same.