[HJay]

Hi, I'm not a native English speaker and I was little confused with the following phrase.

"The supernatant was removed from the precipitate after centrifuging and transferred onto mica for analysis by AFM."
The way I'm understanding the above phrase is that you are transferring "the supernatant" onto mica for analysis by AFM and not the pellet, which just gets thrown away.
Is that correct?

For a second phrase, "A solution of lambda-DNA (100 uL, 500 ng/uL, corresponding to 1.5 mM nucleotides)", can I assume that 1.5 mM nucleotides are equal to 1.5 mM DNA?

I know this is not an English forum, but I'm not really in an English-friendly environment, so I don't have anywhere else to ask but here. So please understand

[chenbeier]

Second one I would say no, because 100 µl with 500 ng/µl = 50 µg DNA and this correspond to 1,5mM nucleotides.

[Babcock_Hall]

To the first question, the supernatant is the liquid portion of a centrifugation experiment, and it sounds as if the supernatant contains the desired product, not the pellet.  People occasionally write things incorrectly.

To the second question, I converted the numbers you provided into 0.5 g/L.  A rough estimate for single stranded DNA is that it is 325 g per nucleotide unit, which works out to about 1.5 mM in nucleotides.  However, phage lambda is double stranded.  I would have used 650 g per nucleotide pair for double stranded DNA.  This is just an educated guess about what might be going on.

[Arkcon]

Its sloppy writing, but you have to provide the context as best you can on your own.  Something has to go onto the mica stage of the Atomic Force Microscope.  What is the topic of the paper -- a powdered precipitate dried there, or a freeze-dried crystalline substance dried there.  What is the later processing, or staining that is performed.  I have to guess as for myself, I haven't done AFM before.

[HJay]

Thank you all for kind answers.
Well, as Arkcon mentioned it, I would have to put the whole paragraph up for people to better understand what's really going on in the paper, but I thought posting the whole paragraph up and making people read was just way too much trouble. So I only brought the sentences I didn't understand.

Anyway, the paragraph that had those two sentences is as follows:

Synthesis of CdS Nanowires in DNA Containing Solutions: An
aqueous solution of Cd(NO3)2 (100 lL, 0.2 mM) was added to a solution
of k-DNA (100 lL, 500 ng lL–1, corresponding to 1.5 mM nucleotides),
and the solution was mixed thoroughly and kept for 24 h at
4 °C. To this solution was added 100 lL of 0.2 mM Na2S in water/ethanol
(1:1, v/v). The solution was mixed thoroughly and incubated for a
further 24 h at 4 °C. Then. 10 lL of 20 mM aqueous Cd(NO3)2 was
added and allowed to interact for 24 h (4 °C) before introduction of
10 lL Na2
S (20 mM) in water/ethanol (1:1, v/v). The solution was
again incubated at 4 °C for 24 h and then allowed to stand at room
temperature. The supernatant was removed from the precipitate after
centrifuging and transferred onto mica for analysis by AFM. The reaction
mixture was allowed to stand at room temperature for further
analysis.


It's a paper from Adv Mater 2007 by Liquin Dong

[mjc123]

Looking at that, it seems virtually certain that it's the precipitate that is transferred to mica for AFM. The "supernatant" is the "reaction mixture", and if something else is done with that, it must be the precipitate that is analysed. This is just sloppy writing, probably by someone whose native language is not English, struggling with the peculiar English style of scientific papers, full of passive constructions. But you should be able to tell, from reading the whole paper, whether the material for AFM analysis is in the precipitate or the supernatant. Failing that, you could always contact the corresponding author for clarification.

Always be sure you understand the full process, don't just follow a recipe blindly.

[HJay]

Looking at that, it seems virtually certain that it's the precipitate that is transferred to mica for AFM. The "supernatant" is the "reaction mixture", and if something else is done with that, it must be the precipitate that is analysed. This is just sloppy writing, probably by someone whose native language is not English, struggling with the peculiar English style of scientific papers, full of passive constructions. But you should be able to tell, from reading the whole paper, whether the material for AFM analysis is in the precipitate or the supernatant. Failing that, you could always contact the corresponding author for clarification.

Always be sure you understand the full process, don't just follow a recipe blindly.

Thank you for the reply.