16 votes
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Would it be possible to sequence human DNA from wastewater treatment plants?

As it turns out, you are not the first to have this idea. Prior research claims that it is, at least in principle, possible to conduct epidemiology of cancer by sequencing on wastewater DNA for ...
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9 votes
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Why are large amounts of DNA required for analysis?

Firstly, A DNA sample obtained from a cell or whatever is never going to contain just the DNA sequence you want but will instead contain the entire genomic DNA, plasmids, RNA sequences and whatnot. By ...
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5 votes
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Explanation of protocol in DNA extraction experiment

The DNA solution has a fixed volume (e.g., 0.1 mL). To a suitable test tube is added 0.2 mL of buffer-saturated phenol. After closing the test tube the mixture is mixed well, typically using a vortex ...
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  • 3,407
5 votes

What are the roles of guanidine-HCl and ethanol in binding of DNA to silica?

Guanidine HCL is a chaotropic salt. Chaotropic salts are critical for cell lysis and binding to the silica resin. Specifically, Chaotropes have two important roles in nucleic acid extraction ...
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5 votes

Would it be possible to sequence human DNA from wastewater treatment plants?

As already hinted in the answer by @jakebeal, the low concentration (high dilution) of human DNA in waste water would mean that we need huge sequencing depth in order to detect something. This is not ...
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  • 3,772
4 votes
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What is the most critical step of plasmid purification?

There are a few critical steps (which sounds horrible if written together, but the method per se is robust and usually without problems): Resuspension of the pellet: Make sure it is really ...
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4 votes

Appropriate Buffer for electerophoresis of DNA & Protein TBE or TAE?

There are already many great answers to your question, however I thought I put my comments in form of an answer. The standard for DNA agarose gel is TAE and for the protein, it depends on the size of ...
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4 votes

Appropriate Buffer for electerophoresis of DNA & Protein TBE or TAE?

Grossly, it does not matter what buffer you use. It is the pH that matters. For DNA electrophoresis EDTA is added in order to chelate divalent cations that serve as cofactors for nucleases. Tris is ...
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4 votes
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Appropriate Buffer for electerophoresis of DNA & Protein TBE or TAE?

The question which buffer for DNA is better is quite old. Both have their pros and cons and I list a few of them: TBE is a better conductor and is thus less prone for overheating the gel Borate is a ...
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4 votes

Appropriate Buffer for electerophoresis of DNA & Protein TBE or TAE?

I have had good experience using a lithium boric acid buffer from Faster Better Media. I use it for RNA gels, but it's advertised for DNA gels. I don't think it can do protein, but I've never tried it....
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4 votes

From a computer science perspective, how is DNA compared for various purposes?

From a computer science perspective, there's nothing at all special about DNA. It's stored as a simple ASCII text file consisting of repetitions of 4-15 different letters. DNA, the molecule, is a ...
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4 votes
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DNA extraction methods for hair?

I've been trying to figure out something that works for some time. I have recently tried 3 cheap protocols using commonly available lab reagents. I was using buccal samples (0.2 ml of spit). 1) ...
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4 votes

How long is saliva viable?

Saliva buffer usualy provides stability at RT for month or even years. Genotyping companies like 23&me use collection kits like Norgen's (https://norgenbiotek.com/product/saliva-dna-collection-...
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  • 243
4 votes

How bad is ethidium bromide in your plasmid for downstream applications?

Purification and isolation of DNA bands by cutting them from agarose gel is commonplace (Lee et al., 2012). The purification step after excision of the band gets rid of most of the EtBr and other ...
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4 votes
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Can I pellet DNA back from dissolved state?

No, you cannot pellet dissolved DNA with ultracentrifugation. Yes, you can recover a pellet with additional treatments, similarly to how you got it in the first place; only instead of your input ...
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  • 5,640
3 votes

Detecting nuclear DNA in suspension of mitochondria

Centrifuge the suspension in Cesium Chloride solution at a particular g value which causes the mitochondria to settle to the bottom of the centrifuge tube but leaves nuclear DNA forming a layer near ...
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  • 506
3 votes

During the process of plasmid isolation, how can we be sure that only plasmid DNA has been isolated and there is no chromosomal DNA?

It comes down to the size of genomic DNA (relatively huge) compared to that of plasmid DNA (rather small). Cell lysis for plasmid extraction involves an alkaline buffer that includes sodium ...
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3 votes
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How long can one leave sample in lysis buffer for DNA extraction?

It should be fine. Unless they have been contaminated with DNase, none of the components will damage or denature DNA. I've left purified plasmid DNA on the bench for weeks with no apparent degradation,...
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3 votes

Purifying large amounts of PCR product

We had to do this frequently. What I would first recognize is that all of your current methods only work for at the small scale and that for you to purify mg quantities of DNA, you need to work with ...
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3 votes

How does the size of insert affects the rate of Homologous Recombination in yeast?

As pointed out by aandreev, the greater the size of the insert relative to the flanks lower will be the recombination rate. This is because the donor DNA essentially becomes non-homologous. See the ...
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3 votes
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DNA content in plant seeds vs. fruit flesh

It depends on the seed and fruit you're talking about. The amount of DNA in your crushed up sample of plant matter depends on only one thing--how many cells are in your sample. Look at this diagram ...
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  • 3,264
3 votes

DNA extraction from oil-containing seeds

The paper "Modified method for combined DNA and RNA isolation from peanut and other oil seeds." has a nice protocol for isolating DNA and RNA (which later can either be differentially digested or ...
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3 votes
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State of extracted DNA

Yes, normal DNA extraction protocols fragment genomic DNA. In my experience, extracted DNA tends to have a size distribution on the order of 10 - 20 kilobase pairs (kbp), independent of the protocol ...
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  • 7,564
2 votes
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Transcription rate expressed in microarray per hour

The units here are relative units of intensity. There may be about a picomole of probes on a microarray spot, but the units of intensity are not scaled to the precise concentration of DNA on the spot....
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2 votes

Effect of 260/230 values on PCR

EDTA carbohydrates, phenol all have absorbance near 230 nm. TRIzol reagent is a phenolic solution which absorbs in the UV both at 230 nm and ~270 nm Guanidine HCL used for most DNA isolations will ...
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  • 3,675
2 votes

Extracting cell-free DNA

To note: I have no personal experience with this protocol. I am forwarding this paper, passed on to me by a colleague There are many kits and methods available that don't rely on Qiagen. Or ...
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  • 2,268
2 votes
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How to make µg/ml concentrations of proteinase-K?

It depends on what form your proteinase K is in. You may have a stock solution of some concentration, in which case you just add a specific volume according to $C_1V_1=C_2V_2$. Example: Let's say ...
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2 votes

0.1 M sodium citrate in 10% ethanol and DNA solubility

The sodium ions will bind to and neutralize the (-) charge on the phospho backbone of DNA. This reduces hydrogen bonding sites for water, which then results in less solubility. Edited for clarity and ...
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  • 1,309
2 votes
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DNA extraction from plants and algae don't use phenol. Why?

CTAB is for removing polyphenols and polysaccharides which are found in plant tissues. Animal cells/bacteria don't have these. You can do an additional phenol-chloroform extraction if you want. See ...
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  • 35.1k
2 votes

Separation of smaller DNA fragments and larger fragments without using gel electrophoresis?

One option is to use SPRI beads, like those sold by Ampure (Ampure XP beads) to separate DNA fragments by size. By adjusting the ratio of beads to sample, you can selectively bind fragments of certain ...
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