DNA, or deoxyribonucleic acid, is the carrier of genetic information for the vast majority of living organisms. The only known exceptions are RNA viruses.
6
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1answer
77 views
What is the effective relatedness of inbreeding?
If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?
6
votes
2answers
665 views
What conditions should I use for Gel Red staining?
What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often ...
6
votes
1answer
411 views
Does extracted DNA degrade after a certain time period?
For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression ...
6
votes
1answer
115 views
What is the origin of “melting” in molecular genetics?
I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that ...
6
votes
1answer
333 views
Basic Amino Acid Residue Binding Mechanism to DNA
I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues ...
6
votes
1answer
228 views
Does every mitochondrion in a cell contain the same DNA?
I know that mitochondria of eukaryotes have their own DNA, more similar to that of bacteria than to the rest of the cell's DNA. I also know that a cell can have plenty of mitochondria, and I ...
6
votes
1answer
96 views
How does Topoisomerase II inhibition affect cancer cells?
Topoisomerase II poisons represent some of the most important and
widely prescribed anticancer drugs currently in clinical use. These
drugs encompass a diverse group of natural and synthetic ...
6
votes
1answer
59 views
(Rough) Model for DNA evolution in E. coli genes
I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone.
Here is what I understand:
Sequences corresponding to genes have both exons and introns, but in bacteria the ...
6
votes
0answers
57 views
DNA modifications other than 5-mC/5-hmC/5-fC/5-caC in vertebrate genomes?
Other than 5-Methylcytosine and the more recently discovered 5-Hydroxymethyl, 5-formil and 5-carboxylcytosine DNA modifications found in DNA sequences, what are other DNA modifications present in ...
5
votes
2answers
549 views
Altering the human genome
I recently had a conversation with a rather unusual gentleman who was, let's say, more than a little partial to conspiracy theories. He has this idea that governments are lowering "nanowires" from ...
5
votes
2answers
83 views
Do somatic cells alter their own nucleotide sequence?
I seem to remember reading that embryonic cells will frequently replicate the section of their genome containing rDNA by splicing in duplicate genes. The cells use this to produce ribosomes at a rate ...
5
votes
3answers
172 views
What would need to be discovered to prove there is extraterrestrial life?
Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment. What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA (or ...
5
votes
2answers
108 views
Are there other mechanisms for mutation besides imperfect DNA replication?
I was reading http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/ and saw:
[...] the evolution of entire species can be changed by a single
mistake ...
5
votes
1answer
98 views
Are there any DNA base sequences that are fully conserved between the genomes of all humans?
That is, they don't differ throughout the entire population. I understand of course that we can't DNA sequence every human, so by "fully" I mean there's an incredibly small probability of there being ...
5
votes
2answers
425 views
Why do DNA and RNA have the functions they have?
I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if ...
5
votes
2answers
83 views
Synthetic biology using existing cells
I was watching the video at this link:
http://www.bbc.co.uk/news/science-environment-17436365
The speaker says that a cell is taken and its original DNA content is stripped out and replaced with ...
5
votes
2answers
52 views
How to find Exons in mRNA Computationally
I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning ...
5
votes
1answer
145 views
How can I predict DNA binding affinities from a protein sequence?
Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?
5
votes
1answer
223 views
How long is DNA stable in a freezer?
Inspired by the post about extracting pet DNA, how long would genomic DNA be stable for in a -20°C freezer? It is common practice to store DNA (double-stranded, plasmid) in a -20°C freezer in ...
5
votes
1answer
136 views
What is the benefit for cells having the ATP production regulated in mitochondria compared to being from the nucleus?
Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role.
Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the ...
5
votes
2answers
224 views
What is a good Non Fluorescent DNA Dye?
Can anyone suggest a dye which specifically targets DNA, but is not fluorescent?
(We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak Signal even a low emission would ...
5
votes
1answer
189 views
Primer Dimer / Hairpin Algorithms
What are the algorithms / methods in use for the calculation of primer dimers and hairpins?
As an example, IDT's OligoAnalyzer tool will generate these analysis given particular sequences.
The ...
5
votes
1answer
82 views
What is the oldest example of DNA identified?
What is the oldest sample of genetic material (presumably DNA) identified? What are the prospects of pushing back much further into the geologic record?
4
votes
2answers
183 views
DNA as an acid? [duplicate]
Possible Duplicate:
Does DNA react in all of the ways most other acids do?
Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
4
votes
1answer
73 views
How do mutations come to be shared by all cells?
It's my understanding that various hazards can damage the DNA in our cells, causing mutations.
But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs ...
4
votes
1answer
127 views
How are DNA polymerase error rates measured?
It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
4
votes
1answer
94 views
Finding exons in DNA problem
My attempt: I looked for the TACs because I thought this would be AUG in mRNA and ultimately Methionine (the start codon). But apparently, that's not how you do this problem. Im confused because ...
4
votes
1answer
88 views
Why are 3 nucleotides used as codons for amino-acid mapping in DNA?
DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length?
A related question can be ...
4
votes
1answer
75 views
How does “inheritance of methylation” of DNA and/or histones work?
What are the current models/ideas describing the mechanisms explaining inheritance of methylation on DNA resp. histone level?
Is there evidance of this "setup" information being really ...
4
votes
1answer
82 views
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
4
votes
3answers
89 views
Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?
I have a vector sequence and would like to find the following nucleotide sequence in it.
AASYWSRA
This query sequence uses several degenerate symbols, defined ...
4
votes
1answer
76 views
How does formaldehyde cause protein-DNA crosslinking?
How does formaldehyde cause protein-DNA crosslinking? I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less ...
3
votes
2answers
163 views
Difference between mice and rats
What is the actual biological difference between mice and rats? Are they actually the same thing with two different names depending on appearance (are they all mice for instance and we call the larger ...
3
votes
2answers
56 views
High sequence similarity but start codon isn't methionine
I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
3
votes
2answers
93 views
What risk to DNA does long-term exposure to low-dose radiation pose?
A new study from MIT scientists suggests that long-term exposure to low-radiation poses no risk of DNA damage for mice (it is also important to note that mice are unusually susceptible to cancer). So ...
3
votes
1answer
44 views
How are atoms in benzopyridines and benzopurines numbered?
I am well-aware of the numbering system used for the traditional bases, as seen below.
My question is how are the atoms in the size-expanded bases seen in xDNA and xRNA numbered?
3
votes
1answer
80 views
What is the fiber axis in the Watson and Crick paper?
I was reading Watson and Crick's article on DNA structure, and the diagram on the lower left of the first page had something called the fiber axis going through the DNA. This axis isn't in modern ...
3
votes
1answer
50 views
How do multiple replication forks function without 'colliding', and what is the benefit of this method?
I'm currently reading a little about DNA replication, and have come accross the following statement;
Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are ...
3
votes
1answer
42 views
mutant down but not out
I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from ...
3
votes
1answer
98 views
What is the DNA/protein charge ratio?
To study DNA-protein interaction, I want to do a DNA retardation test by mixing the protein with DNA and afterwarts loading it on an agarose gel to see if the DNA migrates slower. I've found some ...
3
votes
1answer
100 views
Why re-label the strand ends in 3' DNA labelling?
I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.
I took a diagram from my lesson and tried to understand with it; this is what I understood.
If I’m ...
2
votes
2answers
66 views
Consensus codon optimization by organism
Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
2
votes
2answers
115 views
Translate DNA to Protein
Assuming the sequence shown is read left to right, what is the sequence of the protein produced?
sequence: 5’-ATGTACTTCCATCTGGAATAG-3’
MY ATTEMPT: I know RNA is synthesized 5 to 3. This is ...
2
votes
1answer
70 views
Expanding the SETI initiative to seek intelligent data within DNA sequences?
I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article ...
2
votes
2answers
61 views
Is there a way to measure the amount of bytes that are possible to encode in a DNA molecule?
When I saw a DNA molecule for the first time, it kinda reminded me of a hard drive. It consists of slots and there are some possible combinations for each slot; in the hard drive these possible ...
2
votes
2answers
33 views
Studying changes in DNA for causes of cancer
First of all let me say that I'm not into Biology myself... but I have a question for those of you who are.
From what I've read, cancer is caused by 'faulty' DNA that behaves abnormally. Mutations ...
2
votes
3answers
61 views
Simulating Cell differentiation
I'm a computer programmer deeply interested in Biology.
I wish to write a computer simulation for cell differentiation. I understand there will be seemingly impossible challenges in doing this. But ...
2
votes
2answers
92 views
How distantly related are eusocial insects? Aren't members of a species much more related than 1/4, 1/2, or 3/4? [duplicate]
Possible Duplicate:
How many genes do we share with our mother?
I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, ...
2
votes
1answer
109 views
How does a thymidine block halt DNA synthesis?
The best I've been able to find is that there's a feedback mechanism, but what is this feedback, and how does the mechanism work? If it's just that the concentration of thymidine is too high, why ...
2
votes
1answer
109 views
How to learn DNA Origami
Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics.
Advance thanks for your help
edited: INSILICO
