DNA, or deoxyribonucleic acid, is the carrier of genetic information for the vast majority of living organisms. The only known exceptions are RNA viruses.
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best known indexing method / transformation to coordinates for gene sequences
What would be the best known method to transform a gene or proteine sequence to some coordinate space (so $t(G)$ is the transformed sequence) complying to following rules:
similar sequences ...
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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 ...
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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 ...
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0answers
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What is the purpose of Y-shaped adapters in Illumina sequencing?
Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.
The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.
...
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3answers
2k views
Why do eukaryotic organisms have introns in their DNA?
We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not ...
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4answers
705 views
Why are there exactly four nucleobases in DNA?
Does someone know why DNA is composed of four nucleobases? In particular, is there an explanation for the number? Why four and not two, or eight?
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2answers
41 views
DNA replication Okazaki fragments
I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so ...
5
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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?
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1answer
77 views
can the face of a person be accurately predicted from DNA information?
3/05/creepy-or-cool-portraits-derived-from-the-dna-in-hair-and-gum-found-in-public-places/?utm_source=plus.google.com&utm_medium=socialmedia&utm_campaign=20130503&utm_content=collageartdna
...
6
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2answers
110 views
BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:
It looks like it's ...
4
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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 ...
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3answers
113 views
Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?
My apologies if my question is too basic, and please point me to a more appropriate forum. I am reading the textbook "Essential Cell Biology" by Alberts et al, and am consulting other sources as ...
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1answer
395 views
Is there an advantage to linear chromosomes?
The DNA copying enzymes have a hard time working to the end of a chromosome. For circular chromosomes this is not a problem, since there is not a sharp 'end'. However, for a linear chromosome, without ...
16
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2answers
2k views
What is the advantage of circular DNA in bacteria?
From what I understand, bacteria have circular DNA. What advantages does it have over linear strands like for eukaryotes?
Do there exist bacteria with more than one ring of DNA?
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1answer
27 views
Is episome a plasmid or a virus?
A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell.
In general, in eukaryotes, episomes are closed circular DNA ...
4
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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 ...
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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 ...
33
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3answers
7k views
Why is uracil used in RNA rather than thymine?
What is the advantage gained by the substitution of thymine with uracil? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of ...
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1answer
20 views
Complexity in creating transgenic animals (e.g., mice)
Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With ...
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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 ...
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2answers
31 views
Do individual (free) nucleotides base-pair with other free nucleotides?
I had a student ask me about this and my google-fu let me down. He asked if individual nucleotides (not in a nucleic acid) base-pair with their complementary nucleotides, essentially forming many ...
3
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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 ...
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1answer
39 views
How much can be said about behaviour (future) based on bloodgroup?
My bloodgroup for example is A+. How much information is knowing my bloodgroup? How much information can be known from a blood sample? I expect you to be able to clone if known a complete DNA sequence ...
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1answer
42 views
Can IVF decrease the probability of trisomy in the fetuses of older mothers?
Is trisomy mostly due to complications with fertilization?
If so, does in vitro fertilization reduce the probability of trisomy for the fetuses of older mothers?
If not, can zygotes be screened ...
7
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1answer
55 views
How is instinctual information encoded?
If instincts are passed on through genetics, how is that information encoded in DNA?
For example, spiders instinctively know how to spin webs. Does that imply that the algorithm for web spinning is ...
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1answer
110 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 ...
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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 ...
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2answers
137 views
Can DNA produce ribozyme-like structures?
RNA is known to act as an enzyme via its ability to fold itself in specific ways.
Is DNA capable of such structures? Or is it some biochemical reason stopping the folding?
Have they been observed in ...
6
votes
3answers
75 views
What are the limitations of commercial-grade DNA genotyping compared to full sequencing?
I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what ...
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 ...
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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 ...
5
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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 ...
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0answers
55 views
Papers linking telomeres and aging [closed]
I'm currently writing a piece of work about telomeres and aging, and wondered if you could share some good papers you've either read or know of.
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3answers
2k views
How many agarose gel bands are typical for circularised DNA
I am aware that circular DNA can be both relaxed and super coiled. However when running an agarose gel of the circular plasmid along with singly digested plasmid with BamHI and HindIII, I see 1 band ...
4
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1answer
89 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 ...
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4answers
192 views
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.
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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 ...
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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 ...
3
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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 ...
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votes
3answers
196 views
What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?
Apparently all living humans are matrilineal descendants of a single woman who lived 200.000 years ago. She is called Mitochondrial Eve.
But at the time she lived there was a different matrilineal ...
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1answer
127 views
Can DNA act as a translation substrate?
I get conflicting answers. One would think if it was true, it would be rather seminal and widely known.
There are papers from Khorana[1], Holland[2], and Bretscher[3] (late 60s) that suggest that it ...
3
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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
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
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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?
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1answer
105 views
How realistic is to use DNA for long term storage?
This is mainly a followup question to the recent paper Next-Generation Digital Information Storage in DNA.
Personally, while I agree about the data density of the format, I can't help point out the ...
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2answers
184 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?
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1answer
157 views
Does DNA react in all of the ways most other acids do?
As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of ...
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 ...
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2answers
212 views
What distinguishes “coding” and “noncoding” DNA from each other?
I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA".
I'm just an interested layperson but I thought all combinations of ...
5
votes
2answers
426 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 ...
