Deoxyribonucleic acid (DNA) is the carrier of genetic information, including for all known living organisms. The only known exceptions are RNA viruses.

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Do mitochondrial DNA have repair enzymes?

Mitochondria are considered endosymbionts originated from a prokaryote. So, do they have a DNA repair mechanism ?
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Reassociation of DNA

What is the order in which this DNA samples would would reassociate ? e.coli DNA plasmid DNA viral DNA satellite DNA DNA-RNA hybrid This is a homework question and I have not been given any ...
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546 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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There are linear and rotary molecular motors in the cells. Do any of them have a fixed or stable frequency or speed?

Are there any linear, rotary or oscillatory molecular motors in the cells which can have fixed frequeny and which can be used as a reference for elapsed time timer? This question is with relevence to ...
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What to do with a DNA sequencer? [closed]

My school is very fortunate to have a DNA sequencer, and I want to find an opportunity to learn how to use it. I'm currently taking AP Biology this year, and I hope to do an independent study in ...
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34 views

Genotoxic agent and their metabolic pathway

What are the mechanics (set of biochemical reactions) allowing a given genotoxic agent to modify the mutation rate at a given spot? to induce only a given type of mutation (from Gs to Cs for ...
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887 views

Difference between viral and human genetic material

I have heard that there is a difference between viral and human genetic material. What is that difference? If I take my cells and take DNA out of them and insert only a small part of it having a ...
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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 ...
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Basic text/notes on DNA structure (for non-biologists)

I am a mathematics grad student researching knot theory, and I've recently discovered that there is a connection between knot theory and DNA structure (if I understand correctly, when DNA strands ...
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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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Why can't we observe haplotypes directly?

I am completely a noob to biology and DNAs, but recently I am looking into EM-algorithm used in the case of re-constructing haplotypes from genotype data. I am just wondering what exactly in the ...
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Which organisms have introns?

From Wikipedia: For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, ...
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Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
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126 views

Do spouses begin to share genes over time?

I apologize if this hypothesis sounds strange by I was wondering if any research had been done on a phenomenon which I've seen and have corroborated with many other - the idea that over time spouses ...
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949 views

What happens when cells in your body run out of telomeres?

In my biology book I read about an experiment where the genes encoding telomerase were 'knocked out', but they could still live a normal life and no adverse effects were noticed until the 6th ...
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66 views

How correlated are proximally related CpG sites in human DNA?

Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together. I can only find one paper that ...
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88 views

Complementarity of cDNA

Strictly speaking, what is the definition of cDNA? This confuses me, since usually it is said to refer to DNA that is complementary to mRNA. Is this correct? Is it restricted to mature mRNA? I ...
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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 ...
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278 views

Can replication occur if DNA is methylated?

Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?
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Can retroviral delivery systems “overwrite” genes?

As the question states, what are the limits of retroviral genetic delivery systems? Are they limited to adding additional gene sequences to a cell, or can they actually overwrite specified segments ...
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883 views

When can a virus modify DNA in every cell of a living organism?

I've recently heard about experiments with brain tissue, where a virus is introduced in a rats brain, causing a "glow when electric charge is present" protein to be created. This protein then helps to ...
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559 views

Is there variation of AT/CG ratio along species?

Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T. But what ...
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219 views

How to deduce if RNA virus infection or DNA virus infection

Is there any general rule to say this must be RNA virus infection and the other one DNA virus infection? Example of a case: 5 children develop a bright red rash on the face and turns violet after a ...
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153 views

Suggestions for an experiment? [closed]

I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have >to be fairly ...
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What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
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Is there any other function of DNA?

We all know that DNA acts as a genetic molecule. Does DNA have any other function in the cell other than being a genetic material and carrier of information?
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What triggers DNA to produce proteins?

What is the trigger for DNA to produce proteins or RNA? I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...
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Self pairing in DNA

I know that ssRNA molecule can fold over itself (e.g. in t-RNA). Can DNA do the same? Is there any example of this in nature? Why is this phenomenon more common in RNA than in DNA?
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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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Prenatal Marketing

This is for a short story idea. Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...
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How does the DNA know which chain has error in repairing?

As we know, the DNA has more stability than RNA, if one chain has broken or accidentally distorted, it can be repaired by the other one. Suppose there is a segment AGTC, its peer is GACT. Now its ...
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DNA Replication

I just wanted to understand the basic steps behind the replication of the lagging strand of DNA: Have helicase unwind it first DNA Primase lays down RNA primers in fragments, called Okazaki ...
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Mitochondrial DNA and recombination

Firstly I could do with a brief description of mitochondrial DNA. How does the structure of DNA in mitochondria compare to animal DNA (for the sake of simplicity let's say human - some animals might ...
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Do thymine and uracil ever appear in the same strand of RNA?

Wikipedia says that "in RNA, thymine is replaced with uracil in most cases." I'm curious what are the cases when this does not happen? Does this ever occur in normal functioning, or is it an error? ...
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Can a dNTP be built into a RNA strand?

DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two ...
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Why did high A+T content create problems for the Plasmodium falciparum genome project?

The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
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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 ...
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Are there beneficial genetic mutations identified by consumer DNA genotyping?

I'm looking at services like 23andme, and see that they identify a wide variety of genetic-based risks, like predisposition to diseases, hair loss, cancer, etc. Are there a more "positive" DNA ...
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Transcription factor binding site located in intron

I have noticed that some TF binding sites are located in the introns of the genes. I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during ...
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Is there a DNA test to identify dog mixes?

We adopted a dog at the age of two. Our vet said it was a mix of an Australian Shepherd and Border Collie, which we've told everyone. Based on markings, I think it's likely. I am wondering, however, ...
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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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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 ...
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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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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 ...
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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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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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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 ...
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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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123 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 ...
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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 ...