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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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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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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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 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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57 views

Walk me through microsatellite markers and PCR

Three polymorph microsatellite markers are used to try and narrow down the location of a disease locus, with the use of PCR with 2 flanks on each side of the actual polymorphic area. The PCR ...
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92 views

How fallible are DNA paternity tests?

Is it possible to get either a false positive or a false negative from a DNA paternity test and what would be the likely mechanisms behind this? For example, is it possible that a father's DNA could ...
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The move from RNA to DNA and the necessity of reverse transcriptase

In this piece about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states: In order to move from RNA to DNA, you need an ...
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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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38 views

Gene frequency problem

1/330 of white people in south Africa have a disease called Porphyri. What is the frequency of the gene if it is inherited autosomal recessive? This one I understand. The genotype frequency is $q^2 ...
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104 views

How would you affect bulk DNA gene therapy for a human?

Let's imagine that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to ...
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60 views

How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
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943 views

Telomere shortening during replication

It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the ...
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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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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, ...
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106 views

Restriction sites

I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases: ATTGCAGTCTG and I want ...
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49 views

How do nicks in the DNA strand affect the success of Long Range PCR?

Long Range PCR using NEB Master Mix - Hot Start Taq was working fine for me (amplicon sizes of ~10kb) but stopped working all of a sudden. Is it possible that many freeze-thaw cycles on the DNA ...
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51 views

How do mosquitoes maintain telomere length?

While the vast majority of eukaryotic organisms maintain their chromosome ends (telomeres) via telomerase, an enzyme system that generates short, tandem repeats on the ends of chromosomes, other ...
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37 views

What is the genetic distance where linkage can be ignored?

I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree ...
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414 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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38 views

DNA length and annealing kinetics

I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the ...
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Forensic genetics- why is mtDNA comparison sometimes better than nDNA comparison?

Why is (in forensic genetics) in some cases more appropriate comparison of nuclear DNA but in some other cases comparison of mitochondrial DNA? Is it because geneticists are sometimes unable to find ...
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68 views

Is it possible to insert DNA without cutting the recognition site with CRISPR/Cas9?

We are looking for a way to insert DNA into a genome, but we would like to do it in a way that the recognition site stay intact to be able to add again DNA at the same location. Do you know if it is ...
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95 views

How do genetic chimeras with different blood types not die?

If a person is a chimera and has two different blood types in his veins, how does he not die? Shouldn't the immune system attack one of the blood types? In 1953 a human chimera was reported in the ...
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What percentage of DNA do people share?

If you picked two people in the world at random, sequenced each of their entire genome, and compared their DNA, what would the expected percentage match be?
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How does GC-content evolve?

Background GC-content refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs ...
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138 views

Real-time PCR delay in Cq due to insertion SNP in primer

I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. I am most interested in how much there is a delay in ...
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Transposons and the net amount of DNA

The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost ...
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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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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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588 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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49 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 ...
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229 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 ...
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How stable is linear DNA transfected in eukaryotic cells?

I would like to know, with references from the literature, what is the half life of a linear dsDNA transfected in a mammalian cells. For example, if I transfect human cells with a PCR product ...
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Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)?

The recent work by DeLoache, et al. on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they ...
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Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: ...
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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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Is a single x-ray photon capable of doing enough damage to the DNA of a cell to kill that cell? [closed]

Ionizing radiation is damaging to DNA, but is there such a thing as a safe dose below which no DNA damage could occur? I'm not asking about a minimum safe dose overall, just whether or not there's an ...
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DNA is charged negative. Where is all the positive charge in my body?

DNA is charged negative because of its phosphate backbone. Since charges need to be balanced (so that there are no charges building up somewhere), what is the positive charge which neutralizes this ...
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584 views

Are all body atoms really recycled several times during a life?

I heard a point, that all (human) body atoms are recycled withing short period like few years. Recycled means "old" atoms are replaced by "new" ones during metabolism, leaving only structure ...
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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 ...
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How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
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Why are urban birds still scared of humans?

I understand that animals are naturally scared of humans because we basically slaughtered every living thing we found in our way for millennia. How long does it take for them to genetically 'forget' ...
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What are the major causes of mutations in DNA?

I know that point mutations can change the base sequence of a gene by altering a specific codon that codes for a particular amino acid. Are these mutations purely random events that occur when DNA is ...
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334 views

How does non-homologous end joining (NHEJ) work?

I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it ...
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219 views

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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299 views

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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DNA replacement: new species

This is a hypothetical question What would happen if the DNA of a prokaryote was replaced with the one of a prokaryote of another species, would the cell structures change and adapt to the new DNA ...
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442 views

Can DNA & RNA be considered as nature's programming language?

The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA). If after fertilization the DNA of the zygote could be genetically ...
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Why do three nucleotides code for one amino acid? Why not 5 nucleotides? [duplicate]

We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?
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How does the telomere repeat sequence vary in Eukaryotes?

Question: How does the telomeric repeating sequence vary in non-vertebrate Eukaryotes? If you know the repeating sequence of a given species I would appreciate hearing it. Background: Telomerase is ...