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Questions tagged [dna]

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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Realistic Application of CRISPR in Human Disorders

Human trials recently began to use the genome editing technology CRISPR to treat sickle cell anemia using edited stem cells. Sickle cell anemia is caused by a single DNA Mutation, and is also a ...
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How does the new discovery that mitochondrial dna is inherited from both parents change population genetics and other dates?

This new study seem to have pretty much proven that mtDNA is inherited from both parents. I assume that this would lead to most age estimates of ancient human ...
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Are there any alternatives to the Epicentre product Plasmid Safe?

I need to remove any traces of linear DNA (both single and double stranded) from a ligation reaction while keeping circular DNA intact. Up to now, I have used Epicentre's Plasmid Safe to do the job. I ...
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In vivo delivery of ssDNA

I am looking for a system with which I can deliver (large quantities of) ssDNA in vivo (say in mice). I do not know whether it is of importance but the 5' end of the ssDNA fragments are assumed to be ...
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Do eukaryotes assimilate DNA that is floating in the extracellular membrane?

Prokayotes, which replicate primarily using binary fission, don't get much genetic diversity. For this reason, they take in any genetic material they encounter, in a gambit to help them better adapt ...
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Offspring of parents with different number of chromosomes

Many papers report that dog-whelks (Nucella lapillus) show a distinct chromosomal polymorphism between populations of 2n = 24 up to 2n = 36. Could somebody please tell me how many chromosomes the F1 ...
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How much DNA does a species lose after post-polyploidization genome downsizing?

After whole genome duplication, diploidization takes place, right? A lot of changings in gene organization and expression involving genetic and epigenetic mechanisms (translocations, transpositions, ...
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What are the microscopic mechanisms of plant branching?

For a long time I've been idly interested in how the shape of a complex organism gets determined during development at a microscopic level. Recently I've realized that plants could be a good place to ...
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Is DNA replication a serial or parallel process?

This video entertainingly supplements this 3d animation of DNA strand replication. Does this process happen serially from the beginning to the end of a DNA strand (like having to unzip a six foot long ...
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Why is competence useful for a starving cell?

I know that some bacteria become competent when there is not much food available in their environment. I don't really understand why this is useful for the cell. I've seen some other organisms form ...
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Scaling down amount of DNA for transfection: what factor to consider?

I am interested in transfecting HEK293 cells with a BAC. One paper suggests using 24 ug of DNA to transfect a 55-cm^2/10 ml culture plate. I am using an assay optimimzed for a 96 well plate so I am ...
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How to calculate information content of a DNA sequence

How does one calculate the information content of DNA sequence like ATCGGCT where mutation rate of G's is 10% and the most common mutation product binds with C and A with equal frequency. I know that ...
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Minichromosome maintenance protein structure and function

I am having difficulty answering three homework questions which relate directly to Chong et al. (2000). Questions The authors have determined that MtMCM is able to bind both ssDNA and dsDNA (see ...
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What are the reasons which make intron detection uncertain?

Intron/exon sequence detection seems to involve statistical prediction which can at best deliver a guess (until experimentally confirmed) as to where the splice site is. What are the reasons why ...
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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 (500-...
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CRISPR-Cas Systems

In the context of the bacterial systems (not the gene editing tool), I was wondering what happens to the foreign DNA after the Cas proteins have created a new spacer. It is really not clear to me, ...
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Inter-codon mutations statistical analysis

I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or ...
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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: 5'...
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Can a dividing cell that skipped DNA replication become cancerous?

Let's assume that a cell fails to replicate its DNA during the S Phase of the cell cycle. Let's also assume that the appropriate CDKs are inactive (perhaps due to mutation or lack of cyclin proteins ...
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DNA preservation at room temperature

I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in ...
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Would I expect salt precipitate on fibres of DNA in a NaCl water solution?

I just recently conducted an experiment in my biochemistry class where we had to add DNA to distilled water, isotonic saline and 2.5M NaCl. I noticed different physical aspects depending on the ...
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How is the effect of proof-reading on error frequency during DNA replication determined?

An article in Nature Scitable on DNA Replication and the causes of Mutation states that: When an incorrect nucleotide is added to the growing strand, replication is stalled by the fact that the ...
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How did biologists find out that bacterial plasmids were circular?

I was always curious how it was determined that bacterial plasmids were circular, since there isn't an obvious way to find this out. I heard somewhere that there was a difference when gel ...
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Can a phosphodiester bond form between RNA and DNA?

In the initiation of DNA synthesis: the RNA segments are first synthesized by primase and then elongated by DNA polymerase (Wikipedia). What does 'elongated' mean in this context? Is it possible ...
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DNA Longevity in Keratin, Ivory and other Bioplastics

For how long is DNA viable for extraction and/or sequencing in bioplastics created by the human body? I checked out a few links online, and this article gives a record of about 7000 years for frozen ...
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Why does cell waste energy in meiosis, between meiosis 1&2

As far as I have learnt about meiosis I have read that anaphase 1 is followed by telophase 2 where chromosomes change back to reticulum.but in the very next stage i.e prophase 2 they again start ...
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What happens during fixation of Nucleic acids on nylon membrane

In Southern blotting technique, fixation of DNA to nylon membrane is a step prior to hybridisation with probe. It is done by baking at 80ºC and according to this cross linking between DNA and nylon ...
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How many generations apart can a DNA test for blood relations be valid?

Suppose an American suspects he is a descendant of George Washington and he has a strand of hair of George Washington. Can a DNA test be done to prove that he is indeed a true descendant of the great ...
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Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?

I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory. Note that I am aware of these posts: best book for a comprehensive introduction to biology for a ...
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Difference between Classic Satellite DNA and Microsatellites/Minisatellites

I am very new to this community and have a basic question about repetitive DNA sequences. How is different (classic) satellite DNA from microsatellites/minisatellites? All textbooks give concrete ...
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Is there a method to isolate half of the chromosomes of a cell?

Each cell has 2N number of chromosomes, I wonder if currently there is a technique allows isolation of N number of chromosomes out ?
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Can translocation occur within a gene?

I know genes can be translocated between chromosomes but can nucleotide sequences be moved around within an individual gene? Could the following gene: MEN SAW OLD HEN Become: MSA WOL DHE NEN By ...
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Validity of comparing gene expression levels between alive and <24h postmortem cohort

There is a recent paper about assessment of a suicidal risk in psychotic patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759104/ One of the important points is that the authors compare gene ...
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Do users of CRISPR/Cas iterate or parallelize to try multiple guide sequences?

I've read about on-target efficiency and off-target effects in use of CRISPR/Cas9, and about tools that suggest good guide sequences. I am wondering: how many guide sequences do typical CRISPR users ...
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Which DNA fragments do not have expected sizes on this gel electrophoresis?

The problem is such: After performing a PCR, the vector carrying the PCR fragment with two restriction enzymes (Nhe1 and Asc1). The DNA samples were then separated using agrose gel electrophoresis ...
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Link between macro lncRNA and DNA looping

I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by ...
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How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?

Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and ...
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Does every protein encoding gene necessarily have a transcription factor?

For instance, transcription factor gene A is responsible for activating gene B that encodes protein 1. However, it is possible for genes like gene B to encode proteins without having transcription ...
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How to preserve tissue DNA without using formalin?

Except using formalin to preserve human corpse for autopsy. I heard from the news that technique damages the DNA in the organs Question: Suppose corpse will be investigated next by another juridical ...
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How specific are Vitamin D promotors in the DNA?

As far as I understand there are genes that get regulated by the amount of Vitamin D that comes in contact with DNA. How specific are those promoters? Are there promotors that for example only get ...
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How diverse are the sperm cells of an individual male due to random mutations?

Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species? For instance would it ...
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UV-lamp, DNA and RNA extraction lab

I'm equipping a lab room (~3x5 meters) that's supposed to be used for DNA and RNA extractions. I know about the basic safety precautions when working with RNA and DNA extraction (fresh gloves, ...
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Why is the Mongolian Horse superior in stamina?

I've heard a lot about the Mongolian Horse over the years, especially that it has more stamina than the Arabian Horse. It's a little smaller/lighter than an Arabian. Apparently the Mongol Horse can ...
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Do cells store information other than permanent (chromosome) information

The brain stores information in neurons (i.e. neural networks), and cells store information in DNA. But with DNA, this is permanent information. There is a lot of potential temporary information in ...
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DNA synthesis in nucleus

I read somewhere that according to a research, I don't remember what the date was, that our cells stop synthesising DNA around noon and restart it around the sunset. The research told that it was ...
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What percentage of a complete Denisovan genomes lives on in the union of the sets of overlapping pieces in extant humans

In studies like this one mapping out distributions around the world or the analysis described in this article (suggesting a contribution from a non-Denisovan but Denisovan-like unidentified hominin to ...
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What percentage of genome do slugs and scallops have in common?

We can know genetic distance of thousands of species. The OTT tree of life gives genetic distance for nearly all species. Is there a resource to compare the genomes of any sequenced animals to know ...
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DNA linking number, twist and writhe

The image below is taken from a molecular biology textbook. It is not clear to me that what is happening at the two writhe crossings matches up with the numbers provided. Is there a problem with ...
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What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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Dyes that won’t bind to dna

I am looking for a dye that won’t bind to DNA. I want to add dye to proteinase K to make is visible when adding to clear buffer liquid samples. I need it to not bind to the DNA so it will be removed ...