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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161 views

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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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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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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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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91 views

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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922 views

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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220 views

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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40 views

Why is my DNA band bulging?

This is the only image my the TA was able to get for us. And, we're using it for our lab report. The image isn't even ours. It's another group's image that we're sharing. But I don't understand why in ...
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115 views

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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55 views

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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54 views

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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55 views

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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142 views

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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115 views

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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721 views

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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68 views

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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40 views

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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61 views

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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36 views

Can chain-linked genetic segment data be used to reliably assign unknown relatives to either the donor's mother or father?

I am analyzing DNA matching segment data, and I am trying to broadly group all DNA matches by my donor's parents. Based on documented evidence, I can confidently identify "Person 'B'" as a ...
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102 views

Poly-G tails in NovaSeq Paired-end sequencing from museum samples

I'm currently working with DNA samples originating from museum specimens, this means they have been stored in formaldehyde for the last 50-100 years. The DNA I'm analysing has been sequenced by ...
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30 views

Genes and proteins with a significantly inbalanced composition

According to Wikipedia, the median size of a protein-coding gene is 26,288 bp which makes it possible (from statistical considerations) that the nucleotides C, G, A, T appear in roughly equal amounts ...
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70 views

What is the charge of (bacterial) ribosome?

Ribosomes are negatively charged and thus electrostaticaly repelled from DNA. However, I could not find a good reference that would allow me to estimate the magnitude of negative charge on a ribosome. ...
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32 views

What is the status of the cfDNA ends?

I am working on a protocol to ligate cfDNA, extracted from blood, into some vector. I have looked into the literature but I cannot find any detail about the status of the ends of the cfDNA. Are they ...
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Need help to determine % difference between DNA-strand from two different haplotypes. Known nucleotide diversity and more

Backround: 229 DNA sequences 493 bp in length Haplotype diversity: 0.9956 Average number of nucleotide differences: 12.50544 Polymorphic sites: 145 Nucleotide diversity: 0.02426 Is it possible ...
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115 views

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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225 views

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 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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28 views

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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114 views

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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36 views

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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84 views

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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76 views

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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171 views

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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91 views

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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28 views

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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559 views

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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386 views

How does DNA organise a cell's physical position within a body?

How do cells "know" where they are supposed to be in relation to other cells, in forming the physical shape of the body? If you have ever tried to organise or choreograph the physical positions of a ...
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139 views

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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559 views

What are constrained genetic elements?

I am somewhat of a newbie in evolutionary biology currently taking my first steps in bioinformatics. I was reading a paper when I came across the term "constrained genetic elements", referring to ...
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69 views

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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389 views

Transfect Mammalian Cells with Single Stranded DNA?

Agrobacteria can deliver parts of their DNA to plant cells as T-DNA, transfer DNA. This DNA is delivered as a single strand and can be integrated into the plant genome or can be converted to a double ...
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Will a Kozak sequence within a coding sequence interfere with eukaryotic expression?

I want to make a DNA vaccine for fish by using plasmid pcDNA3.1(+) with a bacterial antigen. Unfortunately, there is a Kozak sequence in the middle of my target gene. I am concerned that this Kozak ...
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DNA extraction from parasitic worm

I have a part of a parasitic worm frozen at -20°C. Do you think that DNA extraction using DNeasy kit without any pre-treatment is sufficient for DNA extraction? Or would you recommend bead beating / ...
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What are the advantages of long read sequencing for cancer oncogenomic research?

Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of ...
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32 views

Why can DNA tests with mixed DNA of several people not be used to detect a criminal in a database?

Scenario: Two males attack another pair of two males with a weapon. The attackers are fought off and the weapon remains. Why does the police require DNA samples of the two who have been attacked to be ...
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How would one model a Neutrophil Extracellular Trap with Hookean Springs?

This is a question based in biology but involves a good amount of physics. Given that a Neutrophil Extracellular Trap (N.E.T) behaves like an aggregate of DNA strands with citrullinated Histones and ...
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Can DNA rings, i.e. plasmids, form as Möbius strips?

I know that plasmids can be present in a coiled form, which keeps the DNA strands together when they degenerate, by forming catenases. I was wondering, however, whether it has been documented to ...
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51 views

Changes in DNA and forensic cases

If DNA changes over time, how is it that forensic DNA gathered decades ago can be matched to a person today for solving crimes?