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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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How, exactly, does single-strand DNA editing (prime,e.g.) work? What happens to the second strand?

When reading or hearing about 'prime' CRISPR editing, it is always stated that the 'prime' advantage of prime editing is that it only affects one strand..... But... What happens to the second, ...
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DNA slippage as the cause of insertion mutations in cancer cells?

I'm a computer science student who has started working with DNA. I know the basics but not everything. While working on the ICGC data, I found a weird pattern in the insertions: In around 60% of the ...
Wassim Jaoui's user avatar
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Understanding DNA Fingerprinting

I am a high-school student learning about DNA fingerprinting. I know that satellite DNA is non-coding DNA and has a lot of repetitive sequences, and the length of each repeat can be either short or ...
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Can bacterial DNA solutions, which include other cellular components, be stored without compromising DNA stability?"

Question Can bacterial DNA solutions, which include other cellular components, be stored without compromising DNA stability?" Details I'm using the boiling extraction method to extract ...
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How do you find the template strand for a sequence where start codon is in both strands?

Maybe I'm missing something very obvious but I can't seem to understand how to find the template strand given a sequence and its complementary strand if both strands contain ATG from 5' -> 3'. ...
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Correlation of Meselson and Stahl with “multifork” replication in E.coli

Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous ...
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Mathematical periodic turns in DNA

Today our college professor gave us a mathematical biological challenge in DNA. He challenged us to find the pattern in which DNA follows the following equation in its periodic turn. How can we crack ...
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Is it possible to plant tardigrade DNA into a human? What would happen even if?

So I have been reading a WEBTOON (A distant sky) and the 2 mcs have tardigrade stem cells in them which gives them the abilities tardigrades have. I am aware that the story is obviously fictional, but ...
pluto134340's user avatar
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Can DNA reveal an approximate chronological generation of a person?

Given complete nuclear and mitochondrial DNA from an individual, would it be possible to approximate in what generation they were born? For example, imagine DNA from someone who lived circa 200 to 700 ...
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Preserving a sample for mtDNA and nuclear DNA analysis

Imagine a person in the early half of the 20th century (1900 to 1950) took some kind of sample(s) from a living human body using any technology of the era. They then stored it using any technology ...
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Change of DNA concentration due to restriction digest?

Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about ...
Michael Gruenstaeudl's user avatar
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How to generate PDB file for custom single strand DNA squence(46 bp)?

I need to generate a pdb for ssDNA to research the interaction of DNA and proteins. I will really appreciate if you can please guide me. Thank you all for your time.
HaiYang Li's user avatar
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Fridge vs freezer for short-term DNA storage – how long until freezer is better?

I know keeping DNA products in the freezer (-20°C) is preferred for long-term storage, but the downside is that freeze-thawing can cause shearing/breaking of the DNA. For short-term storage the fridge ...
Joel's user avatar
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Problem during DNA extraction from blood using automated magnetic beads extraction protocol

We've been using the Perkin Elmer Prepito D instrument + the Blood 250 associated kit for DNA isolation from blood for the last couple of years. It's been working well, however, lately the resulting ...
Safae Simma's user avatar
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Can a deletion occur on only one strand of a human chromosome?

Hello. Is it possible that a deletion can occur in the middle of only one strand of a human autosomal chromosome?
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Can a person have different sex at cellular level?

I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....
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qPCR precipitation

I have performed DNA precipitation using two methods on an amplified 194 bp PCR product: using a PEG method with just cold 80% ethanol PEG worked much better for me. Can the same methods be applied ...
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Are all humans related to one mother and one father? [duplicate]

Are all humans related to one mother and one father ? What is proof for that? If that is case,that mean brother and sister reproduce, this is incest, so how population survived?
user707264's user avatar
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How many base codes are in DNA? Two or four?

We know there are four bases found in a DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). We also know that A always pairs with T and G always pairs with C. Can we say that the DNA is ...
Mehdi Abbassi's user avatar
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Reverse protein biosynthesis in nature

This is more of a funny question to think about, but I am wondering, theoretically if it is possible in cells to synthesize nucleic acids(DNA, RNA) from proteins. What might this be useful for and how ...
bioHacker's user avatar
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How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation?

From 'Protein and DNA Sequence Determinants of Thermophilic Adaptation', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | https://doi.org/10.1371/...
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Ames Assay Confusion: Aren't the odds of spontaneous revertants too low to be able to accurately test the mutagenicity of certain compounds?

I am a student conducting a test with the Ames Assay. This assay uses a strain of bacteria that has a mutation in an amino acid synthesizing operon, which doesn't allow it to synthesize its protein. ...
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How do molecular biologists typically get their oligos?

What's the typical route taken to obtain synthetic DNA/RNA samples in practice? Are they pretty much always custom ordered from a place that prints them using sold-phase synthesis, or can you cobble ...
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Determining the Length of DNA in a Human Spermatozoon

Hello everyone, I’m currently trying to solve a problem related to DNA length in human spermatozoa and could use some guidance. The problem states: “The DNA of one human spermatozoon contains 10^23 ...
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How many generations does it take for the average descendant not to be genetically related to the ancestor?

Parent 1 and 2 have children. Assume infinite, randomly-mating population size. How many generations until the median descendant by lineage of parent 1 has 0 base pairs inherited from parent 1? I ...
BigMistake's user avatar
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Inheritance of child behavior based on daily life experiences of the parent

Our brain is a large network of neurons connected with each other.Our daily experiences change how our neurons are connected.Some experiences create better connections between two neurons A and B and ...
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Calculating pitch of B-DNA

From this question (How pitch of a DNA Helix is 3.4 nm?), I've learnt that for counting the number of axial rise for 10 base pairs in 1 helical turn to measure the pitch of B-DNA, we have to include ...
Apogee Point's user avatar
2 votes
1 answer
131 views

Is it possible to proccess human genome in a local computer?

I have some basic programming knowledge, and I would like to take a look at my genome and search for specific sequences related to mental illness and addiction. The test costs only 1000$ in Spain and ...
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What do alleles look like visually on linear DNA strands?

I've seen many textbook images of alleles on homologous chromosomes with the gene loci identified but how could this be visualised on linear DNA sequences with the bases written out? Is it that you ...
mydearestpotato's user avatar
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Overlapping annotated regions among repetitive families of human genome

I am studying the repetitive elements in the human genome and I have come to know that some genomic locations are not uniquely described by a single repeat family. What's behind this uncertainty? Does ...
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What is the approx. diameter of a completely "folded up" human DNA molecule, in inches?

The human DNA molecule would be about 6ft if stretched out to a straight line. I'm curious what the diameter of the DNA molecule normally is when it is "all scrunched up" or "bundled&...
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ddT-tailed TA cloning, and the fate of a double nicked plasmid in E. coli

In an undergraduate lab class on TA cloning, it was explained that ddNTPs are used as the substrate for terminal transferase when making the T overhangs of the vector. I was told this was to ensure ...
jettosutorimu's user avatar
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What's the significance of DNA replication (S phase) before Meiosis?

From what I'm able to understand, Meiosis should end up with haploid cells with chromosomes having single chromatids (I don't know why it's necessary, but alright) I understand that meiosis has a ...
user76486's user avatar
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Start codon and 5' codon

Here it says: For amino acid-based systems, the start codon of the mature protein is labeled codon 1. The codon 5' to this is numbered -1. So, I assumed the START codon is either -1 or 0. But, when ...
FluidMechanics Potential Flows's user avatar
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How pitch of a DNA Helix is 3.4 nm?

How pitch of a DNA Helix is 3.4 nm? In the image that I have attached, the numbers with prime represent the number of base pair and normal numbers represent the number of gap elements between two base ...
Peter swift's user avatar
1 vote
0 answers
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Does blunt end have a hydrogen bond?

I am an undergraduate student of biology. I saw a lecturer online, who said that sticky ends makes phosphodiester and hydrogen bonds cut. (also here). But why blunt end just makes phospodiester bonds ...
arsy's user avatar
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2 votes
1 answer
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Are DRB3 DRB4 and DRB5 different genes or different version of the same gene

From what I understand, an individual can hold up to two HLA-DRB345 alleles (but can be less) that can each be HLA-DRB3, HLA-DRB4 or HLA-DRB5. However, since HLA-DQB1 and HLA-DQB2 are entirely ...
FluidMechanics Potential Flows's user avatar
1 vote
1 answer
219 views

what are average, median, and minimal dna closeness of stranger peoples, compared to closeness of relatives?

i thought: a parent closeness to a person can be marked as 50%. seems that is 50% of all parts of dna of humans that have variability across all human population. i heard that chimpanzees are 98% ...
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Must RNA and DNA be the way it is?

We're carbon-based based life form with (mostly) iron-based oxygen transportation for apparently good reasons. Is the same true for why life on Earth developed using nucleotides, amino acids, RNA and ...
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How to quantify and measure phenotypic variation?

It is easy to quantify and measure genotypic variation, because genes are digital, like the 1's and 0's of a computer. You just check how many places the gene "letters" A,C,G,and,T differ. ...
user107952's user avatar
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What does 'bend angle' of DNA mean?

Literally, what does the 'bend angle' of DNA mean? I did some googling but I couldn't understand it. How is it defined?
yeseong Bae's user avatar
1 vote
1 answer
50 views

How are probes in capture sequencing synthesized?

In capture sequencing it is common practice to use a panel containing ~10,000 probes. How are these DNA molecules synthesized? I imagine that there is a way to do this in parallel, but I haven't been ...
Peter Wu's user avatar
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1 answer
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If sufficienly many people are born, then is it possible that two persons are genetically identical although they are not twins?

It is my tought experiment. Since for human, the genome information is finite, if so many many people are born, then there exist two people who have the same genome although they are not a twin. Is it ...
with-forest's user avatar
4 votes
1 answer
131 views

What makes protein binding to the DNA random?

We know that the genetic recombination process in known as a random process. On the other hand, it has also been discovered that certain proteins (such as PRDM9) determine what recombination hotspots ...
Alex L's user avatar
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How do we know that the DNA we share with other species (especially primates) isn't fully the result of transposable elements?

I recently read a couple studies that concluded the 25% of genetic similarity between cows and reptiles is actually primarily due to TEs (transposable elements) rather than common ancestry. Here's the ...
Mihir Dhawan's user avatar
2 votes
1 answer
187 views

Telomerase and End Replication in Eukaryote

Here is a picture of using telomerase in solving end replication problem (Courtesy: Molecular Biology of the Cell, Alberts, Garland Science Pub.) Now lets consider the $3'$ end here, we are extending ...
user3001408's user avatar
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1 answer
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Can I have LAMP on the bench / in the field?

I am interested in LAMP for detecting small amounts of DNA (loop-mediated isothermal amplification and yes, I know the initials don't match). I am trying to figure out exactly how clean/(sterile?) ...
Laura's user avatar
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24 votes
3 answers
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How do proteins 'know' where to go?

I've just found once again this famous animation I've been curious about for many years: https://youtu.be/WFCvkkDSfIU?t=213 Here's a screenshot from the animation: The green blobs (proteins, I ...
Vladislav's user avatar
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Population structure and SNP's in Linkage Disequilibrium

I am reading about population structure and how you could as an example use plink to analyze a set of SNPs for individuals in a vcf file to identify a given population structure. I know that LD can be ...
RAHenriksen's user avatar
5 votes
1 answer
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Is Chimpanzee mitochondrial DNA identical to human?

How similar is chimpanzee mitochondrial DNA to human? Does it show the same single ancestor?
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