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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getting PDB file of interested sequence

I want a PDB file of DNA sequence I am interested in (10 base pairs) for docking. I will appreciate if any of you can please clarify some of my doubts. Do you think, I can generate PDB file by using ...
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Can two of a persons relatives who are unrelated to each other, one through each parent, match on the same chromosome segment?

Regarding the title, I would like to emphasize, assuming no recent endogamy. To be clear, let's say they're distant enough that any endogamy would be expected to be less than 5 continuous ...
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What can you do with DNA at home?

I just heard of a simple procedure that involves using salt, dish soap, and water to extract DNA from fruit. I was wondering if there's anything you can actually do with this DNA once it's extracted? ...
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Molecular biology- Protein- gene interaction [closed]

I have a hypothesize that an N-terminal domain of a protein is responsible for sequence-specific interactions with the regulatory region of a gene. Which experimental strategy would be best to test my ...
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36 views

Ordering Primers: When to choose wet vs dry delivery format?

Whenever ordering primers, I'm always asked to specify which delivery matrix I prefer to have the oligos delivered in: wet (in water or some kind of TE buffer) vs. dry. My understanding is that when ...
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Are the complementary base pairs known as genes? [closed]

In my text book ,it is written that a chromosome has 1000s of genes and it is distributed throughout the chromatids except in the centromere. But we know that the chromosomes have DNAs inside them ...
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Is there a standard for how to encode DNA base pairs numerically?

DNA base pairs are made of the chemicals ATGC. Or is it ACGT? Or AGCT? Or TCAG? Etc. I'm curious if there is a standard on what order these chemicals go in, for writing purposes and specifically ...
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76 views

Can we cure cancer with CRISPR dead Cas?

Here's a silly idea I had this morning: Sequence a bunch of normal patient cells. Sequence a bunch of tumor cells from a biopsy. Find a DNA sequence that we're reasonably certain exists in the cancer ...
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98 views

How many different DNA molecule classes does a person have?

Books always refer to human DNA as a unique molecule, and two different humans generally have different DNA molecules. But how many different types of DNA molecule does a person have? In order to make ...
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Why don't we use hybridization instead of PCR? [closed]

So, I would like to ask, why don't we use just DNA hybridization instead of PCR primer amplification to diagnise some illness? I know, when you have a really small amount of DNA from virus or cell you ...
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How to generate PDB file for custom DNA squence(10 base pairs)

I am trying to study docking of drug-DNA interaction and for that I need PDB file. How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)? I will really appreciate if you can ...
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92 views

Why is there no wavelength change in the hyperchromic shift in DNA?

From Wikipedia article on hyperchromicity (emphasis my own): "When the bases become unstacked, the wavelength of maximum absorbance does not change, but the amount absorbed increases by 37%.&...
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300 views

Why can mRNA come out of the nucleus but not enter it?

I am a mechatronics engineer who stopped learning biology after high school - but this is bothering me. mRNA is, if I recall correctly, created in the nucleus of the cells and migrates out of the ...
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78 views

Why does Diphenylamine only react with the deoxyribose of purines?

The deoxyribose in DNA in the presence of acid forms β-hydroxylevulinaldehyde which reacts with diphenylamine to give a blue color with a sharp absorption maximum at 595nm. In DNA, only the ...
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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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Meaning of ‘motif’ in molecular biology

I would like to understand the meaning of the term motif as used in molecular biology. In an article in Nature Biotechnology, Patrik D’haeseleer states: Sequence motifs are short, recurring patterns ...
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47 views

Do same DNA sequences lead to the same proteins in all organisms? [duplicate]

I'm not a biologist, but I am curious about a particular question about DNA. As I understand DNA encodes proteins using special sequences of nucleotides and cells decode these proteins from DNA during ...
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127 views

Why doesn't RNA polymerase just rotate?

I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. ...
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91 views

Does DNA have 5 nitrogenous bases?

Does DNA have 5 nitrogenous bases? I believe they are 5 because Uracil is not the same thing as Guanine, because, first of all, uracil "replaces" thymine, not guanine. And second, uracil ...
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82 views

What are the prospects in synthetic biology, especially in the introduction of biological computers? [closed]

One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I ...
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129 views

Is circular DNA the same as plasmids?

Chloroplasts have circular DNA, but would it be right to say that they have plasmids? Are plasmids and circular DNA even the same thing? Thank you in advance.
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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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How do we know genes that are considered endogenous retroviruses are actually endogenous retroviruses and not just ordinary genes?

What makes these genes different as to be classed as an endogenous retrovirus? I've read the entirity of Wikipedia on retroviruses and didn't find the answer. I think it could be that these genes are ...
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51 views

How is the possibility of beneficial mutations ensured in the genome?

To ensure natural selection and variability, the genome must have a structure in which the occurrence of beneficial mutations has a high enough probability. But how is this ensured? The space of ...
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93 views

What would an organism be like if its entire genome "worked"? [closed]

It is known that a large fraction of the genome of almost any organism "does not work", that is, it does not encode any proteins and does not participate in gene expression, in protein ...
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104 views

Has life on Earth explored the entire space of genomes?

Recently I came across a 2008 article, the authors of which argue that in fact the space of protein sequences is not as large as it might seem, and that life on Earth has most likely already explored ...
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45 views

Is there any way to identify if chromosomes are inherited from the same parent?

I'm a PhD student in bioinformatics working on genomic data, and I was wondering: If I have access to a person's chromosomes, is there an assay that can determine that two chromosomes come from the ...
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40 views

What is targeted gene disruption?

I am a bit confused about what targeted gene disruption means. I was reading this article in which they compare the Pyrococcus Furiosus genome with a genetically tractable strain P. Furiosus variant ...
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77 views

How much genes can be knocked down at the same time

When experimenting on mice, gene knockdown seems to be a useful technique to deactivate individual genes to study what they are doing. In practice what's the maximum of genes that can be knocked out ...
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114 views

What is prochromosome?

My textbook says that prochromosome is a false chromosome present in the nucleoid of prokaryotes. I looked up Wikipedia and all over internet and this word is kinda sus. So I'm asking about it here. ...
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What species is the ancestor of the African Basenji dog?

I thought domestic dogs were descended from the wolf (Canis lupus). However, this article suggests the African Basenji is one of the oldest dog breeds. But the wolf is only marginally native to Africa ...
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Cell location co-ordinates [closed]

I have just had the nails on both my big toes removed. I am much happier. But it got me to thinking, as there is no 'root structure' from which the nail grows, is there an x,y,z, type co-ordinate ...
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Why do more complex DNA strands take longer to anneal?

My textbook and several websites told me that more complex DNA strands take longer to anneal because it is harder to find the correct sequence. A simpler, repeating sequence like ATATATATA would be ...
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Which method of gene amplification for toehold switches?

My team and I are from a high school and are planning to carry out some research investigating some toehold switch riboregulators which we have designed in silico. However, we have little experience ...
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47 views

Does Remdesivir cause bone marrow suppression?

According to Wikipedia, Remdesivir is a prodrug of GS-441524 which is a nucleoside analog. I know that nucleotides are the building blocks of both DNA and RNA, meaning nucleotide analogues that ...
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1answer
59 views

What can be used for DNA preservation?

I am neither a student nor really advanced in biology, I am just writing a tabletop role-playing game scenario that I want as realistic as possible. In the story, the players find an old laboratory ...
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51 views

Genomic library preparation: Why does the restriction enzyme not cut into the gene?

I am currently trying to understand creating a genomic library more profoundly. In most textbooks I read (as well as wikipedia), they mentioned that the genomic library is created by isolating the DNA ...
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65 views

What does does a blood sample tell you about an individual's identity?

I am working on a fiction/mystery scene where blood is found in a particular character's residence but the character themselves is missing. I would like to understand whether the law enforcement/...
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54 views

Virus variant transmissibility: empirical data or spike protein shape?

Well first I am not in the field of Biology or Medical Sciences. Since these days we are waiting scientists to tell us if the Indian variant of SARS Cov 2 is more transmissible than the original virus,...
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103 views

Can a strand not be synthesised in 5' -> 3' direction?

I've been solving some biology questions, and according to one of them ( I have the responses too) the following phrase is false: "Both strands are always synthesised in the 5' to 3' direction.&...
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Why is Somatic Cell Nuclear Transfer (SCNT) less effective for interspecies?

Somatic Cell Nuclear Transfer (SCNT), a process for replacing the nucleus of an egg cell with a nucleus containing genetic information of a different animal, seems to be very useful for cloning and ...
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58 views

Direction of translation/transcription

Perhaps it would not be wrong to say that "translation/transcription goes in the direction of 3' to 5'" or "in the direction of 5' to 3'";that's because these statements are ...
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67 views

How do you determine "in which direction" DNA is shared between groups of people

In popular DNA ancestry tests you can read lines like "you have 2% neanderthal dna" or "you have 20% italian". How can you distinguish between a person having 20% italian vs ...
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How was gene knock out done in pre CRISPR era?

I am trying to understand how CRISPR has made the gene knockout or gene editing process simpler to make transgenic animals. Here is an old (pre CRISPR) flowchart from Manis, 2007 that shows how ...
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Are there any "in vivo" DNA replication fidelity assays?

I haven't been able to find a way to assess the fidelity of DNA replication in vivo as opposed to in vitro. I was wondering, would it be possible to find this by sequencing the DNA of individual cells ...
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75 views

By selecting sex cells after meiosis, would it be possible to create two offspring with inverse parental DNA of one another? [closed]

Would it theoretically be possible to select two sex cells after a male meiosis (filtering out the two where crossover had taken place) and combine each with two sex from a female meiosis (imagining ...
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102 views

Why is DNA replication not 100% accurate

I've been reading about DNA mismatch repair (MMR) and how this process improves DNA fidelity. However, I was wondering, what is stopping MMR from correcting all mistakes in the daughter DNA with 100% ...
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170 views

Forward or Reverse Strand: Is there a difference when encoding genetic devices?

Background: In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic ...
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663 views

What if target DNA doesn’t have restriction sites

All the examples on DNA cloning I have encountered have assumed that the target gene and vector both have compatible restriction sites at just the right locations (probably for ease of explanation). ...
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Geometric Interpretations of the DNA Double Helix

In mathematics, a helix is a shape which has constant curvature and constant torque (see Wikipedia here. What are the biological implications of the DNA double helix having constant curvature and ...

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