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Question: <p>A bodies genetic material provides the blueprint for your appearance. Your predisposition to be tall, freckled, blue eyed and blonde are encoded from birth.</p>
<p>However, external and environmental factors can influence the manner these instructions are carried out. For example malnutrition during childh... | https://biology.stackexchange.com/questions/52410/can-genetic-material-actually-provide-a-physical-description-of-appearance |
Question: <p>Most of my body hair is black however my lip hair is light brown/blonde the rest of my beard region is black. Since hair color is genetic what causes this?</p>
Answer: <p>The hairs you mention are also called "<a href="http://en.wikipedia.org/wiki/Androgenic_hair" rel="nofollow">androgenic hairs</a>", mea... | https://biology.stackexchange.com/questions/16394/why-is-the-human-body-hair-not-uniformly-colored |
Question: <p>Most of the human genes are found to be highly methylated in their 3'UTR region (0.8-0.9%). I was wondering if there is any specific reason for this?</p>
Answer: <p>According to <a href="http://genomebiology.com/2009/10/9/R89">Choi et al. Genome Biology 2009, 10:R89</a>, DNA methylation at both coding bou... | https://biology.stackexchange.com/questions/1541/why-is-the-3utr-region-highly-methylated-in-most-of-the-human-genes |
Question: <p>I don't know if this is a real claim, I live in Mexico City and most of the people I know are more similar to their father than to their mother? Why is that? Are the x and y cromosomes somehow related to the strength of a particular gen?</p>
Answer: | https://biology.stackexchange.com/questions/59639/on-parents-similarity |
Question: <p>This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.</p>
<p>Regarding Evolution, nothing, absolutely nothing, that a person does to herself in... | https://biology.stackexchange.com/questions/884/is-it-the-case-that-all-changes-in-phenotype-during-life-are-not-inheritable |
Question: <p>I was reading "<a href="http://www.wisdom.weizmann.ac.il/~/eran/NucleosomeModel.pdf" rel="nofollow noreferrer">A genomic code for nucleosome positioning</a>" (by Eran Segal et al). And I am having 2 doubts.
<img src="https://i.sstatic.net/7eyzE.png" alt="enter image description here"></p>
<p>The figure(b)... | https://biology.stackexchange.com/questions/30342/doubt-on-genomic-code-for-nucleosome-positioning |
Question: <p>I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to make a Russian doll analogy. I know about epigenetic markings but I am really looking at an example of a DNA ... | https://biology.stackexchange.com/questions/30416/enhancers-of-enhancers |
Question: <p>I was thinking about a fiction world in which all animal (at least vertebrate) could crossbred because they share same number and layout of chromosome but differ in hereditary detail (like human skin color) and/or using epigenetic modifications.</p>
<p>Is it actually possible? And how large of DNA it coul... | https://biology.stackexchange.com/questions/51557/is-it-possible-to-create-dna-of-a-species-that-could-be-any-animal |
Question: <p>So I am trying to brush up on my knowledge of HATs and HDACs.</p>
<p>I am reading the just the 1st paragraph of the background of this <a href="https://www.alzforum.org/therapeutics/amx0035" rel="nofollow noreferrer">study</a></p>
<p>I remember learning that HATs turn things on on, and HDACs turn things ... | https://biology.stackexchange.com/questions/93758/histone-deacetylase-inhibition |
Question: <p><a href="http://en.wikipedia.org/wiki/Polyploid">Polyploidy</a> is the multiplication of number of chromosomal sets from 2n to 3n (triploidy), 4n (tetraploidy) and so on. It is quite common in plants, for example many crops like wheat or Brassica forms. It seems to be rarer in animals but still it is prese... | https://biology.stackexchange.com/questions/935/why-is-polyploidy-lethal-for-some-organisms-while-for-others-is-not |
Question: <p>Recently Southern California experienced extreme wind velocities and afterwards the news reported over 300 trees had fallen in San Diego County. I had either heard or read somewhere that the action of the wind and bending of a tree assists to strengthen the roots ( I suppose as long as the wind is not stro... | https://biology.stackexchange.com/questions/43014/does-the-bending-of-a-trees-trunk-in-the-wind-stimulate-and-strengthen-root-gro |
Question: <p>I'm familiar with how CRISPR works to make either knockdown or amplification effects for a single gene because you can make precision cuts. </p>
<p>What exactly does a pooled crispr screen do & how does it work?</p>
Answer: <p>In the context of pooled CRISPR screen, you first design a library of gRNA... | https://biology.stackexchange.com/questions/92506/simple-explanation-of-a-crispr-screen-vs-pooled-crispr-screen |
Question: <p>"CRISPR" and "Cas9" are different things. When a virus attacks a bacteria, the bacteria stores the viral code of the virus in CRISPR. And when the virus attacks again the Cas9 protein uses the RNA in the CRISPR to find the viral DNA and then destroy it.</p>
<p><strong>So, what is the us... | https://biology.stackexchange.com/questions/100421/is-crispr-being-utilized-when-scientists-use-the-crispr-cas9-system-to-edit-gene |
Question: <p>I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.</p>
<p>CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amoun... | https://biology.stackexchange.com/questions/30839/splice-in-with-crispr-cas |
Question: <p>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. </p>
<p>It is really not clear to me, most of the documentation I have found focuses on the subsequent steps (expression and interference) ... | https://biology.stackexchange.com/questions/34811/crispr-cas-systems |
Question: <p>With CRISPR-Cas9 I have conducted a targeted knockout of a DNA region encoding a certain protein (working with leukocytes). My question is, how long does it take until this protein is not detectable any more (e.g. via surface staining + flow cytometry) after the DNA has been manipulated? Or in other terms:... | https://biology.stackexchange.com/questions/91082/crispr-cas9-knockout |
Question: <p>Are Restriction Enzymes obsolete with CRISPR?</p>
Answer: <p>No.</p>
<p>While CRISPR allows you cut a piece of DNA anywhere, you need to order a guide RNA to target your desired cut site. All standard plasmids still carry traditional restriction sites, and it's often convenient to use these. Using CRISPR... | https://biology.stackexchange.com/questions/74475/are-restriction-enzymes-obsolete-with-crispr |
Question: <p>Using the CRISPR/Cas9 technology, it is possible that after inducing a DSB with the Cas9 endonuclease guided with an RNA designed by the user and using a template DNA, get a desired Knock-In (KI) by homologous recombination.</p>
<p>I have read that for desired KI-s that are less than 200 bp, a olygonuclea... | https://biology.stackexchange.com/questions/30460/crispr-knock-in |
Question: <p>Is the crispr (where the parts of Virus DNA is saved) section of the DNA existing in human cells aswell or is it just in bacteria cells?</p>
Answer: <p>No analogues of the CRISPR-Cas system have been found in any eukaryotic species, including humans. So far, it appears to have evolved only in prokaryotes ... | https://biology.stackexchange.com/questions/78609/crispr-complex-in-human-cells |
Question: <p>I'm learning about CRISPR at my college.<br/> I understand that when viral DNA is inserted into a bacterial cell, the <strong>Cas1-Cas2</strong> proteins identify the <strong>PAM</strong> site in the viral DNA and then cut the protospacer from the viral DNA to make it a spacer in the CRISPR array for the a... | https://biology.stackexchange.com/questions/115330/why-do-bacteria-need-the-crispr-system |
Question: <p>I am doing CRISPR/Cas9 experiment on <em>E. coli</em>. I am introducing recombinant plasmid BPK764 (which carries Cas9 + sgRNA designed and added later in that plasmid) into compentent <em>E.coli</em> cells which already carries another plasmid with GFP gene. sgRNA will be designed so that it corresponds ... | https://biology.stackexchange.com/questions/82134/crispr-cas9-edited-e-coli-on-afm |
Question: <p>The use of crisper-cas systems is currently applied to cells cultivated in vitro. As control of the ‘off target’ effects of Crispr improves and Crispr is used in vivo, why won’t the immune system neutralize it?</p>
Answer: <p>Usually not. the Crispr/Cas proteins can be delivered to the cell as DNA/RNA an... | https://biology.stackexchange.com/questions/94978/does-immunity-to-crispr-proteins-limit-their-effectiveness |
Question: <p>I need to stop some protein from being active and searching for some universal way to do so. In mammalians. </p>
<p>With CRISPR it is possible to knock-out the entire gene. But it's a little complicate (need two gRNA for eg.). There are also another reasons, so I need to do this with only one gRNA.</p>
<... | https://biology.stackexchange.com/questions/31928/mutations-deletions-with-crispr |
Question: <p>If CRISPR is used to modify the DNA sequence to cure a disease - say MS in a woman - will the RNA guides also modify the sequence in her eggs so her children could be born without MS inherited from her.</p>
Answer: <p>First off, CRISPR can't be used to cure diseases in an adult human or, more generally, f... | https://biology.stackexchange.com/questions/62675/inheriting-modified-dna-after-crispr-editing |
Question: <p>If I'm not mistaken only RNA viruses insert themselves into the host genome. As an example of DNA viruses, herpes viruses for example do not insert themselves in the host genome.</p>
<p>Can CRISPR cut DNA that isn't in a chromossome, like a DNA virus?</p>
Answer: <p>Yes, this should in principle work, an... | https://biology.stackexchange.com/questions/81849/can-crispr-also-remove-dna-viruses |
Question: <p>I had a quick questions on the size limitations of a CRISPR guide. More specifically on the shorter end. Can I make a guide that is say 7-10bp and still have an active complex? I transfect using an RNP system. </p>
<p>Just curious. </p>
<p>Thanks in advance. </p>
Answer: | https://biology.stackexchange.com/questions/80464/size-constraints-on-crispr-guide-rna |
Question: <p>As a critical stage in the CRISPR-Cas9 system, two different mechanisms of DNA repair can occur in the target DNA after RNA has been introduced: non-homologous end joining (NHEJ) and homologous recombination (HR).</p>
<p>Can these repair mechanisms be intentionally controlled or manipulated, and if so, wha... | https://biology.stackexchange.com/questions/111668/crispr-cas9-system-dna-repair |
Question: <p>I am currently designing a mock CRISPR knock-out experiment, and I’m wanting to insert a plasmid for selection. Using a restriction enzyme at 2750bp for cutting, would the location of the cut site then be considered position 1?</p>
<p>I’m wanting to run PCR after insertion to confirm it has been successful... | https://biology.stackexchange.com/questions/111705/linearising-plasmids-for-crispr-experiment |
Question: <p>I am collecting literature to start a new project on CRISPR/Cas9 gene editing. I must put together a protocol to start and am intending to use the following paper as guidance:</p>
<p>"Genome engineering using the CRISPR-Cas9 system". Nature Protocol 8(11):2281-308 · November 2013</p>
<p>Could you please ... | https://biology.stackexchange.com/questions/45836/what-is-the-most-up-to-date-crispr-cas9-protocol |
Question: <p>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 <a href="https://pubmed.ncbi.nlm.nih.gov/18077807/" rel="nofollow noreferrer">Manis, 2007</a> that shows how knockouts can be made.
<a href=... | https://biology.stackexchange.com/questions/100416/how-was-gene-knock-out-done-in-pre-crispr-era |
Question: <p>CRISPR-cas9 uses a string of RNA that matches with DNA and makes a double stranded cut at that point. </p>
<p>If the RNA is just a few letters in length, the enzyme would cut DNA in many places. It would be unspecific. But if you can make the RNA string very long, it would only cut at the exact place wher... | https://biology.stackexchange.com/questions/49106/how-specific-are-crispr-cas9-cuts |
Question: <ol>
<li><p>Theoretically speaking, can you insert the gene sequences for cas9, sgRNA, and promoters into the host genome so that the cell perpetually produces CRISPR components?</p>
</li>
<li><p>In this scenario, I'm guessing there would be no way to have the host cell produce DNA templates for HDR?</p>
</li... | https://biology.stackexchange.com/questions/111231/can-the-genetic-sequences-for-crispr-components-be-inserted-into-the-host-genome |
Question: <p>While at school, I learnt about restriction enzymes and how you could insert foreign DNA into an organism.</p>
<p>When I first heard about CRISPR I thought it was very similar except much more precise/targeted.</p>
<p>It seems however that CRISPR only allows editing (substituting nucleotides)</p>
<p>Wha... | https://biology.stackexchange.com/questions/88193/whats-the-difference-between-traditional-genetic-engineering-and-and-crispr |
Question: <p>One confusing thing I have found when reading articles about possible CRISPR based gene therapy treatments in humans is that there is vey little discussion about what percentage of your cells will actually have their DNA edited, the rate at which the editing takes place, and how to quantitatively estimate ... | https://biology.stackexchange.com/questions/74171/mathematical-models-of-gene-editing-using-crispr |
Question: <p>Can CRISPR-Cas9 make changes on a living organism? What's the limit here? E.g. reversing/restoring hearing loss in a living adult mice.</p>
Answer: <p>Answer is yes, but it depends on which kind of phenotype you're going to restore/change. As you can imagine, using crispr cas9 on an high amount of cells r... | https://biology.stackexchange.com/questions/66782/can-crispr-cas9-make-changes-on-a-living-organism |
Question: <p>I am currently reading an article about a particular assay of Cas9 nucleases. In one of the experiments, they have used ApoCas9 (Apo variants of other CRISPR nucleases) as some sort of control. </p>
<p>But the whole article they have not defined ApoCas9? I did check online of definition and activity of Ap... | https://biology.stackexchange.com/questions/85949/what-is-apocas9-in-the-crispr-cas9-system |
Question: <p>I've been researching into the biohacking world where people most notable <a href="https://en.wikipedia.org/wiki/Josiah_Zayner" rel="nofollow noreferrer">Josiah Zayner</a> and <a href="https://www.bbc.com/news/world-us-canada-41990981" rel="nofollow noreferrer">Tristan Roberts</a> have used a CRISPR soluti... | https://biology.stackexchange.com/questions/81004/diybio-crispr-injection-sites-for-targeting-the-abcc11-gene |
Question: <p>I need some help about Crispr / Cas9.
The CRISPR/Cas9 technic consists (for bacterias) in "cut" bacteriophage's DNA, in order to make it unfunctional.
When the RNA is transcribed (RNA which is complementary to the bacteriophage's DNA), it will be associated with crRNA and tracrRNA to form the sgRNA (single... | https://biology.stackexchange.com/questions/58400/functions-of-tracrrna-and-crrna-in-the-crispr-cas9-system |
Question: <p>I've been out of Biology for about a year polishing my programming skills. I know CRISPR/Cas9 allows targeted 'cutting' of DNA via RNA-guidance. Few questions regarding this.</p>
<ol>
<li><p>Regarding to its natural phenomenon, when a virus infects a microbe with CRISPR capabilities, how does the genome g... | https://biology.stackexchange.com/questions/40576/in-crispr-bacteria-how-does-viral-genomes-get-integrated-into-the-spacers-of-cr |
Question: <p>I would like to insert a 1500 bp or longer gene to the broken site in E.coli (or may be <em>bacillus subtilis</em> which support NHEJ) after cut with Crispr-Cas9. Is this possible for both NHEJ or HDR?</p>
Answer: | https://biology.stackexchange.com/questions/79267/can-crispr-cas9-be-used-to-insert-a-large-gene |
Question: <p>I am new to the CRISPR Cas9 genome editing system and I have the above basic question.</p>
<p>Another way to think about this: what would happen if after cells are transfected, the cultures are left to grow without any selection. Thus, if a mutation disrupts a cell cycle gene (e.g. p53), such cells will p... | https://biology.stackexchange.com/questions/46094/why-selecting-cells-after-gene-editing-with-crispr-cas9 |
Question: <p>I am trying to knockout huntingtin gene from HeLa cells (human epithelial cells). I used CRISPR explorer and benchling.com to determine the best guide RNA sequence that would bind to the target DNA sequence and cas9 could then make the cut. The gRNA I have is as follows:</p>
<p>GGAGGCCTCGGGCCGACTCG
Strand ... | https://biology.stackexchange.com/questions/59627/crispr-guide-rna-design-and-primer-synthesis |
Question: <p>From what I understand, in a CRISPR cas9 complex, gRNA is comprised of tracrRNA and crRNA. I've read that crRNA is the part which is matched to the DNA which is targeted, but what role does tracrRNA play in the process? That I'm not clear about. Also, unless this should be its own question; how is gRNA ... | https://biology.stackexchange.com/questions/54690/what-is-the-role-of-tracrrna-in-crispr-cas9 |
Question: <p>I'm a student started who has started learning about CRISPR/Cas9. As I understand it, CRISPR/Cas9 is an enzyme that is used to cut a gene at a specific sequence. I would like to know how scientist do the next step to insert/edit a genome.</p>
<p>For example, say I have an original sequence ...AAATTT... I... | https://biology.stackexchange.com/questions/50562/how-to-edit-insert-new-gene-after-cutting-with-crispr-cas9 |
Question: <p>Can gene knockout (e.g. by CRISPR) be referred to as gene inhibition? I am trying to use precise words for a manuscript. We first showed siRNA of a gene has effect X. We also found knockout of the gene has the same effect. For the MS, could I say:</p>
<p>Knockout of the gene showed effect X, confirming inh... | https://biology.stackexchange.com/questions/104967/can-crispr-knockout-of-a-gene-be-referred-gene-inhibition |
Question: <p>I've been reading up a bit on the CRISPR-Cas9 system for gene manipulation. From what I read, it introduces double-strand breaks at specific points determined by the choice of sgRNA. But how do you get from double-strand breaks to editing genes in incredibly specific ways? As far as I read you can fix poin... | https://biology.stackexchange.com/questions/29735/how-is-the-type-of-genetic-manipulation-determined-in-crispr-cas9 |
Question: <p>Although I believe there is a good reason -- or reasons -- why this theory, that CRISPR could disable the genes for division in cancerous cells, is incorrect, I haven't been able to find them.</p>
<p>In short, the theory is that multiplexed CRISPR could knock out the genes responsible for cellular division... | https://biology.stackexchange.com/questions/113734/could-multiplexed-crispr-disable-the-mitotic-and-meiotic-genes-of-cancerous-cell |
Question: <p>Here's a silly idea I had this morning:</p>
<ol>
<li>Sequence a bunch of normal patient cells.</li>
<li>Sequence a bunch of tumor cells from a biopsy.</li>
<li>Find a DNA sequence that we're reasonably certain exists in the cancer cells but doesn't exist in normal cells.</li>
<li>Create a guide DNA that ma... | https://biology.stackexchange.com/questions/104755/can-we-cure-cancer-with-crispr-dead-cas |
Question: <p>I read this article <a href="https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/" rel="nofollow">https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/</a> and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the very same t... | https://biology.stackexchange.com/questions/41050/difference-between-micro-rna-and-short-interfering-rna-and-crispr-cas-9-system |
Question: <p><a href="https://knowyourmeme.com/memes/people-with-blue-eyes" rel="nofollow noreferrer">Blue eyes are unsaleable garbage.</a> How would you use CRISPR and gene editing to change a man's eye color from blue to dark brown?</p>
Answer: | https://biology.stackexchange.com/questions/116480/how-can-i-using-gene-therapy-crispr-change-my-eye-color |
Question: <p>I know that <em>Vibrio Cholerae</em> infects the body through the GM1 ganglioside. So, would it be possible to engineer a CRISPR gene editing tool to prevent <em>Vibrio Cholerae</em> from getting into our cells?</p>
<p>Specifically, would it be possible to insert a piece of DNA into our genes that allow t... | https://biology.stackexchange.com/questions/88889/how-to-design-a-permanent-vaccine-to-cholera-using-crispr |
Question: <p>In a CRISPR-Cas9 experiment, the protein cuts the site matching the cRNA part of the gRNA. My question is: How many cuts are possible if multiples sites matching the cRNA are found in the cell?</p>
<p>Especially, considering DNA is made of multiple chromosomes, if more than one chromosome have a site match... | https://biology.stackexchange.com/questions/111127/how-many-cuts-are-done-during-crispr-cas9-in-one-cell |
Question: <p>CAS9 is the RNA-guided endonuclease that cleaves DNA as specified by the RNA sequence and is used to target viruses that infect bacteria. So why doesn't this RNA+endonuclease combo also cleave the original CRISPR spacer sequences (which also have the same DNA?). Is it the same reason that the bacterial gen... | https://biology.stackexchange.com/questions/54696/why-doesnt-cas9-cleave-the-original-crispr-sequence-in-the-bacterial-genome |
Question: <p>So from what I understand, in gene editing, the CRISPR vector expresses a small RNA sequence comprised of a small guide-RNA that is complementary to your target sequence. The sgRNA comprises a 20 Bp CrRNA and a truncated (cut down) TracrRNA right ? </p>
<p>My main question is how does this truncation enab... | https://biology.stackexchange.com/questions/57503/crispr-cas9-what-are-the-main-differences-between-sgrna-and-the-crtracrrna |
Question: <p>Does anyone have experience with the CRISPR/CAS9 platform performed on MEF? Or does anyone recall any relevant articles?</p>
Answer: <p>From <a href="http://genesdev.cshlp.org/content/27/23/2602.long" rel="nofollow">this</a> paper:</p>
<blockquote>
<p>We chose to test for Cas9-driven targeted mutagenes... | https://biology.stackexchange.com/questions/19829/has-anyone-used-crispr-cas-to-induce-a-knock-in-in-mef-cells |
Question: <p>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 try -- i.e. is there any iteration or parallelism involved?</p>
<p>I think the answer is yes for some use c... | https://biology.stackexchange.com/questions/49133/do-users-of-crispr-cas-iterate-or-parallelize-to-try-multiple-guide-sequences |
Question: <p>In <a href="http://elifesciences.org/content/2/e00471" rel="nofollow">Jinek et al.</a>, the authors show nuclease activity of their CRISPR/Cas9 system using the so-called <em>Surveyor assay</em> method. This assay recognizes small mismatches in dsDNA which are introduced by error prone non-homologuous end-... | https://biology.stackexchange.com/questions/38933/why-is-dsdna-nuclease-activity-by-crispr-cas9-only-shown-indirectly |
Question: <p>In <a href="https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(15)00274-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0167779915002747%3Fshowall%3Dtrue" rel="nofollow noreferrer">this</a> paper<sup>1</sup>, I read that mutant versions of Cas proteins such as a deactivate... | https://biology.stackexchange.com/questions/76567/what-is-the-role-of-crispr-dcas9-in-grna-dcas9-transcription-regulator-complexes |
Question: <p>Are scientist able to correct mutiple gene defect in whole body by using CRISPR recently?</p>
<p>AS i know, it is in a beginning stage</p>
Answer: <p>Certainly not yet - there is not yet any evidence that this can be used to correct specific deficiencies in an adult, though the in vivo applications are g... | https://biology.stackexchange.com/questions/42862/are-scientist-able-to-correct-mutiple-gene-defect-in-our-body-by-using-crispr |
Question: <p>I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and Zinc finger nucleases. </p>
<p>I understand that there may be a few metrics used for analyzing any genome e... | https://biology.stackexchange.com/questions/20665/when-did-crispr-cas9-evolve-and-what-is-the-likelihood-that-a-superior-system-fo |
Question: <p>According to <a href="https://www.sciencedirect.com/science/article/pii/S109727651830546X" rel="nofollow noreferrer">this diagram</a>, the high efficiency and the high specificity of CRISPR lies in its reversible binding with the target DNA. The Cas protein unzips the target DNA and have the gRNA to base p... | https://biology.stackexchange.com/questions/108213/is-crispr-mediated-rna-editing-less-specific-and-less-efficient-than-dna-editing |
Question: <p>There are multiple widely-used plasmids for using CRISPR/Cas9 with a dual lentiviral vector strategy (Cas9 & sgRNA on different vectors) in mammalian hosts with a Blasticidin selection selection marker.</p>
<p>In particular:
<a href="https://www.addgene.org/73310/" rel="nofollow noreferrer">Lenti‐Cas9... | https://biology.stackexchange.com/questions/109257/what-are-the-differences-between-dual-vector-crispr-cas9-lentiviral-plasmids-len |
Question: <p>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 possible or if it is already the way CRISPR/Cas9 does it? Apparently multiple systems were already engineere... | https://biology.stackexchange.com/questions/30347/is-it-possible-to-insert-dna-without-cutting-the-recognition-site-with-crispr-ca |
Question: <p>I have to make an exposition in my university about Crispr-cas9 edition and I have some questions about the method. In the knock out/knock in technique is used a plasmid containing the DNA that codifies for the Cas9 protein and guideRNA and a <strong>Donor template</strong> that has a gene for puromicine r... | https://biology.stackexchange.com/questions/51857/what%c2%b4s-the-role-or-function-of-the-homologous-arms-in-a-donor-template-in-a-knoc |
Question: <p>In the paper on CRISPRs, the following figure is shown:
<a href="https://i.sstatic.net/gnwUp.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/gnwUp.png" alt="enter image description here"></a></p>
<p>I added the light-green boxes.</p>
<p>What do the red arrows and the line with a filled cir... | https://biology.stackexchange.com/questions/38706/in-this-illustration-about-crispr-function-what-do-these-objects-mean-image-pr |
Question: <p>I have recently studied how CRISPR works but there is something that I do not understand at all. I have heard a lot of people claiming that with this method it is possible to modify any genome by inactivating, activating, removing or adding genes. However, as far as I have understood, DNA regions can only ... | https://biology.stackexchange.com/questions/69273/can-a-gene-be-inactivated-using-crispr-if-it-is-not-in-the-interspace-of-short-p |
Question: <p>I have here my hypothesis, does this make scientific sense? Assume this situation is occurring in a closed environment with only bacteria and bacteriophages.</p>
<p>The effectiveness of CRISPR/Cas9, being an adaptive defence system, is heavily reliant on the phages that it, or its ancestor has previously h... | https://biology.stackexchange.com/questions/107756/would-viral-diversity-result-in-a-change-in-the-effectiveness-of-crispr-systems |
Question: <p>This paper seems to describe the use of a plasmid delivered by a gene gun to depigment rat skin;</p>
<blockquote>
<p><a href="https://www.nature.com/articles/3302264" rel="nofollow noreferrer">https://www.nature.com/articles/3302264</a>
Published: 27 May 2004
Seeing the gene therapy: application of gene gu... | https://biology.stackexchange.com/questions/96043/can-we-change-the-eye-hair-color-by-knocking-out-the-oca2-herc2-and-mc1r-genes |
Question: <p>The CRISPR/Cas9 method allows new genes to be inserted. After Cas9 cuts the Target-DNA, it can use a homologous piece of DNA as a donor template for homology-directed repair. But HDR only occurs when there are sticky ends, and Cas9's cuts end in blunt ends.</p>
<p>What did I miss?</p>
Answer: <p>According... | https://biology.stackexchange.com/questions/111256/crispr-cas9-how-can-inserted-dna-be-used-as-a-donor-for-the-homology-directed-r |
Question: <p>Since i had my first cell class at university i have heard about Cripsr Cas9 method. But I am quite surprised about one fact. Why actually wasnt rewarded by Nobel price? Is it something like Einsteins relativity (to early to reward it)?</p>
Answer: <p>My guess is that some people (likely Jennifer Doudna,... | https://biology.stackexchange.com/questions/70708/crispr-cas9-method-and-nobel |
Question: <p>It seems that to modify DNA a guide RNA and Cripr are introduced.</p>
<p>But I'm unable to understand how the Guide RNA is made or created.</p>
<p>Is it a simple method which can be done with simple lab equipment or is it complicated?</p>
<p>What is the equipment need to create it?</p>
Answer: | https://biology.stackexchange.com/questions/66646/how-is-the-guide-rna-created-for-crispr |
Question: <p>I read that Cas9 protein along with guided RNA binds at a specific DNA fragment of foreign organism integrated in a host organism DNA. To make the host immune to virus infection Cas9 along with gRNA which is complementary to viral DNA attaches to it host DNA by unbinding it and then cuts the DNA at this si... | https://biology.stackexchange.com/questions/38915/how-does-cas9-interact-with-crispr |
Question: <p>I am researching a fatty acid amide hydrolase (FAAH) SNP RS324420 and FAAH out microdeletion that together lead to reduced pain sensitivity and reduced anxiety (<a href="https://www.sciencedirect.com/science/article/pii/S0028390807002146" rel="nofollow noreferrer">Moreira et al 2008</a>).</p>
<blockquote>
... | https://biology.stackexchange.com/questions/96379/if-an-snp-were-edited-using-crispr-what-are-the-chances-that-absent-artificial |
Question: <p>I understand CRISPR-mediated bacterial immunity to occur in the following simplified steps:</p>
<ol>
<li>A CRISPR array is transcribed from promoters in the leader sequence to yield a precursor CRISPR RNA (pre-crRNA).</li>
<li>The pre-crRNA is processed by ribonucleases (<em>e.g.</em> Cas6 in Type III syst... | https://biology.stackexchange.com/questions/104533/does-ribonuclease-processing-of-pre-crrnas-happen-co-transcriptionally |
Question: <p>I know, that the CRISP/Cas approach for "cutting" the human genome is not completely suitable if we can't say not suitable at all. Because we have many repeats and this approach can bring to our genome additional breaks in DNA and after DNA-repair it causes unwanted mutations. If so, why scientist still co... | https://biology.stackexchange.com/questions/45655/crispr-cas-for-editing-the-human-genome |
Question: <p>I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually designed them yourself in software that lets you design and alter the components. </p>
<p>Am I correct so far?</... | https://biology.stackexchange.com/questions/89402/what-software-do-i-need-to-read-write-cas9-and-dna-files |
Question: <p><strong>My goals are to use a free webtool to:</strong></p>
<ol>
<li><em>Identify guide RNAs</em> (direct-repeat sequence followed by the targeting sequence) appropriate for use with <em>AsCpf1</em> in order <em>to target a specific segment of genomic DNA</em>.</li>
<li><em>Estimate efficiency and specifi... | https://biology.stackexchange.com/questions/59027/webtool-to-design-guide-rna-grna-for-use-with-crispr-ascpf1 |
Question: <p>all,</p>
<p>Is it only happens in certain phases, like S, G1,...or it can happen any time....or maybe, it has some perferences.</p>
<p>Put it in another word, does it going to processe edit if the cell is not growing ?</p>
<p>Thanks for any helps or comments.</p>
<p>Best</p>
<p>Bill Zhang</p>
Answer:... | https://biology.stackexchange.com/questions/73812/crispr-cas9-genome-editing-is-actually-processed-at-which-phase-of-cell-cycle |
Question: <p>I am new to this technology and don't quite understand how it works. Hope someone can give some suggestions! Thank you.</p>
Answer: <p><em>Short Answer:</em>
No, for CRISPR/Cas9 knockout you do not need to add donor DNA.</p>
<p><em>Little bit more detail:</em>
CRISPR/Cas9 allows you to cut at a given po... | https://biology.stackexchange.com/questions/94021/does-using-crispr-cas9-knockout-need-to-add-donor-dna-in-the-process |
Question: <p>Sometimes people wanna use primary cells to do gene-editing because the cells normally have more interesting characteristics, but can we really do so?</p>
Answer: <p>The most efficient CRISPR-based editing of primary cells that I've read about used a technology called <a href="https://en.wikipedia.org/wik... | https://biology.stackexchange.com/questions/94044/can-crispr-be-used-in-editing-primary-cells-how-is-the-transfection-efficiency |
Question: <p>I'm talking about CRISPR system. I know the crRNA is transcribed from the palindromic repeat and the "spacer" but I don't know where the tracrRNA comes from.</p>
Answer: <p>Usually the tracrRNA is a part of the CRISPR locus and is encoded in the the vicinity of the CRISPR array (e.g. upstream or downstrea... | https://biology.stackexchange.com/questions/65776/where-does-tracrrna-comes-from |
Question: <p>In research of seed breeding, I'm trying to understand the impact of genetic engineering techniques like CRISPR (This is the main one as I understand) on traditional seed breeders. Through searching on the internet, I believe to have found the following two types of impact:</p>
<ol>
<li>research: increase... | https://biology.stackexchange.com/questions/67100/what-impact-do-genetic-engineering-techniques-have-on-seed-breeders |
Question: <p>I am new to these concepts in biology and need some help understanding. My main concern is how to find the enhancer of my gene of interest, specifically the sequence of the enhancer. I am working on a project where I will be attempting to use CRISPR- mediated deletion of the promoter region and enhancer re... | https://biology.stackexchange.com/questions/88850/how-to-find-the-enhancer-region-of-a-specific-gene |
Question: <p>As a computer scientist, I'm interested in the ability of the Cas9 protein to function as an if-gate for DNA. It opens up so many questions for me. Right now the protein works as "if the sequence matches, cleave", but perhaps you could customize it to do "if the sequence matches, [do arbitrary action]". Ho... | https://biology.stackexchange.com/questions/52480/is-cas9-unique-in-its-ability-to-act-in-response-to-a-specific-dna-sequence |
Question: <p>Sorry for the possibly confused question, my knowledge of genetics is limited to medical training only but I have a question.</p>
<p>Are gene editing techniques such as CRISPR used on both of the chromosomes in a pair or just on one of them?</p>
<p>Some of the general searching I have done suggests that ... | https://biology.stackexchange.com/questions/80008/when-gene-editing-are-both-chromosomes-in-a-pair-changed |
Question: <p>Reading Jennifer Doudna's fascinating book on CRISPR. So she describes rare cases where a mutation in a single cell removes the gene responsible for a genetic disease. The cell proliferates and the disease is cured. What I don't understand is--aren't all the aberrant cells also still dividing and passing o... | https://biology.stackexchange.com/questions/64247/mutated-cell-proliferation |
Question: <p>The CRISPR/Cas defense mechanism uses spacer sequences between palindromic repeats to search for the sequence to cut by an endonuclease. But how are these spacers created?</p>
<p>Let's take Bacteriophages, for example, which insert and integrate their genome into the prokaryotic genome. How does this infec... | https://biology.stackexchange.com/questions/111138/how-are-spacer-sequences-created-in-a-prokaryotic-genome |
Question: <p>I'm interested in the idea of using exosomes as an alternative transfection agent / delivery mechanism for gene editing applications (CRISPR/cas9, etc). </p>
<p>Information on the matter is sparse.. Does anyone know of any practical techniques for manufacturing exosomes in the lab?</p>
Answer: | https://biology.stackexchange.com/questions/65788/are-there-any-techniques-for-manufacturing-exosomes-in-the-lab |
Question: <p>Non-biology background here.</p>
<p>I read this very interesting article: <a href="https://www.wired.com/story/crispr-eradicate-invasive-species/" rel="noreferrer">https://www.wired.com/story/crispr-eradicate-invasive-species/</a></p>
<p>However I am having a hard time wrapping my head around something:<... | https://biology.stackexchange.com/questions/71545/how-could-a-species-be-engineered-to-go-extinct |
Question: <p>I'm working on a project where I'm trying to use virophages as viral vectors in introducing CRISPR-Cas proteins into other viruses. I was wondering where I might be able to find replication-defective Sputnik virophages or other virophages for this kind of experiment?</p>
Answer: | https://biology.stackexchange.com/questions/90146/where-can-i-obtain-sputnik-virophage-samples |
Question: <p>I've been transforming E. coli via heat shock in order to insert oligonucleotides (around 50 nt); however, none of my experiments have given positive results so far. I begin to question the efficiency of chemical transformation, especially for short DNA fragments. Is there such a notable difference between... | https://biology.stackexchange.com/questions/73150/heat-shock-vs-electroporation |
Question: <p>Let's say a human cell mutates cancerously, we identify the mutated gene sequence and use CRISPR to mutate the patient's cells to include some variation of the cas genes and spacer sequences matching the mutated cancerous sequence.</p>
<p>Then design a virus to "infect" cells (cancerous and healt... | https://biology.stackexchange.com/questions/97604/what-obstacles-would-be-most-prevalent-in-an-attempt-to-use-virotherapy-to-inj |
Question: <p>I live in Egypt, and I do want to perform CRISPR-Cas9 genome modification, but there are no reliable sources of Cas9. I can order some Cas9 online from the US, but not much. So... my question is, is there any way I can replicate a small amount of Cas9 to get a bigger amount? Or maybe extract some from S. P... | https://biology.stackexchange.com/questions/71189/a-reliable-source-of-cas9 |
Question: <p>I have many questions about the Cas9 enzyme. When the Cas9-guideRNA (crRNA and transcrRNA) complex is attached to the DNA sequence, what is the type of bond that cuts the Cas9? Does the Cas9 degrade all the sequence of DNA complementary to the guide RNA?</p>
<p>If the question before is "Not", then how is... | https://biology.stackexchange.com/questions/52360/can-the-cas9involved-on-the-crispr-cas9-mechanism-be-considered-as-a-restric |
Question: <p>Researchers have proposed the application of CRISPR/Cas9 and <a href="https://en.wikipedia.org/wiki/Gene_drive" rel="nofollow noreferrer">gene drive</a> to genetically alter wild mosquito populations such that they don't transmit malaria. The government of New Zealand has announced a <a href="https://en.wi... | https://biology.stackexchange.com/questions/58604/could-we-eradicate-mosquitoes |
Question: <p>As a someone with beginner knowledge on biology, I have come across the terms "RNA editing".</p>
<p>Take this paper for example : <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793859/" rel="nofollow noreferrer">RNA Editing with CRISPR-Cas13</a></p>
<p>From my understanding, DNA -> RNA -> Protein... | https://biology.stackexchange.com/questions/84567/what-is-the-difference-between-dna-vs-rna-editing-in-the-context-of-gene-therapy |
Question: <p>Articles about ’prime’ CRISPR editing generally state that a major advantage is that it only affects one strand…</p>
<p>…But what happens to the second, complementary strand of the genome? Doesn’t it have to eventually change to match the first?</p>
<p>Or is that edited portion of the genome forever ‘open... | https://biology.stackexchange.com/questions/114552/what-happens-to-the-second-strand-in-single-stranded-prime-editing |
Question: <p>The lysis-lysogeny state of bacteriophage lambda is well known. Under certain conditions, the phage will enter the lysogenic state after infection of a bacterium. Then, after a while, the phage switches to the lytic state and breaks the bacterium. I forgot the details but the phage must expressed some prot... | https://biology.stackexchange.com/questions/110620/how-bacteria-respond-to-toxic-viral-proteins |
Question: <p>The use of viruses as transfection or delivery agents for gene editing (CRISPR/cas9, etc) is well known. However, one problem with using viruses to deliver DNA into cells is the possibility of triggering an adverse immune response.</p>
<p>Cells already use exosomes to transport various cargo in and out of... | https://biology.stackexchange.com/questions/65786/are-exosomes-useful-as-a-transfection-or-delivery-mechanism-in-gene-editing |
Question: <p>I know how plasmids and restriction enzymes work to change the dna of a bacteria cell, but I do not really understand how a bacteriophage works to edit the genome of a cell. Is it related to crispr since its a virus which inserted genetics in bacteria? Also, is it during the lysogenic or lytic stage that t... | https://biology.stackexchange.com/questions/62854/bacteriophages-and-their-role-in-genetic-editing |
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