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1

B-form DNA is wrapped around histones in a left-handed manner resulting in a left-handed solenoidal superhelix (see that, that and this). The reason for this wrapping is that it reduces the helical tension. This post has more information about DNA helical tension. Also note that exceptions exist (i.e. right-ended direction) especially for histone at the ...


4

Either the gene is present in multiple copies (especially possible if it is in a plasmid) or multiple RNA polymerases are transcribing it, each beginning from the start site one after the other with some amount of time delay, much like multiple ribosomes translate the same mRNA to increase rate of protein production.


5

Multiple RNA Polymerase transcription complexes engaged on the lacZ gene at the same time, staggered along the gene.


2

Would something like CRISPR fit your criteria? CRISPR is essentially an adaptive immune system for bacteria. When a bacteria encounters foreign DNA (usually from an invading bacteriophage), it can cut it up and insert part of it in between palindromic repeats called CRISPRs. This small piece of DNA can be transcribed and then used as a template to recognize ...


6

In multicellular organisms there are specialised cells called gametes that are responsible for sexual reproduction (sperm/ egg cells). Mutations occurring in these cells can be passed on to offspring (germ line mutations). Mutations occurring in others cells affect only the given individual (somatic mutations). Edit: For unicellular organisms it is pretty ...


1

I can't unequivocally say, at least without further literature review, that both sister chromatids are transcribed equally everywhere, especially since the cell does have mechanisms to differentiate between the old and new DNA strands (such as methylation state). It would be conceivable to expect, however, that the same regulatory factors that were present ...


1

To measure the frequency of indels at the ligation site you can use a vector with a unique restriction site in the lacZ gene. With a colorimetric assay you can count the number of white cfu. Perfect ligation in-frame yields blue cfu


3

The best resource for troubleshooting ligations I found (and use frequently) is this NEB page. That is assuming you've already referred to the instructions provided with the enzyme you're using. In my case it's T4 Ligase, again from NEB. It's helpful to check the FAQs and the references listed on that page. Also, you can make use of their Molar ...


2

Addition to the answer provided by Teige. Transcription factors bind to both the strands however your question also included proteins in general. DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) ...


11

The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding proteins obviously bind one strand but they do this in a non-specific manner. RNA-binding proteins recognise the sequence on a single strand by inserting ...


8

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen. In the "classical" way the silencer is bound by a transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the ...


2

Excellent question! You would definitely be able to find quite a few sequences of DNA that are undamaged (in fact most of them would be undamaged), but it is very unlikely that any cells in his/her body would have a perfect copy of the entire original genome. I'm sure that cells closer to the skin (exposed to more radiation) would have more mutations, but ...


1

You've asked a number of questions here, but yes -- mutation rates have been studied extensively in humans as well as in model organisms. And as you suggest, they vary substantially across tissues. One starting point to read about how mutation rates are measured and how they vary across species, tissues, etc., is a 2010 Trends in Genetics review by Mike ...


3

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how to make our genome do what we want, but it's a >major refactor. We're going to have adjust 10-15% of our DNA. I think we both recognise that this is a very ...


0

Look into site-specific recombination. You can use a site-specific recombinase, specifically an integrase, that can insert a sequence of DNA at a certain attachment site. You can add an identical attachment site into the DNA sequence to insert, allowing for the reintegration of a new attachment site. Note however that you might get SSR onto the insertion ...


5

Not very common, and not found so far in nature, but they exist and are called deoxyribozymes. Additional information: Deoxyribozymes are the equivalent of ribozymes in the DNA world and can function as catalysts for different biochemical reactions, such as DNA cleavage. While DNAzymes (short name) were synthesized in a laboratory context (In-vitro) and ...


4

Even though you - or the problem did not clarify, I assume in my answer that you work with eukaryote system, even though the principle of the replication is the same. dNTPs do have an OH group on their 3rd carbon atom (for eg. check this wiki-page for dCTP) so I don't think that's the issue here. My guess is that the first tube contains the radio labeled ...


2

MicroRNA (miRNA) are gene-regulatory RNAs that are loaded onto the RNA-induced silencing complex (RISC) and interact with partially-complementary targets on mRNA to suppress protein expression. The miRNA is originally double-stranded and composed of strands about 21 nucleotides long; on loading onto RISC, one strand is degraded and the other, the "guide" ...


4

This question can't be answered with a simple yes/no, but I would say that the analogy of DNA being the "code" used by cells is a reasonable one, if taken with a number of other considerations. DNA function When Watson and Crick first described the structure of DNA (being a double-stranded sequence of the nucleotides Adenine, Cytosine, Guanine and ...


4

DNA is not analogous to computer code which renders your search for similar constructs in it meaningless. To give a couple of simple examples why this is: Computer code has a sequential order of execution; DNA acts in parallel and out of sequence, it is not "executed". Computer code has a strict and consistent meaning so the line if x==4 : x=7 always does ...


1

Genome editing techniques like CRISPR-Cas and TALEN use non-specific recombinases coupled to a DNA-recognizing part that can be designed to be specific for any stretch of sequence, as it is constructed out of single zinc-finger 'modules' that each specifically bind a couple of nucleotides (one nucleotide each in the case of TALEN).


6

Just to add to previous answers, but transcriptional interference (see e.g. Shearwin et al., 2005) can be seen as a form of IF-statement (or WHILE) in the sense that: if(x transcribed){not y transcribed} The interference does not have to be binary though, and more common are graded responses. Transcriptional interference can also take place at the RNA ...


3

As WYSIWYG said there is no equivalent for function calls, as there will always be some interference. However one could argue that some modular pathways (eg. apoptosis signalling) can be seen as a "code block" where a certain input will (almost) certainly lead to a certain effect. The analogy with function calls is that, in describing many different ...


46

Biological examples similar to programming statements: IF : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only with the death of the cell. So the IF statement is always a part of a loop. WHILE : Transcriptional repressor; gene will be transcribed ...


9

There are certainly some comparisons that could be made between the way genes are expressed from DNA and logic functions, but they aren't great. But synthetic Biology is really a blossoming new field that is attempting to integrate logic functions into biology, see e.g. Siuti et al (2013). The above paper is a brilliant example of a group using using ...


3

So this question is difficult to answer because it has some errors in it, in that lifeforms being dependent on rarely used elements is a different question than lifeforms using different DNA bases, but I will answer both. So for the question about whether or not organisms could exist that use DNA bases not found in organisms on earth, the answer is ...


2

It depends what you mean by "predict". Consider that the faces on genetically identical individuals, such as identical twins, are very similar, even in old age. If you look at the processes of development over the life of an individual as a more-or-less deterministic and predictable phenomenon, then you might argue that faces are predictable from DNA info. ...


5

Retroviruses depend on being able to convert their RNA genome into a DNA copy, and have a reverse transcriptase enzyme to do that. This unique activity is not found in human cells, allowing for potential antiviral therapy if a drug can be used to inhibit the reverse transcriptase while not affecting the human enzymes. AZT is one such drug, by mimicking the ...


2

This recent Cell paper mentions a ribozyme (RNA enzyme) that ligates two oligonucleotides into itself. Given a sufficient source of input oligonucleotides and the correct conditions, it can catalyse its own replication and undergo Darwinian evolution, and can be thought of as a rudimentary form of RNA-based life. The authors hypothesise that ligase-based ...


1

Since these cells are there by the development of the immune system, the immune cells recognize them as self. By blood transfusion with incompatible blood type, the immune system recognizes the blood cells with different histocompatibility antigens (A,B,Rh etc...) as non-self, that's why it attacks them.



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