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6

Though this is a basic question (a few google searches will provide all answers) and you have asked a lot of questions, I shall answer them one-by-one. Why is RNA single stranded (and not double stranded like DNA)? dsRNA is less stable than dsDNA. See this: http://en.wikipedia.org/wiki/RNA#Structure. An important structural feature of RNA that ...


6

A clarification on introns and exons. While it is true that introns are not a part of the mRNA as March Ho said, they are essentially transcribed. This may seem trivial but it is important to note. So: Both introns and exons arise from the transcribed region Exons need not necessarily form the ORF (i.e. be translated to proteins) Regarding intronic ...


6

Most (almost all, AFAIK) mRNAs and lncRNAs start with exons for the reasons already mentioned by David. In a typical splicing event, the nucleotide that is 5' to the splice donor site (lets call it pre-donor) and the one that is 3' to the acceptor site (lets call it post acceptor) are joined together and the intronic sequence between them is removed. If ...


5

It sounds like you have considered most of the obvious alternatives (and thank you for clarifying the question). I suppose the first question in an alternatively spliced transcript with a retained intron is whether the open reading frame of the protein is maintained. If there is a termination codon that now becomes in-frame due to the intron then the ...


5

You call it a thought experiment but something like this has actually been done. Not entirely similar as they don't switch 2, but still they replace a codon. An overview: https://en.wikipedia.org/wiki/Expanded_genetic_code Big thing: in the two articles leading up to this one they replaced all 314 UAG stop codons in E.coli K12 and used the now unused UAG ...


4

There are no animals or plants with RNA genomes. There was a mistaken belief in the 1920s that plant genetic material was RNA whereas animals had DNA, but this was finally disproved by JN Davidson in the 1940s.


4

mRNAs encode specific genes and perform specific functions whereas the other two perform housekeeping functions in all cells. Changes in their expression are related to global changes in the cell. The expression of rRNA and tRNA is affected in certain conditions such as stress and also possibly cancer (may be due to high replication rates). However, even if ...


4

While Ankur's answer is correct, it must be noted that not all non-coding RNAs are introns. An intron must be excised from an mRNA, which therefore means that any non-coding RNA that is not part of an mRNA cannot be an intron. For example, rRNA and tRNA are all examples of non-coding RNAs that are not introns, since they are not part of mRNA. miRNA may ...


4

One can prepare rabbit ribosomes from reticulocytes (immature red blood cells), and by providing a few cofactors required for an active extract, create an in vitro system that will translate virtually any eukaryotic mRNA that contains the correct sequence determinants. You can purify mRNA from your cells or tissues of choice, or you can synthesize an mRNA in ...


4

Qiagen and Life Technologies call it RNA content, total RNA, or total cellular RNA.


4

As far as I am aware, transcripts always start and end with exons. The reasons I wouldn’t expect otherwise (apart from my observations when examining Drosophila transcripts) are given below. As you will be aware, the spliceosome (at least for mRNA) is a highly sophisticated multi-component ribonuclear protein complex, and has functions to both splice out ...


3

Comparing Biopython MetlingTemp to other calculators. I have written the recent version of MeltingTemp in Biopython's SeqUtils. I have extensively tested the Tm calculations against other programs like MELTING and Primer3Plus and other online Tm calculators with consistent results, thus I'm pretty confident that there is no gross error in the module. The ...


3

Some suggestions. For identifying function do a homology search. There is little functional annotation of lncRNAs. So homology based information can be obtained only for protein sequences. So you can try these: Check the coding potential. Find ORFs (perhaps set a minimum length cutoff). To be stringent you can also check for Kozak consensus sequences (for ...


3

With many non-coding RNAs, the RNA is the functional endpoint. Therefore, ncRNA "expression" simply refers to the production of that functional component. Similarly to with proteins, this involves looking at differential tissue production of that noncoding RNA (i.e. in which tissues the RNA is produced). Gene expression is defined in the Oxford Dictionary ...


3

RNA and proteins are not electrical systems, but the idea of translating a signal between incompatible systems can be applied here. Proteins are made through a process called Translation, where instructions stored in a piece of mRNA are used by the Ribosome to make protein. tRNAs adapt the mRNA nucleotide sequence into a protein's peptide sequence by ...


3

Hasn’t your question already been answered by those organisms (and organelles) that have a different genetic code from the standard genetic code (originally known as ‘universal’)? Essentially they have performed the experiment for you by developing machinery to decode mRNA differently (transfer RNAs with appropriately different anticodon/amino-acid accepting ...


2

Why DNA for the genetic material? I think the correct and sufficient answer to this is the one so frequently repeated that it is difficult to find the original source. For example, G.F.Joyce wrote in a 2002 Nature review article: The primary advantage of DNA over RNA as a genetic material is the greater chemical stability of DNA, allowing much larger ...


2

Palindrome sequences are important in bioinformatics understanding, it helps us to extract patterns in the genomic sequences. I'll give an example in HIV (very important application). HIV has a nasty requirement that the virus must keep the cell alive. It does that by inserting itself into the host's genome. We know from biology that cutting and pasting of ...


2

My knowledge of biology is extremely limited, but this is what I know of palindromic sequences: Palindromic sequences are their own reverse complements. I have seen many restriction sites be palindromic. Also, some Transcription Factor Binding sites are palindromic. The canonical E-box site, for example, can be expressed as CANNTG. Also, these palindromes, ...


2

According to Lewin's Genes XI - Kreb's et. al on Eukaryotic Transcription, RNA Splicing, and Processing It is not clear whether RNA polymerase II actually engages in a termination event at a specific site. It is possible that its termination is only loosely specified. In some transcription units, termination occurs more than 1000 bp downstream of the ...


2

The residue numbering convention in the PDB is more-or-less entirely up to the depositor of the structure. While generally speaking sequential numbers are next to each other, there is no guarantee of that fact. For example, the PDB allows for what are called "insertion codes", which are extra residues which interrupt the regular sequence progression. For ...


2

The CRISPR Cas 9 system is used to introduce insertion or deletion in a genomic sequence not mRNA. https://www.addgene.org/CRISPR/guide/


2

what is the thing that gives the ribosome its functionality ( to synthesis the protein ). RNA strands can fold themselves in a sequence specific manner. In fact ribosomes are highly structural being able to hold tRNAs having a hole which a polypeptide goes through during protein sysnthesis. I do not know, but it could work. I do not know if it works ...


2

Here is the results summary of the study that describes the discovery of DNA:RNA hybrid virus: Results Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence ...


2

Cis-regulatory elements are simply DNA regions upstream or downstream of a gene that can affect its expression (basically they have to be in the same chromosome). DNAse-I hypersensitive sites (DHS) are regions of chromatin that get digested during the DNAse treatment because they are exposed i.e. not protected by a protein (complex). The protein complex can ...


2

There are many studies that have used RNAi against the plant parasite M. incognita. The fundamental idea is that RNAi is directed against one of the vital genes of this nematode. Since, RNAi causes downregulation of the target gene, the nematode dies (or becomes ineffective in infecting) because of the loss of function of these important genes. As you might ...


2

For 1, that is how retroviruses such as HIV work, and of which scientists have utilised to use in gene therapy. It requires a process called reverse transcription. However, this would only show you the gene the mRNA was from, but no information about its location, or if it is repeated elsewhere. As for 2, this is to do with the fact that one base cannot ...


2

It is not unusual for RNA sequences to be reported with T instead of U; the writer is reporting the cDNA sequence instead of the RNA sequence. In RNA at the boundary of the minor intron, there is a uracil. In the following page, the writers follow the oft-used convention of describing RNA with T instead of U (writing the cDNA sequence). https://en....


2

Thank you for a great question. I would like to start by clarifying some terminology. First, nascent RNA refers to an RNA molecule that is currently being transcribed and has not been processed. Processing can include the splicing out of introns or polyadenylation at the 3' end, for example. Mature RNA is (typically) spliced and polyadenylated. Second, ...


2

On one hand, designing an experiment which would kill (and resurrect) a cell is not possible: once a cell malfunctions, it's likely damaged beyond repair. However, other than that I don't think this experiment kind of cannot actually be done. You would just have to simultaneously expose different cultures (grown in the same conditions) to different inserted ...



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