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If you don't want acrylamide in your preparation, don't use it, as you will always have some carry-over in the solution. And you will not get rid of it completely, as it at least partly co-precipitated with the nucleic acids (it's used as a co-precipitation agent for this purpose). I think the best solution is to use chromatography, either size-exclusion ...


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Knowing the secondary structure of nucleic acids is very useful in many cases when working with them. The simplest case, and probably the most often used case is when you order or synthesize a small RNA or DNA and actually don't want this to have any stable secondary structure. There are many methods where you use a small nucleic acid that can bind to a ...


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Short answer I can think of at least a dozen applications for which it would be useful to know the secondary structure of a given sequence of RNA off of the top of my head. In no particular order: Simulation/visualization of RNA Riboswitches MicroRNA RNA interference (RNAi) RNA-RNA interactions RNA-DNA interactions RNA-protein interactions Ribosomal ...


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Addition to Jvrek's answer based on the comments. Most RNA degradation mechanisms catalysed by different RNAses (RNAse-A and RNAse-S, for example), involve the 2'-OH. Therefore the repertoire of RNAses is selective towards RNA and not DNA because of the 2'-OH.         ...


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Nice question which leads to the fundamentals of DNA and RNA. DNA (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA ...


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I opened Lehninger (Principles of biochemistry, 4th ed.) on page 293. The slow Cytosine deamination reaction seems innocuous enough, but is almost certainly the reason why DNA contains thymine rather uracil C is deaminated to U in a rate of 10^-7 in 24 hours, which means 100 mutations a day for a mammalian cell which would have lead to a A-U genome ...


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Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact lifetime). Deadenylation generally precedes 3'→5' degradation by exosome but I am not sure if that is a prerequisite. However tailless mRNAs can be stabilized by ...


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I'm no expert at this but I don't think you need a Turing machine to achieve this, at least for DNA, since in conventional sense (not including carcinogenic factors such as UV) the most probable stage in which a DNA mutation can happen is during DNA replication so DNA polymerase engages in proofread to ensure accurate DNA replication, and then the DNA can ...


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There are always exceptions but you can consider some general rules. A is 1 i.e the sequence that is perfectly complementary (2 is complementary but direction is parallel — cannot base-pair), then B would be 1 (siRNA). Reasons (some are just based on general rules of siRNA design): siRNAs have to be perfectly complementary The size is also perfect for a ...


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It doesn't seem like a homogenization problem. Nonetheless you can try this: Suspend the heads in trizol Homogenize by passing through 30/31G needles (insulin syringe) up to 10-15 times. Heating a little might help but I think it is unnecessary for these tissues. Insulin syringe is much better than the hand held homogenizer. Freeze-thaw 1-2 times if you ...



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