RNase A – pretty pretty pretty pleaaaaase stay away!!!!!! RNase. RNase. RNase. This is the name for “RNA cutters” and I’m writing it over and over because, even though I think (and worry) about them a lot (especially these last couple days as I’ve struggled to eradicate certain ones), capitalize the name correctly, I often do not! I always write RNAse! A while back I saw it written “RNAse” in a paper and felt so happy and vindicated! But, in a journal article is basically the only place I want to find these (at least the generic ones). Because RNases are everywhere – they’re secreted by us and by microbes to degrade viral RNA etc. which is good. But they can also shred up RNA you’re trying to work with, which is not good….

video added 4/19/22

For example, a couple days ago I ran one of those urea-PAGE gels I was telling you about – the technique we use to separate and look at pieces of RNA. And I saw that, instead of a nice crisp band indicating a (lots of copies of) a single piece of RNA, of defined length), I saw multiple bands, indicating degradation. Eek! So I’ve been on a quest to vanquish the contaminating RNase. I remade all the solutions I’ve been using from scratch (spent over 2 hours yesterday preparing solutions before I could even start my experiments!) and hope that fixes things…. Update – it worked!

But how can we prevent RNases from doing damage in the first place? In addition to keeping things super clean when working with them (about the only time you’ll see me working with a clean bench…) we can use a chemical called DEPC (DiEthyl PyroCarbonate) to put a permanent safety shield on the RNAse (ugh, I mean RNase) scissor blades. Some RNases will be inhibited by a chemical called EDTA, which hides metals, but not RNase A… EDTA doesn’t protect against RNaseA because these scissors don’t need the help of metal to cut RNA.

As the “-ase” ending indicates, RNases are enzymes (reaction-speeder-uppers). And what this type of enzyme speeds up is RNA cutting. RNA and DNA are a category of biochemicals called nucleic acids and they’re used to store genetic information. DNA is used for “permanent storage” whereas RNA is used for “temporary copies” like the messenger RNA (mRNA) copies of protein recipes that allow for a “seasonal assortment” of proteins to be made. More on this here: http://bit.ly/31IwofL & here: http://bit.ly/2FqasfN

But basically there are times when your cells want to destroy RNA – whether it’s foreign RNA from viruses or proteins you’re done making for now. So your cells have proteins called RNases that can catalyze (speed up) the hydrolytic cleavage of RNA (using water (hydro) to cut (lytic) the phosphodiester bond connecting the individual RNA letters (nucleotides). And, in the lab, we often want to keep them from doing this in our samples.

Different RNases have different “Achille’s heels” because the enzymes aren’t really the scissors themselves. Instead, they’re more like the scissors holders – they hold the blades in place so they can cut. Lots of nucleases use metals to help do this, so we can use EDTA (a chelator that “bites down” on a metal in multiple places) to “hide their metals” and inactivate them. But this trick doesn’t work for RNaseA because, instead of needing a metal to convince water to attack it, it convinces the RNA to attack itself! (and then uses amino acids (protein letters) sticking out into active site) to convince water to finish the job.⠀

One reason RNA, and not DNA, is used for “temporary” purposes is that RNA is easier to degrade. And this is because it has an extra “leg.” The D in DNA stands for “deoxyribose” and it indicates that it has one less oxygen than the ribose sugar you find in RNA. Instead of having a 2’ OH (right leg), DNA just has an H there. And H is much more “boring” than OH. Speaking of boring, that O can “get bored” and go looking for excitement if conditions are right (or wrong depending on what you’re wanting….)

Atoms (like the individual O’s, C’s, and H’s) are made up of smaller parts called subatomic particles: positively-charged protons, neutral neutrons, and negatively-charged electrons. Atoms join together to form molecules by sharing pairs of electrons in strong, covalent bonds. Oxygen doesn’t share fairly when it does this because it’s highly electronegative (electron-hogging). So, in that 2’OH, the oxygen hogs the electrons it shares with hydrogen. And since those electrons are negatively charged, this makes the oxygen partly negative & the hydrogen partly positive (we call such bonds polar covalent bonds).

But that’s not the only effect. Because the O is  pulling the electrons away from the hydrogen, it’s kinda like the H has “already lost” so it has less to lose by getting lost!

The more the O pulls away, the easier it is to break the O-H bond. When that bond breaks and the electrons stay with the oxygen, a proton (H⁺) is released. (H only had 1 proton & 1 electron to begin with, and if it leaves the electron behind, it’s now just a proton). If this happens, we say the OH has been deprotonated and has “acted as an acid.”

Once deprotonated, the O now has more electrons than it can neutralize, so it is negatively charged (another way to remember this is that you have to have conservation of charge and the H⁺ is positive so the other part must be negative). O likes having that extra electron but it doesn’t like having that charge. So it wants to find something positive to help it neutralize the charge.

One place you’ll positively find positive charge is a nucleus (the dense central core of an atom) because that’s where the positively-charged protons live. So we call such positivity-seekers “nucleophiles”. Nucleophiles often have a lone pair of electrons, so you can remember nucleophiles by thinking of the u as the smile of a smiley face with the lone pair as the eyes. Sometimes, but not always, nucleophiles have a negative charge. 

The “opposite” of a nucleophile is an electrophile. An electrophile has “too much” positive charge – sometimes this is enough to make it positively charged, though sometimes it’s still neutral.

When you remove the hydrogen from that -OH of ribose (the one that RNA has but DNA doesn’t), the O can “get bored” and when it gets bored it goes looking for fun. For a nucleophile, fun is found with electrophiles. So it looks for an electrophile and finds one right nearby in the phosphate group.⠀

Wait, isn’t that negative? Overall yes, but not the phosphorus! A phosphate ion has a phosphorus atom hooked up to 4 oxygen atoms. And each of those oxygens is pulling electrons away from the phosphorus. So even though the phosphate is negative overall, the phosphorus at the center is partly positive. And thus it’s electrophilic and attractive to nucleophiles.

Left alone, if the 2’ OH “gets bored” it can attack the phosphate connecting it to the next nucleotide, kicking that nucleotide off, creating a cyclic 2’,3’ phsopshodiester and releasing a 5’ O-nucleoside. Or, instead of kicking off the other nucleotide & thus breaking the chain, it can just swap which leg it’s connected to, forming a 2’,5’-phosophodiester instead of the normal 3’-5’.

These are “transesterification reactions” and you don’t want them to happen when you don’t want them to happen or else you’d get jumbled shredded RNA! But you do want them to happen when you do want them to happen! So we want to “selectively bore” specific oxygens and RNases are great at this.

A reason you can have charge-seeking without “full charges” is that you can have “partial charges” – like in water, the O pulls electrons away from the H’s so the O’s are partly negative & the H’s are partly positive. If an H⁺ leaves, you get those full charges, but the charges were already “in the works” before you split it – kinda like a frayed cord stretched to the limit. Things can make an -OH more reactive by pulling harder on that cord, making it easier to break. So RNases have active sites that hold RNA in position and pull on that cord, making the oxygen bored!

But how likely is that H⁺ to leave? To predict its pH-ate you have to look to pH! pH is a measure of how many free H⁺  there are – the more there are, the lower the pH & the more acidic the solution. Under acidic conditions, there are plenty of H⁺ around, so each O can be an OH. But under basic (alkaline conditions) there are fewer H⁺, so the O is more likely to “donate”

So, if you want to deprotonate the -OH, you want to raise the pH. But you don’t want to increase the pH everywhere or you’d get shredded RNA. Instead you want to do it in a localized, controlled fashion. The histidine (one of the amino acid building blocks or “letters” that make up proteins) in the active site of RNase A acts as a sort of local pH raiser – it’s kinda like it tricks the RNA in that location into thinking that the H⁺ stock’s running low, so the OH deprotonates and gives that proton to His.⠀

His can do this because it has an N with a lone pair of electrons and that lone pair can act as a “general base,” pulling off that proton, turning the 2’ OH into a 2’ O⁻ which is now very nucleophilic & can attack the phosphate.

I thought you said this was a hydrolysis reaction?! Where’s the water come in? Well, when the O attacks the P you get a 2’-3’ cyclic intermediate. Water is used to get that phosphate to uncyclize in a way that the phosphate ends up back on the 3’ leg where it “belongs.” It does this with the help of another histidine, this time coming from the other side. Instead of directly attacking, though, it convinces a water to attack. And this back-forthness of the His-mediated protons regenerates the His, letting it do it again.

A lot of DNA cutters (DNases) as well as some other RNases use metals to help them do this type of reaction. Metal atoms are particularly good for things involving DNA & RNA because metal atoms are usually positively-charged (cationic), whereas DNA & RNA are negatively-charged (anionic). This negative charge is what allows us to separate DNA & RNA pieces by length using electricity to bribe them through a gel mesh using positive charge to bribe them. And it also is what allows positively-charged molecules to grab them.

Nucleases have positively-charged binding pockets, where the positive charge comes from basic amino acids like lysine & arginine. That helps the binding, but when the reaction is actually occurring, when that phosphate is getting attacked, you have a really unstable, highly negatively charged pentacovalent (5 things attached) intermediate that needs some extra charge stabilization in order for the cleavage to occur. Some nucleases use metals for this, holding metal cations such as Mg²⁺ in the active site to help stabilize that intermediate (and activate the nucleophile). So you can inhibit those nucleases with EDTA or other chelators (things that bind metals in multiple places), which strip the nuclease of the metal they need. http://bit.ly/2SV2156

But RNase A and some other nucleases don’t need metal. Instead, they use positive-charged amino acids like Lys & Arg instead of positively charged metals.

So, how can we stop RNase? One way is using DEPC (DiEthyl PyroCarbonate). Instead of taking away something the RNase needs, it adds something to hide what it needs. It alkylates the catalytic His residues, sticking carbethoxyl groups on those crucial N’s preventing them from doing that proton ping-pong. This is a covalent inhibition (the DEPC part gets added onto the catalytic residue “permanently” instead of just competing with it).

But it’s not specific for *just those* N’s. It can alkylate any Ns. and lysine & cysteines, and tyrosines. So you don’t want to just stick it into your reaction mix. Instead, we usually only use it to neutralize any RNase A in water we want to use when working with RNA. And after we treat the water, we autoclave it, which heats it up really hot under high pressures. https://bit.ly/autoclavessteam

Surprisingly, although that would kill almost any “normal” protein, such autoclaving doesn’t permanently inactivate all the RNase A – this beast can survive autoclaving – at least some of it – autoclaving can kill some of its activity but this protein has a lot of disulfide bonds that can withstand the high heat and keep the protein partly folded so that it can more easily retold when time comes.

Autoclaving might not inactivate all the RNase A, but it does permanently inactivate the DEPC by causing it to fall apart, forming CO₂ & ethanol. Which can evaporate away.

Tech note: you can use DEPC-treated, autoclaved, water to make buffers that contain Tris, HEPES, or other amines. But you can’t (or at least you shouldn’t) directly treat amine-containing buffers because DEPC isn’t picky. In addition to just the active site amino acids of RNases, it reacts with “any” amines, thiols, & alcohols. And once it reacts, it’s “useless.” Kinda like a party popper – you can only pop it once. So you want to make sure you start with enough poppers and don’t accidentally set them off before you’re ready. Then, the point of the autoclaving is to pop all the poppers that haven’t gone off before you add it to something where you don’t want it to go off. (and you don’t don’t want it to go off and leave confetti stuck to your reaction!)

ThermoFisher suggests ~0.1% DEPC. If you go lower, you might not inhibit all the RNase. But if you go too high, you might not inactivate all the DEPC before you go use it in your reactions. Or, even if you do inactivate it all, some of the DEPC by-products can inhibit some of those reactions you’re going to use it with (such as in vitro translation) and potentially even modify RNA instead of just RNases.

If you’ve ever worked with DEPC-treated water and noticed a fruity smell and gotten kinda freaked out that it had gone bad or something – don’t worry! That smell comes from a type of chemical called esters that are formed when ethanol given off during the RNase-killing reacts with trace amounts of carboxylic acid contaminates.

Perhaps one of the most important things to keep in mind when working with DEPC-treated water is that the water is only as clean as you keep it! Since you’ve inactivated all the DEPC, there’s nothing in there to protect against any RNases that are subsequently introduced.

And there are a lot of RNases a lot of places – There are a lot of different RNases. Some do more specific things in our cells and work in a more controlled fashion. For example, the protein I study, Argonaute cuts RNA but only when that RNA matches an RNA guide that Argonaute is bound to in a process called RNA interference (RNAi). https://bit.ly/rnainterference

So I like that RNase :). But these generic guys are the ones we really worry about. RNase A is the name for the bovine version of one of them. The most similar one in humans is RNase 1. They’re both referred to as “pancreatic-type” cuz they’re secretory RNases made by the pancreas – but that name is kinda misleading because they’re also made by most cells – especially endothelial cells (cells lining body tubing and compartments) – so we can secrete it in our spit & sweat, etc. to add a barrier of protection against viruses before they can even get in. Bacteria & fungi and other tiny life forms also do this – and they’re the main source we worry about in the lab.

In addition to DEPC treatment and cleaning well, we take other precautions when working with RNA including using filtered pipet tips which prevent RNases from getting pushed out of the pipet into the sample when you’re pipetting. 

source of figure & more info: https://bit.ly/32KTllv

In addition to DEPC treatment and cleaning well, we take other precautions when working with RNA including using filtered pipet tips which prevent RNases from getting pushed out of the pipet into the sample when you’re pipetting. 

source of figure & more info: https://bit.ly/32KTllv 



more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 

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