![]() The base-pair complementarity is super nice because it makes it WAY easier (and cheaper) to design probes for different sequences than it does to make probes for different proteins like those you use in western Blots – for proteins you usually use antibodies which are little proteins that recognize specific parts of other things – they can take a long time to produce and production usually involves injecting animals with the thing you want antibodies made to recognize, then letting the animal’s natural immune system select and amplify antibodies that recognize it as foreign. The “oligo” in oligonucleotides refers to “few/several” but you don’t want too few! ![]() Regardless of letter type, you usually you use longer sequences that are less likely to occur by chance (like the reason you should use longer passwords. Thanks to the “RNA can pair with RNA or with DNA” thing, you can use either type of “oligonucleotide” probe, but DNA is more stable. if you’re looking for the sequence 5’-GAUUACA-3’ you can design a probe that’s 3’-CTAATGT-5’ (if you use a DNA probe) or 3’-CUAAUGU-5’ (if you use an RNA probe). Since A binds U (T in DNA) and C binds G, you can design probes that bind the thing you’re looking for with specificity! (e.g. The northern blot is a technique used to test for pieces of RNA that contain a specific sequence, utilizing the 1:1 base-pairing specificity of nucleotides (DNA & RNA letters). They could break the cell open (lyse it) and isolate all the RNA, but if they were to label all the RNA, they’d be labeling tons and tons of different RNAs, not just the one they want. But a lot of times scientists don’t know what and/or how much of a specific RNA is in some mixture – like the insides of a cell at different times. I haven’t actually done it personally because I do in vitro (in a test tube) work where I know exactly what RNAs I put into my reactions, so I can label all the RNA and know all the signal I see is from the one I’m interested in. The western blot isn’t the only technique to hop onto the direction name train – there’s a 3rd main type of blot called the northern blot and, as someone who studies small RNAs, I come across it in papers a lot. This is why you capitalize the S but not the w. The western blot is a way to test for the presence of specific proteins and it’s named after the Southern blot which tests for specific pieces of DNA – and the “Southern” name comes from the name of the scientist who invented the technique, Edwin Southern. In last week’s Bri*fing, we looked at the western blot. And they utilize different types of “probes” to do so – antibodies for western blots, and little pieces of sequence-complementing DNA for the others. If the probe finds a match, a band you will see, but what kind of molecule will it be? For western blots, you’re looking for specific proteins, Southern blots look for specific DNA, and northern blots look for specific RNA. No matter what “direction” is in the name – the basic premise is the same – take a mix of biomolecules and separate (typically by size) then transfer to a membrane and probe to analyze.
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