Psi_Locybe (Hive Bee)
03-02-03 09:55
No 412988
      Help! SDS/ALS, et al... please?  Bookmark   

I have an immense, life-and-death need to sequence my own X chromosome.  Thankfully ('cause I'm a tad... slow), the 'death' side of this isn't quite terribly immediate.

  Unfortunately, I'm an utter ghetto chemist - and not the best one at that; bear with a newbee?  (yes, I *know* it says 'Hive Bee;' I also know I'm an idiot)

Necessity 1 : Sodium Dodecyl Sulfate (SDS)

This is in shampoo (it's also known as 'sodium lauryl sulfate,' often (apparently) in high enough degree to make it cheaper than buying it online - plus, worst comes to worse, I can just have friends steal shampoo samples from the hotel they work at...

...some shampoos contain ammonium lauryl sulfate; I may be an idiot, but I *should* be able to convert.  ;)  (Cook baking soda at 500f for 3-5 hours, and...)

Does anyone know properties/solubilities of SDS/ALS?  A simple 15-common-solvent wash/precipitation?  ;)  Means of chromatographic determination with a ghetto lab?  ( rather looks like it would be hard as hell to swap sodium for, say, tryptamine, track acids under blacklight...then again, how weak an acid *is* dodecyl sulfate?  Can I swap with a little tryptamine acetate, let the strong acid and the strong base leave the weaker acid and the weaker base?)

Protienase K :
So - company X wants $600/g for it.  What part of my flesh do I eviscerate and chromatograph to aqquire it?  Better yet, what common food product contains it, ideally?  Beef liver?  Again, any hints at tracking the damned thing?

Alternately, is there anything else which will maul complex protiens into dissolveable chunks leaving DNA intact? 

Phenol :
...err, the closest I can immediately come is paradiphenol (baking soda at 500f again, and a few mothballs)... I don't suppose the protien fragments are soluble in Zippo fluid, by any chance?

...alternately, are there any common OTC uses for phenol?  Is it hidden in my local grocery store in .999 purity under some stupid common name?  Hell, in any purity, and I'll even take hardware stores... ;)

EtOH precipitation :
EtOH is beyond my means... I'll go with IPA.  :)  It works, according to a lovely little PBS special on tracing humanity's earliest roots..., this seems like a decent time to ask - does anyone know a reasonable means of seperating the X from the rest?  Anyone have the molecular structure/formula of quinacrine?  (is it found in nature?)  Does anyone know if quinacrine damages the DNA?  (I presume G and C banding does)

Sequencing; electrophoresis :

 Umm... unlike such general categories as "psychoactives" or "plant fibers" or "nACha4b2 agonist/AChE inhibitor," I fail to note agarose growing in my backyard... (the last one is the alkaloid galantine from daffodils, BTW)

...will electrophoresis on blotter paper work, by any chance?  Or is these molecules just a tad too large?

Restriction enzymes :
...not a bad idea; I don't suppose they're naturally found within the body?

If not, I guess I'll just grab an extra-long roll of Bounty, do my electrophoresis over a long, long time with a lot of space to do it in...

Dideoxy flourescent single-unit nucleotides :
Clemmensen?  Ammonium Nitrate/Clemmensen?  RP/Iodine?  (okay, so a few of these are sort of tongue-in-cheek - I'll have to buy this, won't I?  ::sigh::  THAT, my dear friends, is the point of idiocy; surrender - asking stupid questions (like this post) is, in contrast, merely a lack of knowledge)...

...just in case, though, I don't suppose anyone has the properties for adenosine, cytosine, thymine, and guanine?  The DEA might get pissed if I start making phosphate esters of deoxy and dideoxy sugars, but... damn... really *is* a war on science, rather than a war on drugs, isn't it?

Just checked Aldrich's lates - DAMN the dideoxy's are expensive... anyone have any hints at blasting DNA into single nucleotide/ribose pairs? 

Hell - anyone have just anything they think might be helpful?  I'm a bit frustrated at the apparent impossibility of contributing my X chromosome to the sum of human knowledge...

I'm quite open to suggestions, here - help?

Rev. Psi Locybe, insane alchemist.
(Chief Bee)
03-02-03 11:55
No 413021
      Please give up before you waste any time  Bookmark   

If I were you, I'd invest my time and money into finding a biochem company to do it for you... I have sequenced enough nucleotides myself to be able to say with authority that you will never be able to pull it off outside a professional lab.
(Hive Bee)
03-03-03 00:27
No 413185
      /me bursts into tears...  Bookmark   

::sigh::  I suppose this means that the years spent bringing my last (known) science up to its usual 'operational but sub-standard' levels has resulted in nothing more than the first truly useless knowledge I have ever found?

Damn, damn, damn...

...thanks for the advice; I'll increase the favor I show to the 'pay someone else to do it' option - which was already pretty large in its favor at the costs of protienase K and the dideoxys, plus the frustration at the inability to truly stand on my own two feet, entire, but instead procure the reagents.

  Damn... I'll keep trolling for info, then, though - for knowledge is its own end, in its own right.

Someday, I will do this in my basement - simply because I must, in order to hold some self-respect... but until that time, it looks like I'll be shopping around.

Rev. Psi Locybe, insane alchemist.