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NucleotideCompositionofRNALEVELII
Materials
- RNAsample
- 1Nand0.1NHCl
- Boilingwaterbath
- Whatman#1filterpaper(forchromatography)
- Chromatographytank
- 20µlmicroPipette
- Aceticacid:butanol:water(15:60:25)solvent
- UVlightsource
- UVspectrophotometer
Procedure
- PlaceaportionofyourRNAsample(approximately40mg,hydrated)intoaheavywalledpyrextesttube.Add1.0mlof1NHClandsealthetube.
- Heatthetubeinaboilingwaterbathfor1hour.
- Coolthetube,openitandplacethecontentsintoacentrifugetube.Centrifugethecontentsat2,000RPMinaclinicalcentrifugetoremoveanyinsolubleresidue.ThesupernatantcontainsyourhydrolyzedRNA.
- PrepareWhatmanfilterpaperNo.1forstandardone-dimensionalchromatography.12
- Usingamicropipette,spot20µlofyourhydrolyzateontothepaper,beingcarefultokeepthespotsassmallaspossIBLe(repeatedsmalldropsarebetterthanonelargedrop).Allowthespotstocompletelydrybeforeproceeding.
- Placethepaperchromatogramintoyourchromatographytankandaddthesolvent(aceticacid:butanol:water).Allowthesystemtofunctionforanappropriatetime(approximately36hoursfora20cmdescendingstripofWhatman#1).Removethepaperanddryitinacirculatingairovenat40°Cforabout2hours.
- Locatethespotsofnucleotidesbytheirfluorescenceunderanultra-violetlightsource.ExposethepaperchromatogramtoaUVlightsourceandoutlinethespotsusingalightpencil.Theorderofmigrationfromthepointoforiginisguanine(lightbluefluorescence),adenine,cytilicacidandfinally,uridylicacid.
DonotlookdirectlyattheUVlightsource.UseacABInetdesignedtoshieldfromharmfulUVrADIation.
- Aftercafefullymarkingthespots,cutthemoutwithscissorsandplacethepapercutoutsintoseparatelylabeled15mlconicalcentrifugetubes.Add5.0mlof0.1NHCltoeachtubeandallowthetubestositforseveralhourstoelutethenucleotidesfromthepaper.
- Packdownthepaperwithaglassrod(centrifugeinaclinicalcentrifugeifnecessary)andremoveanaliquotoftheliquidforspectrophotometricassay.
- MeasuretheabsorbanceofeachofthefournucleotidesattheindicatedUVwavelength(havingfirstblankedtheinstrumentwith0.1NHCl).
Base | Wavelength | MolarExtinctionCoefficient |
---|
Guanine | 250nm | 10.6 |
Adenine | 260nm | 13.0 |
Cytidylicacid | 280nm | 19.95 |
Uridylicacid | 260nm | 9.89 |
- Usethemolarextinctioncoefficientstodeterminetheconcentrationofeachbaseinthesample.Calculatethepercentcompositionofeachbase,andthepurine/pyrimidineratio.
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