Help with size selection

ptery · 06-17-2015, 11:56 AM

I want to remove a 33nt RNA from a small quantity pool of total RNA (couple hundred ng). What kind of technique/kits should I use? Does Ampure XP beads work for RNA? or there is another beads for RNA size-selection? In ion total RNA V2 kits, there is a Nucleic Acid Binding Beads for purification of fragmented RNA. I'm wondering if it's Ampure XP beads? If Ampure XP beads works, may I titrate PEG4000/aqueous phase ratio for size selection? Any recommendation is welcome.

Thanks

jwfoley · 06-17-2015, 12:18 PM

RNAClean XP is the RNA version of AMPure XP. As far as I can tell (and according to Beckman support), it's the same beads in a different buffer, RNase-free. See our homebrew version for examples, although we don't know what's actually in Beckman's buffers.

33 nt is below the range you usually expect to recover by SPRI. However, I've heard you can retain smaller molecules by adding isopropanol to the mix. Maybe give that a try? Or if your goal is to isolate the small molecules from the large ones, you could also just use regular conditions and keep the supernatant instead of the beads.

ScienceGrrl · 07-17-2015, 01:31 PM

Beckman has a protocol for miRNA selection using their SPRIselect beads and isopropanol.

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06-17-2015, 11:56 AM	#1
ptery Junior Member Location: San Diego Join Date: Apr 2014 Posts: 3	Help with size selection I want to remove a 33nt RNA from a small quantity pool of total RNA (couple hundred ng). What kind of technique/kits should I use? Does Ampure XP beads work for RNA? or there is another beads for RNA size-selection? In ion total RNA V2 kits, there is a Nucleic Acid Binding Beads for purification of fragmented RNA. I'm wondering if it's Ampure XP beads? If Ampure XP beads works, may I titrate PEG4000/aqueous phase ratio for size selection? Any recommendation is welcome. Thanks

06-17-2015, 12:18 PM	#2
jwfoley Senior Member Location: Stanford Join Date: Jun 2009 Posts: 181	RNAClean XP is the RNA version of AMPure XP. As far as I can tell (and according to Beckman support), it's the same beads in a different buffer, RNase-free. See our homebrew version for examples, although we don't know what's actually in Beckman's buffers. 33 nt is below the range you usually expect to recover by SPRI. However, I've heard you can retain smaller molecules by adding isopropanol to the mix. Maybe give that a try? Or if your goal is to isolate the small molecules from the large ones, you could also just use regular conditions and keep the supernatant instead of the beads. Last edited by jwfoley; 06-17-2015 at 12:20 PM.

07-17-2015, 01:31 PM	#3
ScienceGrrl Junior Member Location: Indianapolis, IN Join Date: Jul 2015 Posts: 8	Beckman has a protocol for miRNA selection using their SPRIselect beads and isopropanol.