DOH Workshop Part 2: Promega Pronex protocol

Natalie Ring, Bryan Wee, Vesa Qarkaxhija

Published: 2024-03-08 DOI: 10.17504/protocols.io.8epv5xwx5g1b/v1

Abstract

This protocol is to purify extracted dsDNA, removing contaminants (e.g., buffers, proteins, salts, etc.) and low molecular weight DNA (e.g., dsDNA adapters, ssDNA oligonucleotides and nucleotides).

Before start

Ensure that the Pronex Wash Buffer is prepared according to instructions on them (i.e.adding appropriate amount of Ethanol).

Attachments

Steps

Promega Pronex protocol

1.

Resuspend the Pronex beads by vortexing for 0h 0m 10sor longer.

Note
Shake well before use
Shake well before use

2.

Into your extracted DNA tube pipette 80µLof Pronex beads and mix into the sample by slowly pipetting 10 times.

Note
If sticky clumps of bead-bound DNA form, be careful not to take any beads either in the pipette tip or on the outside of the pipette tip.

3.

Leave at Room temperature for 0h 10m 0s.

4.

Place the sample on a magnetic rack for0h 2m 0s (or longer if necessary) until the solution becomes clear and the beads form a pellet.

5.

While leaving tubes on the magnet, carefully remove and discard supernatant without disturbing the beads using a P1000.

6.

While the tube is on the magnetic rack, add 200µLof Pronex wash buffer without flushing directly onto the pellet. If 200µLis not enough to submerge the pellet, use more wash buffer.

Note
Wash Step 1

7.

Allow to incubate for 0h 0m 30s-0h 1m 0s .

8.

While leaving tubes on the magnet, carefully remove and discard wash buffer without disturbing the beads using a P1000.

9.

Keeping the tube on the magnetic stand, carefully add 200µL of Pronex Wash Buffer without flushing directly onto the pellet. If 200µL is not enough to submerge the pellet, use more wash buffer.

Note
Wash Step 2

10.

Allow to incubate for 0h 0m 30s-0h 1m 0s .

11.

While leaving tubes on the magnet, carefully remove and discard wash buffer without disturbing the beads using a P1000.

12.

Allow the sample to air dry with lids open for 0h 2m 0s-0h 5m 0swatching it until the pellet is no longer shiny.

Note
Be careful not to over-dry
Be careful not to over-dry

13.

Remove the sample from the magnetic stand.

14.

Remove the tube from the magnetic rack and add 32µL of nuclease free water. Resuspend the beads by slowly pipetting or stirring with the pipette tip.

Note
Be as gentle as possible while ensuring that pellet is resuspended.
Pipette gently, be careful not to shear DNA
Pipette gently, be careful not to shear DNA

15.

Leave for0h 5m 0s at Room temperature to elute the DNA.

16.

Pellet beads on magnet for 0h 1m 0s until solution becomes clear and slowly pipette DNA eluate into a new LoBind tube.

Note
Save the tube with Pronex beads in case of incomplete DNA elution, so you can repeat.
Pipette gently, be careful not to shear DNA
Pipette gently, be careful not to shear DNA

17.

Quantify 1µL of DNA elute using the Qubit™ dsDNA HS Assay Kit or QuantiFluor® ONE dsDNA System.

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