What is in Illumina's Normalization Beads?

[JMB]

Illumina's normalization beads have formamide, are very stinky, must be used in a hood and use NaOH to render the DNA single stranded. I looked into alternative bead normalization products (one from Qiagen and one from MagBio) and they do not seem to have any of the nasty chemicals in them. I think they are just concentrated AMPure with PEG and NaCl.

Has anyone figured out what is in Illumina's beads? Does anyone have experience with the commercial bead normalization products other than Illumina's or have made your own cocktail? Any ideas on why the ingredients are different or why one would be better than the other?

I am asking because library qPCR takes soooo long when processing high throughput!

[luc]

I am guessing the Illumina beads are coated with P5 and P7 oligos (or the Nextera transposase sequence) and your library is hybridizing to it. Thus the libraries end up being at an extremely low concentration - but I would assume that the normalization is more precise as compared to all the other systems which precipitate dsDNA onto magnetic beads.

[nucacidhunter]

My guess is that S5xx primers has some moiety at 5’ end (maybe biotin) that binds to beads coated with limited number of interacting molecules. After binding and wash they melt the strand without moiety from bead by using NaOH.

There are other normalisation products as well:
1- Bead based normalisation products which work by AMPUre bead based principal but those beads have a low binding capacity. The beads are saturated to their maximum capacity and then extra fragments in supernatant are washed. The eluted fragments are dsDNA. They work well but the short coming is that they require 3-4x more input for consistent output. One has to miniaturise them for lower input.

2- Normalisation plates with coated wells that work by ChargeSwitch binding. This also requires 3-4x more concentrated input than output, but is less flexible for miniaturisation.

[JMB]

Thank you for the replies. I can definitely see Illumina having a complimentary sequence or some sort of moiety on their products. They love to be sneaky like that. I seem to get pretty good yields from my library prep, so I may try out one of the AMPure methods or commercially available kits.