---+ Use of degenerate bases Spoke with IDT about some of their recommendations related to incorporation of degenerate bases in oligos. ---++ Machine Mix vs Hand Mix option * Machine Mix: 1 Bases are mixed at equal molar concentrations. 1 Each base has a different coupling efficiency which leads to different incorporation rates. * Automated message states that this is a difference in delivery rates, but that appears to be somewhat misleading. 1 Results in the following incorporation ratio for a single "N": * 30:26:24:20 T>G>C>A 1 Ratio is per base, and a string of N's does not change the ratio. 1 No additional charge. * Hand Mix: 1 Can be used to correct the machine mix ratio. 1 Percents entered are the incorporation percents, not the mixture percents. * ie: entering 25:25:25:25 would result in them decreasing the amount of T and increasing the amount of A to achieve 25:25:25:25 final diversity. 1 Claim their formula is accurate to within less than 1%. 1 Additional cost required. ---++ PAGE and HPLC problems 1 Each base (A,C,T,G) has a slightly different migration rate than each other. 1 IDT uses a very conservative selection to ensure that all product is full length. 1 Results in loss of diversity. 1 Works against hand mixing. 1 Suggested that can try standard desalting and doing our own less conservative PAGE purification to eliminate truncated product. Warning that this can still lead to elimination of some diversity. -- Main.DanielDeatherage - 22 Jan 2013
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Topic revision: r1 - 2013-01-22 - DanielDeatherage