Wobbles - Degenerate Bases

Wobbles - Degenerate Bases

Standard degenerate bases or "wobbles" are equimolar mixtures of two or more different bases at a given position within the sequence.

Wobbles are often incorporated into oligonucleotide probes designed to hybridize to an unknown gene that encodes a known amino acid sequence. Since the genetic code is degenerate (e.g., histidine could be encoded by CAC or CAT), the oligo probe is prepared with wobbles at the degenerate sites. Oligos with wobbles are also useful in random mutagenesis and combinatorial chemistry.

The universal codes for specifying a wobble are: R = A/G, Y = C/T, M = A/C, K = G/T, S = C/G, W = A/T, B = C/G/T, D = A/G/T, H = A/C/T, V = A/C/G, and N = A/C/G/T.

Please note that oligonucleotides with wobbles can be ordered salt-free or HPLC purified. PAGE purification, 2-step HPLC or 2-step PAGE are not available for wobble oligonucleotides. The broad variety of sequences produced in the synthesis of degenerated oligonucleotides does not allow PAGE purification of standard performance. In general Eurofins Genomics does not recommend further purification of wobble oligonucleotides. Any HPLC purification of wobble oligonucleotides will cause a loss of particular sequences created by the wobbles.

Oligonucleotides with non-equimolar wobble mixtures can be synthesized at the 5’ terminus or internally. Custom wobbles should be indicated in an A/C/G/T order and in the following format: [15-10-65-10]. This designator represents a mixture of 15% A, 10% C, 65% G, and 10% T. Please contact Eurofins Genomics’s technical support specialists for additional information.

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Modification	[Designator]	Availabilty
2'-O-Methyl Equimolar Wobble	[2OMeN]	5', internal
Custom Mixed N Wobble	[25-25-25-25]	5', internal
B Wobble (C+G+T)	[B]	5', internal
3' B Wobble (C+G+T)	[B-Q]	3'
D Wobble (A+G+T)	[D]	5', internal
3' D Wobble (A+G+T)	[D-Q]	3'
H Wobble (A+C+T)	[H]	5', internal
3' H Wobble (A+C+T)	[H-Q]	3'
K Wobble (G+T)	[K]	5', internal
3' K Wobble (G+T)	[K-Q]	3'
M Wobble (A+C)	[M]	5', internal
3' M Wobble (A+C)	[M-Q]	3'
Pre-mixed N Wobble (A+C+G+T)	[N]	5', internal
3' N Wobble (A+C+G+T)	[N-Q]	3'
R Wobble (A+G)	[R]	5', internal
3' R Wobble (A+G)	[R-Q]	3'
S Wobble (C+G)	[S]	5', internal
3' S Wobble (C+G)	[S-Q]	3'
V Wobble (A+C+G)	[V]	5', internal
3' V Wobble (A+C+G)	[V-Q]	3'
W Wobble (A+T)	[W]	5', internal
3' W Wobble (A+T)	[W-Q]	3'
Y Wobble (C+T)	[Y]	5', internal
3' Y Wobble (C+T)	[Y-Q]	3'
dP + dK mixture	[dPdK]	5', internal