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The AUMsilence platform

Sequences per target

Not every position along a transcript is equally available. The RNA folds back on itself and proteins sit along it, so some sites are open to an antisense oligonucleotide and others are closed. That is why several sequences against one target do not perform alike.

When 5 sequences of AUMsilence sdASO or AUMlnc sdASO are designed against one target, each is placed in a different region of the target RNA. Every candidate is checked for RNA folding, secondary and tertiary structure, protein binding, GC content and off-target matches before synthesis.

Order against a target

Target site selection

Conventional design and the AUMsilence platform

Conventional design places sequences along the target RNA, and a sequence can land on a folded stretch or on a protein-binding region.

The AUMsilence platform tries to avoid secondary and tertiary structures and protein-binding regions, which gives a higher chance of success. Every candidate is weighed against the scientific literature and the design parameters, including GC content and off-target matches. The platform uses algorithms, machine learning and AI systems in combination with our extensive experience in antisense design.

How a sequence is designed

Schematic Sequence placement on one mRNA
Conventional design and the AUMsilence platform, on one mRNATwo copies of one messenger RNA stand side by side, each drawn from its 5′ end at the top to its 3′ end at the bottom. Each has a 5′ untranslated region, a coding sequence and a 3′ untranslated region. Both carry the same hairpin, the same two hairpins meeting at their loops and the same two bound proteins. Each of these closed stretches is a hatched band across both copies, named in the right margin: secondary structure, tertiary contact and bound protein. On the left, under conventional design, 1 sequence lands on the hairpin, 1 on the two hairpins in contact and 1 under a bound protein. On the right, on the AUMsilence platform, the sequences sit in open stretches: 1 in the 5′ untranslated region, 3 in the coding sequence and 1 in the 3′ untranslated region.ConventionaldesignAUMsilenceplatform5′ UTRCodingsequence3′ UTRSecondarystructureTertiarycontactBoundproteinBoundprotein5′3′5′3′
  • Untranslated region (UTR)
  • Coding sequence
  • Secondary structure
  • Tertiary contact
  • Bound protein
  • Closed stretch
  • Designed sequence
On the same mRNA, conventional design can place sequences on secondary and tertiary structure and under bound proteins. The AUMsilence platform tries to place them in open stretches. A schematic, not a map of real positions. It shows no outcome and no rate.

Regions of the target RNA

Sequences in different regions of the target

The sequences designed against one target are placed in different regions of the target RNA. On an mRNA they sit across the coding sequence and the untranslated regions (UTRs), and on a long non-coding RNA (lncRNA) along its length.

Designing them in different regions gives more chances of finding a site that is open and meets the design criteria.

Schematic Sequence positions on an mRNA and a lncRNA
Sequence positions on an mRNA and a lncRNAThe first schematic is a messenger RNA from its 5′ end to its 3′ end, with its 5′ untranslated region, coding sequence and 3′ untranslated region. Its designed sequences are numbered 1 to 5, each in a region of its own. Sequence 1 sits in the 5′ untranslated region, sequences 2, 3 and 4 in the coding sequence, and sequence 5 in the 3′ untranslated region. The second is a long non-coding RNA from its 5′ end to its 3′ end, with its designed sequences, numbered 1 to 5, spread along its length. The drawing does not mark which sequences work.mRNA5′ UTRCoding sequence3′ UTR123455′3′lncRNA123455′3′
  • Untranslated region (UTR)
  • Coding sequence
  • Long non-coding RNA
  • Region of one sequence
  • Designed sequence
On an mRNA the 5 sequences sit across the 5′ UTR, the coding sequence and the 3′ UTR. On a lncRNA they sit along its length. A schematic: it shows where the sequences sit, not which of them work.

How many to test

1, 3 or 5 sequences

AUMsilence sdASO and AUMlnc sdASO are supplied as 1, 3 or 5 sequences per target.

  • 1 sequence

    An established design

    Testing 1 sequence suits a published sequence being reproduced, or one used in earlier experiments.

  • 3 sequences

    The standard first pass

    Testing 3 sequences covers 3 regions of the target.

  • 5 sequences

    The first pass with the knockdown guarantee

    Testing 5 sequences covers 5 regions of the target. It suits an experiment that cannot easily be repeated, such as work with primary cells from a single donor or with an animal cohort. It also suits a transcript with few open sites.

Sequences per target, by product

ProductSequences per targetPlacement
AUMsilence sdASO mRNA knockdown1, 3 or 5The sequences designed against one target sit in different regions of the mRNA, across its coding sequence and untranslated regions.
AUMlnc sdASO lncRNA knockdown1, 3 or 5The sequences designed against one target sit in different regions along the length of the lncRNA.
AUMantagomir sdASO microRNA inhibition1An AUMantagomir sdASO is supplied as 1 sequence, which hybridizes to the whole mature microRNA.
AUMmimic sdASO microRNA mimic1An AUMmimic sdASO supplies a microRNA rather than hybridizing to one.
AUMsilence toASO and AUMlnc toASO Transfection-optimized antisense1-4Each is supplied singly, or as a pool of 4 different sequences against one target.
AUMantagomir toASO Transfection-optimized antisense1An AUMantagomir toASO is supplied as 1 sequence, which hybridizes to the whole mature microRNA.
AUMsiRNA Chemically modified siRNA1-5AUMsiRNA is supplied singly, or as a pool of siRNAs against different regions of the same mRNA.
2'-MOE, locked nucleic acid and 2'-OMe oligonucleotides Antisense oligonucleotides1-5Each is made to the supplied sequence, or designed using the AUMsilence platform for the named target, and supplied separately.

Ordering

The knockdown guarantee

If you use 5 sequences and none of them works, we will give more compounds free of cost.

The guarantee covers an order of 5 sequences designed by AUM BioTech of AUMsilence sdASO or AUMlnc sdASO against one target, but not an order of 3.

The guarantee is subject to the terms and conditions.

Order against a target

A scramble control is recommended in every experiment, and a labeled control shows uptake in the cells before the first knockdown experiment.