Gapmer Layout

Assemble and assess an antisense wing-gap-wing oligonucleotide layout.

Description

A gapmer combines left wing, central gap and right wing sequences.

A gapmer combines left wing, central gap and right wing sequences. Sequence assembly alone does not specify the chemical modifications that make a gapmer functional.^[1]

Assemble and assess an antisense wing-gap-wing oligonucleotide layout.

When to use Gapmer Layout

Use this tool to assemble and assess an antisense wing-gap-wing oligonucleotide layout.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Gapmer Layout and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter leftWing, gap, rightWing, minimumGapLength using the field table and calculation rules, then run the tool.
Read oligo, lengthNt, wingBalance, gapValid. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
leftWing	Left wing	string	Required
gap	Gap	string	Required
rightWing	Right wing	string	Required
minimumGapLength	Minimum gap length	number	Required

Enter three nonempty nucleotide-only A/C/G/T/U segments and minimum gap length at least one. Concatenate without converting T/U, report total length and signed wing balance, and compare gap length inclusively with the criterion.

oligo=uppercase(leftWing+gap+rightWing); wingBalance=leftLength−rightLength

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
oligo	Oligo	string
lengthNt	Length nt	number
wingBalance	Wing balance	number
gapValid	Gap valid	boolean

json

{
  "input": {
    "leftWing": "ACG",
    "gap": "TTTT",
    "rightWing": "GCA",
    "minimumGapLength": 3
  },
  "output": {
    "oligo": "ACGTTTTGCA",
    "lengthNt": 10,
    "wingBalance": 0,
    "gapValid": true
  }
}

Limitations and assumptions

No chemical modifications, target complementarity, RNase-H activity or off-target effects are encoded. DNA/RNA letters can be mixed, and a passing length is only a supplied layout screen.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use siRNA GC Screen: Screen siRNA GC percentage against user-selected design bounds. For a complementary task, use miRNA Seed Matcher: Locate reverse-complementary miRNA seed matches in a target RNA.

References

Gapmer Layout — tool.io

Similar or alternative tools

siRNA GC Screen
Screen siRNA GC percentage against user-selected design bounds.
miRNA Seed Matcher
Locate reverse-complementary miRNA seed matches in a target RNA.