NUPACK: Design input

Nucleic acid type:

RNA

DNA

Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.

Temperature:

°C

Enter the temperature (default 37 °C).

Number of designs:

The number of independent sequence designs to perform.

Target structure:

Enter the target secondary structure in dot-parens-plus notation (each unpaired base is represented by a dot, each base pair by matching parentheses, and each nick between strands by a plus). Target structures must be connected and free of pseudoknots.

For example:

..(((...((((((..+.)))))).((((....)))))))

yields:

Preview:

If a valid target structure is entered, a visual preview is provided. Each base is shaded according to sequence constraints specified under Advanced options: A = green, U/T = red, G = black, C = blue, all others = gray.

Advanced options

RNA energy parameters:

For RNA, there are two parameter sets: (Serra and Turner, 1995; default) and (Mathews et al., 1999; valid only at 37 °C). For DNA, there is one parameter set: (SantaLucia, 1998).

Dangle treatment:

None: no dangle energies are considered.
Some(default):a dangle energy is incorporated for each unpaired base flanking a duplex (a base flanking two duplexes contributes only the minimum of the two possible dangle energies).
All: a dangle energy is incorporated for each base flanking a duplex regardless of whether it is paired.

Na⁺:

1.0 M

For RNA, the salt concentrations are 1.0 M Na⁺ and 0.0 M Mg⁺⁺. For DNA, the user-defined salt concentrations can be set in the ranges 0.05 – 1.1 M Na⁺ (SantaLucia and Hicks, 2004; default 1.0 M) and 0.0 – 0.2 M Mg⁺⁺ (Koehler and Peyret, 2005; default 0.0 M).

Mg⁺⁺:

0.0 M

Sequence constraints:

Specify sequence constraints starting at the 5' end using standard nucleic acid codes (depicted below for RNA; T replaces U for DNA).

N	A,C,G,U
R	A,G
Y	C,U
M	A,C
K	G,U
S	C,G
W	A,U
V	A,C,G
H	A,C,U
B	C,G,U
D	A,G,U

Prevented sequence patterns:

Specify patterns to be prevented in the designed sequences. Enter one pattern per line using standard nucleic acid codes (depicted below for RNA; T replaces U for DNA). No design will be produced if the sequence constraints cannot be satisfied. Example patterns: AAAA, CCCC, GGGG, UUUU, KKKKKK, MMMMMM, RRRRRR, SSSSSS, WWWWWW, YYYYYY.

N	A,C,G,U
R	A,G
Y	C,U
M	A,C
K	G,U
S	C,G
W	A,U
V	A,C,G
H	A,C,U
B	C,G,U
D	A,G,U

Email address:

Enter your email address for notification of job completion (required for long jobs).