nupack logotype
Try out the all-new NUPACK Cloud alpha test site!
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 or DU+ notation. Target structures must be connected and free of pseudoknots.

Using 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 (Zadeh et al., J Comput Chem , 2011).

Using DU+ notation, a duplex of length x base pairs is represented by Dx and an unpaired region of length x nucleotides is represented by Ux (Zadeh, PhD Thesis, California Institute of Technology, 2011). Each duplex is followed immediately by the substructure (specified in DU+ notation) that is 'enclosed' by the duplex. If this substructure includes more than one element, parentheses are used to denote scope. A nick between strands is specified by a '+'. For example:

is denoted ..(((...((((((..+.)))))).((((....)))))))
in dot-parens-plus notation and U2 D3 (U3 D6 (U2 + U1) U1 D4 (U4)) in DU+ notation.

Dot-parens-plus notation DU+ notation
((((((((((((..........)))))))))))) D12 U10
((((((((((((+)))))))))))).......... D12 + U10
((((((((((((+..........)))))))))))) D12 ( + U10 )
Preview:
If a valid design is entered, a visual preview is provided. Drag and drop thumbnails to enlarge. Large previews can be zoomed using the mouse wheel and panned by clicking and dragging the image.
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
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).
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.
NA,C,G,U
RA,G
YC,U
MA,C
KG,U
SC,G
WA,U
VA,C,G
HA,C,U
BC,G,U
DA,G,U

Depict target structure:
Draw circles on the probability plot indicating the target structure
Email address:
Enter your email address for notification of job completion (required for long jobs).