Design Input
Design sequences for one or more strands intended to adopt an unpseudoknotted target secondary structure at equilibrium.
Nucleic acid type:
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.
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 )
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:
Select among available energy models, specify dangle treatments, specify salt concentrations, and define pattern prevention requirements.
Email address:
Enter your email address for notification of job completion (required for long jobs).
Start sequence optimization.