Design Input
Design sequences for one or more strands intended to adopt an unpseudoknotted
target secondary structure at equilibrium.
Select RNA (default) or DNA for strand type. DNA/RNA hybrids
are not allowed.
Enter the temperature (default 37 °C).
The number of independent sequence designs to perform.
Enter the target secondary structure in
dotparensplus notation or DU+ notation. Target structures must be connected and free of pseudoknots.
Using dotparensplus 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 dotparensplus notation and
U2 D3 (U3 D6 (U2 + U1) U1 D4 (U4))
in DU+ notation.
Dotparensplus 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.
Select among available energy models, specify dangle
treatments, specify salt concentrations,
and define pattern prevention requirements.

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).

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.

For RNA, the salt concentrations are 1.0 M Na^{+} and 0.0 M Mg^{++}.
For DNA, the userdefined 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).

Specify patterns to be prevented in the designed sequences.
Enter one pattern per line using standard nucleic acid codes (depicted
above 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.
Enter your email address for notification of job completion (required for long jobs).
Start sequence optimization.