|
The functionality described in this
topic is only available when you mark Show
Advanced Options.
Finalize
In this step, you can select to add a linker sequence to the 3' ends of all probes and then specify the parameters for the linker. When you are finished making selections for the linker, you can finalize the design.
Append linker to 3' end
Mark this check box if you want to add a linker to the 3' end of your probes.
Linkers are DNA sequences that move the hybridizing portion of the probe farther from the glass microarray substrate. Adding linkers can decrease steric hinderance and make the probe better able to hybridize target sequences. Agilent provides a default linker sequence that is designed to avoid hybridization to any sequence in the DNA sample.
Linker Length
Select one of the options for linker length:
· Make probes of length - Select this option to add a linker to each probe that results in a specified probe length. Type the desired probe length into the adjacent field. If a probe in your design exceeds the length that you specify, SureDesign does not add a linker.
· Add linker of length - Select this option to add a linker of a specified length to each probe. Type the desired linker length into the adjacent field (must be from 1- 49 bases). If the linker sequence you select in the Linker Sequence parameters (see below) is shorter than the length that you enter, SureDesign replicates the linker sequence to fill in the length.
Linker Sequence
Select one of the options for linker sequence:
Use Agilent - Select this option to use the Agilent-designed linker sequence. This sequence was designed to avoid hybridization to sequences in the DNA sample. The Agilent linker sequence is displayed in the adjacent field and cannot be edited.
Use customer - Select this option to enter your own linker sequence. In the adjacent field, type the desired linker sequence.
When you are ready, click Finalize Design
to finish the design creation process. The wizard advances to the Design
Complete step.