Stealth RNA™ siRNA oligonucleotides are 25-base-pair double-stranded RNA oligonucleotides with proprietary chemical modifications. Compared to siRNA, Stealth RNA™ siRNA molecules provide decreased nonspecific stress responses for clearer results, high potency for more powerful knockdown of genes, and improved stability both in cell culture systems and in vivo.
You can reconfigure 19-mer siRNA sequences into 25-mer Stealth RNA™ siRNA sequences using the RNAi Designer. Select the siRNA to Stealth design option at the top of the Designer page. Then enter a sequence for the gene that you want to target or a database accession number for that sequence, and the 19-mer siRNA oligo sequence(s) that you want to convert to Stealth RNA™ siRNA.
You can copy and paste a nucleotide target sequence directly into the Nucleotide Sequence field, or you can enter a database accession number for the sequence in the Accession Number field. If you enter an accession number, the Designer will link to the Entrez search engine and search the crosslinked databases at the National Center for Biotechnology Information (NCBI), including GenBank and OMIM. Then the sequence associated with the accession number will be automatically downloaded into the Designer.
Note: If you enter an accession number in RefSeq format (e.g., NT_123456), the Designer will check the sequence for known single-nucleotide polymorphisms (SNPs). Designs that include SNPs will be rejected by the Designer. SNP identification will not be performed if you paste in nucleotide sequences or enter GenBank-format accession numbers.
Nucleotide Sequence: Type or paste your single-stranded target sequence into this box. The designer accepts sequences in text, FASTA, or GenBank format.
The sequence should be oriented from 5' to 3'. Because Stealth RNA™ siRNA molecules must be highly specific, the input sequence should contain only the following 1-letter base code abbreviations: A, C, G, T, U (case insensitive). Any regions of the sequence containing ambiguous bases (e.g., N) or other letters will be skipped when generating the designs. If your sequence includes too many ambiguous bases or other letters, you will be prompted to re-enter the sequence. White spaces and numerals in the sequence will be ignored.
Note: If you are having difficulty generating Stealth RNA™ siRNA designs, check your input sequence to make sure that it contains only the letters A, C, G, T, or U.
Accession Number: Enter the database accession number for your sequence in this field. The Designer will link to the Entrez search engine and search the crosslinked databases at NCBI, including GenBank and OMIM. The sequence associated with the accession number will be automatically downloaded into the Designer.
RefSeq-format accession numbers begin with two letters followed by an underscore and six digits (e.g., NT_123456). GenBank accession numbers are usually a combination of a letters and numbers, such as a single letter followed by five digits (e.g., U12345) or two letters followed by six digits (e.g., AF123456). If you enter an accession number in RefSeq format (e.g., NT_123456), the Designer will check the sequence for known single-nucleotide polymorphisms (SNPs). Designs that include SNPs will be rejected by the Designer. SNP identification will not be performed if you paste in nucleotide sequences or enter GenBank-format accession numbers.
In the siRNA Sequences field, enter each 19-mer siRNA sequence that you want to convert to a Stealth RNA™ siRNA oligo. Each sequence should be oriented from 5' to 3' and should be complementary to the target sequence that you specified above. Enter each siRNA sequence on a separate line in the field.
Click on Submit to begin the conversion process. The BLOCK-iT™ RNAi Designer uses statistical analysis of multiple validated Stealth RNA™ siRNA sets and a proprietary algorithm to analyze the target gene sequence and determine the optimal Stealth RNA™ siRNA oligo configuration for silencing the gene.
A Stealth RNA™ siRNA sequence will be generated for each siRNA molecule, and you will be prompted to select negative control sequences for the Stealth RNA™ siRNA. See Stealth RNA™ siRNA Negative Control Sequences for more information.