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GenScript siRNA Construct Builder

Recommendation:

Loop: The default is a 10-nucleotide spacer (TTGATATCCG), and other spacers have been reported as well: CCACC [1], CTCGAG [2], AAGCTT [2], CCACACC [1], TTCAAGAGA [3].
Transcription Start Site: RNA Polymerase III prefers to initiate transcription with a purine [4]. If the hairpin insert does not start with a "G" or "A", an additional "G" will be added to the 5' end of the hairpin insert sequence.

Vector: Vector specific sequences will be added based on vendor recommendation. Those sequences could include:

  • 5' Sequence
  • 3' Sequence
  • Loop Sequence
  • Transcription Start Site
Dinucleotide Leader Sequence: Please do not include the dinucleotide leader sequence "AA" in the sense target sequence. The "AA" leader is not required for vector-based siRNA contruct.

Orientation of hairpin insert:. Hairpin insert can be constructed in these orientations: antisense-loop-sense (Default), or sense-loop-antisense (Reverse). Both orientations can function effectively [5].



Use this tool to build small hairpin inserts for use as siRNA expression vectors.

Instructions:

  1. Paste each sense siRNA sequence in the boxes below or use our batch build form to input several sequences at once.
  2. Please do not include the dinucleotide leader sequence "AA." You may specify the loop sequence or use the default sequence for each target sense siRNA.
  3. Select your desired vector, if any.
  4. For larger orders, indicate the number of targets and click here:
Gene: Quantity:

Vector:

Orientation: Default Reverse
Target 1: Loop Sequence:
Target 2: Loop Sequence:
Target 3: Loop Sequence:
Target 4: Loop Sequence:
Target 5: Loop Sequence:
Target 6: Loop Sequence:
Target 7: Loop Sequence:
Target 8: Loop Sequence:
Target 9: Loop Sequence:
Target 10: Loop Sequence:

 

 

References:

  1. Jacque JM, Triques K, and Stevenson M. (2002) Modulation of HIV-1 replication by RNA interference. Nature 418: 435-438.
  2. Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC, and Shi Y. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99(8): 5515-5520.
  3. Brummelkamp TR, Bernards R, and Agami R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553.
  4. Zecherle GN, Whelen S, and Hall BD. (1996) Purines are required at the 5' ends of newly initiated RNAs for optimal RNA polymerase III gene expression. Mol. Cell. Biol. 16:5801-5810.
  5. Harborth J, Elbashir SM, Vandenburgh K, Manninga H, Scaringe SA, Weber K, Tuschl T. (2003) Sequence, Chemical, and Structural Variation of Small Interfering RNAs and Short Hairpin RNAs and the Effect on Mammalian Gene Silencing. Antisense Nucleic Acid Drug Dev. 13(2):83-105.
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