Abstract
Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered "undruggable". However, properties associated with the native RNA structure limit drug development, and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5′-end using computational screening with the high-resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5′-end nucleotide need not engage in Watson-Crick (W/C) H-bonding but must fit the general shape of the 5′-end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5′-end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5′-end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogues for siRNAs.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 17069-17077 |
| Number of pages | 9 |
| Journal | Journal of the American Chemical Society |
| Volume | 135 |
| Issue number | 45 |
| DOIs | |
| State | Published - Nov 13 2013 |
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ASJC Scopus subject areas
- Chemistry(all)
- Catalysis
- Biochemistry
- Colloid and Surface Chemistry
Cite this
Short interfering RNA guide strand modifiers from computational screening. / Onizuka, Kazumitsu; Harrison, Jason G.; Ball-Jones, Alexi A.; Ibarra-Soza, José M.; Zheng, Yuxuan; Ly, Diana; Lam, Walter; Mac, Stephanie; Tantillo, Dean J.; Beal, Peter A.
In: Journal of the American Chemical Society, Vol. 135, No. 45, 13.11.2013, p. 17069-17077.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Short interfering RNA guide strand modifiers from computational screening
AU - Onizuka, Kazumitsu
AU - Harrison, Jason G.
AU - Ball-Jones, Alexi A.
AU - Ibarra-Soza, José M.
AU - Zheng, Yuxuan
AU - Ly, Diana
AU - Lam, Walter
AU - Mac, Stephanie
AU - Tantillo, Dean J.
AU - Beal, Peter A.
PY - 2013/11/13
Y1 - 2013/11/13
N2 - Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered "undruggable". However, properties associated with the native RNA structure limit drug development, and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5′-end using computational screening with the high-resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5′-end nucleotide need not engage in Watson-Crick (W/C) H-bonding but must fit the general shape of the 5′-end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5′-end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5′-end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogues for siRNAs.
AB - Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered "undruggable". However, properties associated with the native RNA structure limit drug development, and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5′-end using computational screening with the high-resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5′-end nucleotide need not engage in Watson-Crick (W/C) H-bonding but must fit the general shape of the 5′-end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5′-end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5′-end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogues for siRNAs.
UR - http://www.scopus.com/inward/record.url?scp=84887671758&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84887671758&partnerID=8YFLogxK
U2 - 10.1021/ja4079754
DO - 10.1021/ja4079754
M3 - Article
C2 - 24152142
AN - SCOPUS:84887671758
VL - 135
SP - 17069
EP - 17077
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
SN - 0002-7863
IS - 45
ER -