Contribution of 3'T and 3'TT overhangs to the thermodynamic stability of model siRNA duplexes.
3′-dangling ends
DNA
RISC selection
RNA
Thermodynamics
siRNA
Journal
Biophysical chemistry
ISSN: 1873-4200
Titre abrégé: Biophys Chem
Pays: Netherlands
ID NLM: 0403171
Informations de publication
Date de publication:
03 2019
03 2019
Historique:
received:
14
08
2018
revised:
21
12
2018
accepted:
30
12
2018
pubmed:
21
1
2019
medline:
21
3
2019
entrez:
21
1
2019
Statut:
ppublish
Résumé
Herein, we report comprehensive thermodynamic studies on 36 RNA/DNA duplexes designed as siRNA mimics to determine the energetic contribution of 3'T and 3'TT dangling ends. The thermodynamic effect induced by the presence of 3'T overhangs on the stability of RNA duplexes ranges from -0.28 to -0.92 kcal/mol and strongly depends on the type and orientation of the adjacent base pair. Further extension of the 3'-dangling end length, by a second T residue, results in additional stabilization of 0.14 to 0.21 kcal/mol. The results revealed that the thermodynamic contribution of 3'-dangling T and TT on RNA duplexes differs from the influence of 3'-dangling U and UU on RNA duplexes and 3'-dangling T and TT on DNA duplexes. This data suggests that using the contribution of 3'-dangling T values for RNA duplexes, instead of 3'-dangling T values for DNA duplexes or 3'-dangling U values for RNA duplexes, would improve the prediction of the stability of siRNA duplexes.
Identifiants
pubmed: 30660935
pii: S0301-4622(18)30259-X
doi: 10.1016/j.bpc.2018.12.006
pmc: PMC6386172
mid: NIHMS1519048
pii:
doi:
Substances chimiques
3' Untranslated Regions
0
RNA, Double-Stranded
0
RNA, Small Interfering
0
Uracil
56HH86ZVCT
Thymidine
VC2W18DGKR
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
35-39Subventions
Organisme : NIGMS NIH HHS
ID : R15 GM085699
Pays : United States
Informations de copyright
Copyright © 2019 Elsevier B.V. All rights reserved.
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