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. Author manuscript; available in PMC: 2017 Jul 6.
Published in final edited form as: Nature. 2017 Jan 18;541(7637):339–346. doi: 10.1038/nature21351

Table 1.

Structural effects of modified nucleotides in RNA

Modified base Structural effects Proposed conformation in doubled-stranded RNA Effects in double-stranded RNA Protein interactions
graphic file with name nihms872769t1.jpg Watson-Crick base pairing blocked44 Base stacking enhanced44 graphic file with name nihms872769t2.jpg Base pairing destabilized44 Helix unwinding44,45 Adjacent helices stabilized44 Binds to hydrophobic pocket (YTH domain proteins)49,50
graphic file with name nihms872769t3.jpg Watson-Crick base pairing blocked58 graphic file with name nihms872769t4.jpg Base pairing blocked58 Helix unwinding58 Possible electrostatic nteractions
graphic file with name nihms872769t5.jpg Base stacking enhanced59 graphic file with name nihms872769t6.jpg Base pairing possibly stabilized49 Increase in major groove hydrophobicity Possible hydrophobic nteractions
graphic file with name nihms872769t7.jpg Conformationa flexibility possibly reduced65 graphic file with name nihms872769t8.jpg Base pairing stabilized63 Increase in major groove polarity Tertiary interactions stabilized65 Possible polar interactions in the major groove
graphic file with name nihms872769t9.jpg Pairing preference altered73 graphic file with name nihms872769t10.jpg Base pairing destabilized78 Helix unwinding75 Non-selective base pairing Unknown

Modifications that have a destabilizing effect on Watson-Crick base pairing and helix stability are indicated by red circles. Modifications that have a stabilizing effect are indicated by green circles.