The boys, aged 13, 14 and 15, were arrested following incidents earlier this week when two lorries and a coach were damaged by objects allegedly thrown from the bridge between junctions 7 and 8 for Reigate, Surrey, on the M25.
The suspects, who have not been named, will appear before South East Surrey Magistrates' Court in Redhill on August 21.
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A mobile DNA screening unit has been set up in a village where detectives are working to find a grandmother's killer.
Tuesday night's weather for the east of the region
Tuesday night's weather for the west of the region