Stain the chest in the study (6)
I believe the answer is:
darken
'stain' is the definition.
(I know that darken is a more specific form of the action stain)
'chest in the study' is the wordplay.
'chest' becomes 'ark' (historical term for a chest).
'in the' is an insertion indicator.
'study' becomes 'den' (term for a study or office).
'ark' going inside 'den' is 'DARKEN'.
'the' is the link.
(Other definitions for darken that I've seen before include "Grow less light" , "Dim" , "Make less light" , "Cloud over" , "Grow blacker" .)