Penicuik Estate, situated to the south-west of Edinburgh at the foot of the Pentlands, has been owned by the Clerk family since the middle of the 17th century. In 1654 the merchant John Clerk (1611-1674), who had made his fortune in Paris, purchased the Estate with the existing house Newbiggin from the heirs of Margaret Scott, the Countess of Eglinton. In 1647 John Clerk married Mary Gray, fourth daughter of Sir William Gray of Pittendrum by whom he had five sons and five daughters. He married for a second time in 1670 to Elizabeth Johnston, and upon his death he was succeeded by his eldest son, John Clerk, who became the 1st Baronet in 1679.
Sir John served as a shire commissioner for Edinburghshire in the Scottish Parliament from 1690-1702, and in addition to Penicuik Estate, in 1700 he acquired the lands and Barony of Lasswade, to the south of Edinburgh. He was married twice, first to Elizabeth Henderson by whom he had three sons and three daughters, and second to Christian, daughter of the Reverend James Kilpatrick by whom he had a further four sons and four daughters. He died in 1722 and was succeeded by his son, also John, the second Baronet.