An “abandoned composition” by Leonardo da Vinci has been discovered underneath one of his most discussed paintings, which will take centre stage at a ground-breaking exhibition dedicated to the Renaissance master.

The National Gallery, which is hosting an “immersive exploration” of the artist’s work, found the unfinished earlier version after conducting scientific research into the Virgin of the Rocks. The London gallery’s researchers found the Leonardo’s initial designs for the angel and the infant Christ, with “significant differences to how they look in the finished painting”.

“Why Leonardo abandoned this first composition still remains a mystery,” a spokesperson said. “Handprints resulting from patting down the priming on the panel to create an even layer of more or less uniform thickness can also be seen, probably the work of an assistant – but perhaps even by Leonardo himself.”

Detail from the macro x-ray fluorescence map of The Virgin Of The Rocks, revealing the angel and baby of the first composition. Photograph: National Gallery/PA

A team of six experts started using the latest imaging techniques on the composition in January, and because the drawings were made with material containing zinc, they could be seen in macro x-ray fluorescence (MA-XRF) maps, and with infrared and hyperspectral imaging – the same technology that was used by US Navy Seals to examine Osama bin Laden’s compound in Pakistan in 2011.

“Both figures are positioned higher up in the drawing, while the angel, facing out, is looking down on the infant Christ with what appears to be a much tighter embrace,” the National Gallery spokesperson added.

The discovery comes as the gallery announces the an exhibition of Leonardo’s work as a painter, focusing exclusively on the Virgin of the Rocks, which originally stood as an altarpiece in a chapel devoted to the immaculate conception of Jesus’s mother, Mary. The museum’s ground-floor galleries will be transformed into a space that investigates the painting and there will be “multisensory experiences” in four rooms, including a chapel-like environment to recreate what its original setting may have looked like.

Dr Gabriele Finaldi, director of the National Gallery, said the exhibition would give “visitors the opportunity to explore Leonardo da Vinci’s creative process in making this masterpiece”. The gallery’s head of conservation, Larry Keith, said there could be more discoveries as the team continued to look for more changes.

The exhibition has been co-created with 59 Productions, which worked on the V&A’s David Bowie exhibition in 2013. “It’s somewhere between an exhibition and an experience,” said Richard Slaney, the company’s managing director.

“Da Vinci’s view of the world meant he was fascinated at looking deeply into anything that interested him and by giving people the chance to refocus on one painting we’re allowing people to do the same thing. It’s a bit like mindfulness in a way, as it slows things down and people can focus on one idea,” he added.

Slaney said the exhibition would reveal a different aspect of the painting in each room before the main work, the Virgin of the Rocks itself, was revealed at the end. “This is scholarly research that has been turned into an experience that feels theatrical,” he said. “You’re learning by seeing rather than reading a paper.”

In 2010, the Guardian art critic Jonathan Jones looked into the provenance of the painting. “Since it was bought by the National Gallery in 1880, the Virgin of the Rocks has been exhibited as a ‘Leonardo’,” he wrote. “But the small print was more complicated.” Jones said that for a long time the gallery believed it was mostly the work of assistants, with possibly only the basic design recognisable as Leonardo’s.

In 2005 researchers discovered that the Virgin’s pose had been changed, and in 2008 its restoration started. This included the oil and varnish that was applied in 1949 being cleaned and the work being installed in a new frame that was constructed from fragments of a 16th-century original.

In May this year, a sketch of a bearded man – found in among the Leonardo drawings contained in the Royal Collection – was identified as a work by the painter.

“It is a very quick casual sketch of Leonardo; it is the closest that we get to a snapshot of Leonardo during his own lifetime,” said Martin Clayton, head of prints and drawings at the Royal Collection Trust. “It may be trivial as a work of art but it’s hugely important, even moving, as a record of the man himself.”