An American-educated neuroscientist with alleged ties to the al-Qaeda leadership was captured with a list of potential targets for a “mass casualty attack” that included New York landmarks such as the Statue of Liberty and the Empire State Building, according to prosecutors.

Details of the handwritten list were disclosed as formal charges were lodged against Aafia Siddiqui, a Pakistani mother of three with a biology degree from the Massachusetts Institute of Technology (MIT) and a doctorate in behavioural neuro-science from Brandeis University.

Ms Siddiqui, 36, is due to appear in court in New York today to face charges that she snatched a US soldier’s rifle and tried to kill her interrogators after her arrest in Afghanistan on July 17. She was wounded in the exchange of fire. Her lawyers say that she is innocent.

Ms Siddiqui, the daughter of a British-trained Pakistani doctor, became a cause célèbre when she disappeared with her three children in Pakistan in 2003. Her family claim that she was abducted and held in a secret US detention facility.

The US Government denies that she was in custody until her arrest in July and says she is married to a nephew of Khalid Sheikh Mohammed, the mastermind of the September 11 terror attacks. In 2004 Washington named her as one of seven suspected al-Qaeda associates feared to be planning an attack against the US.

US officials see Ms Siddiqui as a potential treasure trove of information about terrorist supporters or sleepers in the US. “She is the most significant capture in five years,” John Kiriakou, a retired CIA officer who led the team that apprehended the first key al-Qaeda figure, Abu Zubaydah, told ABC News.

“Her education troubled us. We know that she’s extremely bright. She’s radicalised. We knew that she had been planning, or at least involved in the planning, of a variety of operations, whether they involved weapons of mass destruction or research into chemical or biological weapons, whether it was a possible attempt on the life of the President,” Mr Kiriakou said.

“We knew that she was involved with a great deal.”

The US Government alleges that Ms Siddiqui has links to at least two of the 14 high-level al-Qaeda suspects who were moved from secret detention facilities to the Guantanamo Bay prison camp in September 2006.

Ms Siddiqui allegedly opened a post office box in Maryland for Majid Khan, a former Baltimore resident now being held in Guantanamo Bay who allegedly planned to attack petrol stations in the US.

Ms Siddiqui also married Ali Abd al-Aziz Ali, known as Ammar al-Baluchi, an alleged al-Qaeda fixer now in Guantanamo, who is a nephew of Khalid Sheikh Mohammed and a cousin of Ramzi Yousef, who was convicted of the 1993 bombing of the World Trade Centre in New York.

An indictment that was issued on Tuesday says that Ms Siddiqui was carrying handwritten notes referring to a “mass casualty attack” and listing a number of US locations, including Wall Street and the Brooklyn Bridge, as well as an animal-disease laboratory that works with viruses on Plum Island, off the east end of Long Island, New York.

The indictment says that other notes referred to the construction of radiological “dirty bombs” and chemical and biological weapons, and discussed the mortality rates of such weapons. Also included were notes about bringing down reconnaissance drones and using underwater bombs and gliders for attacks. Prosecutors say that Ms Siddiqui had a computer flash drive containing correspondence that referred to specific cells and attacks by cells.

Gideon Oliver, Ms Siddiqui's lawyer, said she that would enter a plea of not guilty in court today. He said that her legal team has been unable to see her in person since her first court appearance almost a month ago because she refuses to undergo the strip search required for every visit.

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