Dzhokhar Tsarnaev, the surviving suspect in the Boston Marathon bombings, was charged at his hospital bed on Monday with using and conspiring to use a weapon of mass destruction, a count that carries a possible death penalty.

The charges were announced a week after two devices exploded near the finish line of the Boston Marathon, killing three people and injuring more than 180.

A magistrate judge read the charges to Dzhokhar Tsarnaev, 19, the younger of two brothers suspected in the bombing, in a special session as he lay seriously injured in Beth Israel Deaconess hospital in Boston. According to the criminal complaint, he has gunshot wounds to the head, neck, legs and hand.

A transcript of the extraordinary bedside court hearing shows that Tsarnaev was read his Miranda rights – the process in US law where a suspect is informed of his right not to incriminate himself. It appears that despite his injuries, Tsarnaev managed to speak one word: answering "no" to a question about whether he could afford a lawyer.

Tsarnaev had escaped police on Thursday night after a frenzied shootout in the Boston suburb of Watertown in which his elder brother, Tamerlan, 26, was killed. He was eventually captured on Friday evening, bloody and wounded, hiding in a boat in a suburban backyard after a day in which Boston and surrounding areas were virtually locked down.

"Although our investigation is ongoing, today's charges bring a successful end to a tragic week for the city of Boston, and for our country," said the US attorney general, Eric Holder. The US attorney for Massachusetts, Carmen Oritz, said the impact of the crimes had been "far-reaching, affecting a worldwide community that is looking for peace and justice".

Rick DesLauriers, special agent in charge of the FBI's Boston division, said the events of the week had moved at "breakneck speed" and praised the "collective effort of our law enforcement and intelligence partners".

The charges include one count of using and conspiring to use a weapon of mass destruction – an improvised explosive device or IED – against persons and property within the United States resulting in death, and one count of malicious destruction of property by means of an explosive device, resulting in death. US prosecutors did not announce whether they would seek the death penalty.

The federal complaint gives more details of the evidence against Tsarnaev. Video footage, it says, shows him stopping in front of the Forum restaurant on Boylston Street and dropping his backpack to the ground. He then is seen to use his cellphone, finishing the call just seconds before the first explosion.

"Virtually every head turns to the east (towards the finish line) and stares in that direction in apparent bewilderment and alarm," the complaint reads. "Bomber Two, virtually alone among the individuals in front of the restaurant, appears calm."

According to the complaint, Tsarnaev then moves rapidly to the west. Ten seconds later, the second blast occurs at the spot where he left his bag.

Daniel Genck, the FBI special agent in whose name the complaint is filed, said he had examined video and photographs from the site of the second explosion from a number of different angles and viewpoints, including from directly across the street. "I can discern nothing in that location in the period before the explosion might have caused that explosion, other than Bomber Two's knapsack," he writes.

The complaint offers chilling new details of the carjacking that began Thursday night's dramatic chase and shootout. The victim, who is not named in the complaint, told law enforcement officers that when one of the suspects got into his car, he pointed a gun and said: "Did you hear about the Boston explosion? I did that." The suspect then removed the magazine from the gun to show the victim there was a bullet in it, adding: "I am serious".

A transcript of the special court hearing at Beth Israel hospital, released later on Monday, indicated that there were at least 10 people in the room: Tsarnaev, the judge, a clerk, two representatives of the US attorney's office, three from the public defender's office, a court reporter and a doctor.

The proceedings opened with the judge, Marianne B Bowler, asking the doctor to rouse Tsarnaev. "How are you feeling? Are you able to answer some questions," asked the doctor, trauma surgeon Dr Stephen Odom. "The defendant nods affirmatively," the transcript reads.

After outlining the charges to Tsarnaev, Bowler read him his Miranda rights. She then asked him: "Do you understand everything I have said about your right to remain silent?" In reply, Tsarnaev nodded. "Again, I note that the defendant has nodded affirmatively," the judge said.

Tsarnaev did not enter any plea or make any other statement other than to indicate that he understood the charges and his rights. "I find that the defendant is alert, mentally competent and lucid," the judge said. When Tsarnaev said that he could not afford a lawyer, the judge formally appointed one. The next hearing was scheduled for 30 May.

Shortly before the charges against Tsarnaev were announced, the White House insisted he would be tried in the US civilian court system, despite pressure from Republicans for him to be treated as an enemy combatant in the "war on terror". Jay Carney, the White House spokesman, said: "We have a long history here of successfully prosecuting terrorists and bringing them to justice and the president fully believes that the process will work in this case."

Carney said the decision was taken by Holder and supported by Barack Obama's national security advisers. "We had no choice under the law," said Carney. "He is a US citizen."

In addition to the federal charges, Dzhokhar Tsarnaev is likely to face state charges in connection with the fatal shooting of an MIT police officer, Sean Collier, in Cambridge, said Stephanie Guyotte, a spokeswoman for the Middlesex district attorney's office.

The Tsarnaevs' father, Anzor Tsarnaev, has said he will fly from Russia to the US, in order to seek "justice and the truth". His wife, Zubeida Tsarnaeva, told journalists on Monday that her husband planned to fly to the US on Wednesday and that the family would try to bring the body of Tamerlan Tsarnaev back to Russia.

Wife did not suspect Tamerlan Tsarnaev

Authorities were also seeking to interview Katherine Russell Tsarnaev, Tamerlan's American wife, according to the family lawyer, Amato DeLuca. DeLuca said that his client had not yet spoken to federal agents: "We're deciding what we want to do and how we want to approach this," he told the Associated Press.

DeLuca said that on Thursday, Tamerlan Tsarnaev "was home" when his wife left for work. DeLuca also said that Katherine Russell Tsarnaev had been working 70 to 80 hours a week as a home healthcare aide and did not suspect her husband of anything. While she was at work, her husband was looking after their young daughter.

"When this allegedly was going on, she was working, and had been working all week to support her family," DeLuca said, adding that nothing had seemed amiss. She had only learned her husband was a suspect in the bombing when she saw it on the television.

DeLuca added that Katherine did not see Dzhokhar, who lived with them, at her apartment "at all", because he was in college.

In Massachusetts on Monday, governor Deval Patrick asked residents to observe a moment of silence at 2.50pm, the time the first of the two bombs exploded near the marathon finish line.

Hundreds gathered at a private funeral on Monday for Krystle Campbell, a 29-year-old restaurant worker, one of three killed in the blasts; and a memorial service was held in the evening at Boston University for 23-year-old Lu Lingzi, a graduate student from China. Lu, an only child, was described as an exceptional student of statistics and sweet-hearted woman who was passionate about piano, her studies and life. Boston University has launched a scholarship fund in Lu's name.