All Boston residents have been ordered to stay in their homes as the search for the surviving suspect in the marathon bombings continues after a night of violence that left the other suspect - reportedly his brother - dead.
Boston Police Commissioner Ed Davis announced that the entire city should stay indoors and Governor Deval Patrick said the remaining suspect, described as a dangerous terrorist, was still on the loose.
Transport to and from the Boston area is virtually shut down, with the exception of aircraft, which continue to take off and land at Logan International Airport.
Amtrak has stopped trains about an hour south of the city in Providence, Rhode Island.
The Massachusetts Bay Transportation Authority, which operates commuter trains into Boston as well as the city's subway - called the T - and the city's buses suspended all operations.
JetBlue, the largest airline in Boston, is allowing anybody scheduled to fly to or from Boston to change their ticket for free.
Megabus has cancelled at least 18 buses between Boston and New York, New Haven, Hartford, Burlington, and Philadelphia.
The developments came after the men killed an MIT police officer overnight, injured a transit officer in a firefight and threw explosive devices at police during their getaway attempt.
As the manhunt intensified, reports said the men were brothers from the Russian region near Chechnya.
Their uncle confirmed that the name of the dead suspect is Tamerlan Tsarnaev, the older brother of Dzhokhar A Tsarnaev, 19. Tamerlan Tsarnaev was killed in a gun battle with police in Massachusetts overnight.
Connecticut State Police say a vehicle believed to be linked to Dzhokhar Tsarnaev has been recovered.
The grey Honda CRV with Massachusetts plates was found in Boston. Authorities had said earlier that the vehicle "could possibly be occupied by" the suspect in the Boston attacks.
An uncle of the suspects, Ruslan Tsarni of Montgomery Village, Maryland, said the men lived together near Boston and have been in the United States for about a decade.
Officials warned that Dzhokhar Tsarnaev, "may be armed and dangerous."
In Boston, authorities suspended all public transport and as they searched for the remaining suspect, a man seen wearing a white baseball cap on surveillance footage from Monday's deadly bombing at the marathon finish line.
"We believe this man to be a terrorist," said Mr Davis. "We believe this to be a man who's come here to kill people."
All modes of public transport were shut down, including buses, subways, trolleys, commuter rail and boats, said Joe Pesaturo, spokesman for the Massachusetts Bay Transportation Authority.
The White House said President Barack Obama was being briefed on developments overnight by Lisa Monaco, his assistant for homeland security and counterterrorism.
The suspects' clashes with police began only a few hours after the FBI released photos and videos of the two young men, who were seen carrying backpacks as they mingled among marathon revellers. The bombings on Monday killed three people and wounded more than 180 others, and authorities revealed the images to enlist the public's help finding the suspects.
The images released by the FBI depict two young men, each wearing a baseball cap, walking one behind the other near the finish line. Richard DesLauriers, FBI agent in charge in Boston, said the suspect in the white hat was seen setting down a bag at the site of the second of two deadly explosions.
Authorities said surveillance tape recorded late last night showed the suspect known for the white hat during a robbery of a convenience store in Cambridge, near the campus of MIT, where a university police officer was killed while responding to a report of a disturbance. The officer died of multiple gunshot wounds.
From there, authorities say, the two men carjacked a man in a Mercedes-Benz, keeping him with them in the car for half an hour before releasing him at a gas station in Cambridge. The man was not injured.
The search for the vehicle led to a chase that ended in Watertown, where authorities said the suspects threw explosive devices from the car and exchanged gunfire with police. A transit police officer was seriously injured during the chase, authorities said.
In Watertown, witnesses reported hearing multiple gunshots and explosions early today. Dozens of police officers and FBI agents were in the neighbourhood and a helicopter circled overhead.
Watertown resident Christine Yajko said she was awakened at about 1:30 am by a loud noise, began to walk to her kitchen and heard gunfire.
"I heard the explosion, so I stepped back from that area, then I went back out and heard a second one," she said. "It was very loud. It shook the house a little."
She said a police officer later knocked on her door and told her there was an undetonated improvised explosive device in the street and warned her to stay away from the windows.
"It was on the street, right near our kitchen window," she said.
Yajko said she never saw the suspect who was on the loose and didn't realise the violence was related to the marathon bombings until she turned on the TV and began watching what was happening outside her side door.
State police spokesman David Procopio said, "The incident in Watertown did involve what we believe to be explosive devices possibly, potentially, being used against the police officers."
Boston cab driver Imran Saif said he was standing on a street corner at a police barricade across from a diner when he heard an explosion.
"I heard a loud boom and then a rapid succession of pop, pop, pop," he said. "It sounded like automatic weapons. And then I heard the second explosion."
He said he could smell something burning and advanced to check it out but area residents at their windows yelled at him, "Hey, it's gunfire! Don't go that way!"
Doctors at a Boston hospital where a suspect in the marathon bombings was taken and later died are saying they treated a man with a possible blast injury and multiple gunshot wounds.
MIT said right after the shooting that police were sweeping the campus in Cambridge and urged people to remain indoors. They urged people urged to stay away from the Stata Centre, a mixed-use building with faculty offices, classrooms and a common area.
The suspects' images were released hours after President Barack Obama and first lady Michelle Obama attended an interfaith service in Boston to remember the dead and the wounded.