Boston Police say a college student wanted in connection with the Boston Marathon bombings is in custody, after a manhunt that left the city virtually paralysed and his older brother dead.

Police announced on Twitter that Dzhokhar Tsarnaev, 19, was in custody.

His brother Tamerlan, 26, was killed in a furious attempt to escape police on Thursday night.

The brothers are suspects in Monday's marathon bombings, which killed three and injured more than 180.

The men are also suspected of killing a Massachusetts Institute of Technology police officer in his vehicle on Thursday.

US President Barack Obama pledged that the US will find out whether the two brothers received any help.

President Obama appeared in the White House briefing room after police arrested the lone surviving suspect in the Boston suburb of Watertown, ending the manhunt.

"Obviously tonight there are still many unanswered questions. Among them: why did young men who grew up and studied here as part of our communities and country resort to such violence? How did they plan and carry out these attacks, and did they receive any help?" Mr Obama said.

The president said Americans are in debt to the people of Boston and Massachusetts for their resilience in responding to the twin blasts.

Residents and police officers cheered and clapped when Mr Tsarnaev was caught after an exchange of gunfire with police.

A Massachusetts State Police spokesman said Mr Tsarnaev was bleeding and in serious condition in a hospital.

He had been hiding in the stern of a boat parked in the backyard of a house in Watertown, police said. A resident called police after seeing blood on the boat.

The Boston Police Department said in a message on Twitter: "CAPTURED!!! The hunt is over. The search is done. The terror is over. And justice has won. Suspect in custody."

Boston Mayor Tom Menino said "we got him" on Twitter.

Earlier, authorities in Boston suspended all mass transit and warned close to one million people in the city and some of its suburbs to stay indoors as the hunt went on.

Gunfire was heard as dozen of police cars and armoured vehicles converged on a street in the Boston suburb of Watertown as authorities searched for the surviving suspect in the Boston Marathon bombings.

Minutes after police rushed to a street in Watertown, gunfire broke out, with dozens of shots being heard in rapid succession, a witness said.

Black Hawk helicopters and heavily armed police descended on Watertown.

Earlier, the normally traffic-clogged streets of Boston were empty as the city went into virtual lockdown after a bloody night of shooting and explosions.

Public transport was suspended, air space restricted and famous universities, including Harvard and MIT, closed after police ordered residents to remain at home.

Details have emerged about the brothers, including their origins in the predominantly Muslim regions of Russia's Caucasus, which has experienced two decades of violence since the fall of the Soviet Union.

The fugitive described himself on a social network as a minority from a region that includes Chechnya, Dagestan and Ingushetia.

Monday's bombing on the finish line of the world-famous Boston Marathon, which killed three people and injured 176, was described by President Obama as "an act of terrorism".

A man who told reporters he was an uncle of the brothers said they came to the US in the early 2000s and settled in the Cambridge, Massachusetts, area.

Ruslan Tsarni, who lives in suburban Washington and has not spoken to the brothers since 2009, said the bombings "put a shame on our family. It put a shame on the entire Chechen ethnicity".

Others remembered the brothers as friendly and respectful youths who never stood out or caused alarm.

The FBI said the twin blasts were caused by bombs in pressure cookers and carried in backpacks that were left near the marathon finish line as thousands of spectators gathered.

Authorities cordoned off a section of Watertown and told residents not to leave their homes or answer the door as officers in combat gear scoured a 20-block area for the missing man, who was described as armed and dangerous.

"We are progressing through this neighbourhood, going door-to-door, street-to-street," Massachusetts State Police Colonel Timothy Alben said.

SWAT teams moved through in formation, leaving an officer behind to ensure that searched homes remain secure, a law enforcement official said.

Police expanded their search to Dartmouth, Massachusetts where Dzhokhar Tsarnaev was enrolled as a student at the University of Massachusetts.

Two Black Hawk helicopters circled the area. Amtrak suspended train service between Boston and New York indefinitely.

The Boston Red Sox postponed their night baseball game at Fenway Park, as did the Bruins hockey team.

The events elicited a response from Russia condemning terrorism and from the Russian-installed leader of Chechnya, who criticised police in Boston for killing an ethnic Chechen and blamed the violence on his upbringing in the US.

"They grew up and studied in the United States and their attitudes and beliefs were formed there," Ramzan Kadyrov said in comments posted online. "Any attempt to make a connection between Chechnya and the Tsarnaevs is in vain."

The Islamic Society of Boston Cultural Center, the biggest mosque in the area, said in a statement that "after the terrible and sad events of last night, the criminal of the bombings on the loose" it was shutting its doors until further notice.

The brothers had been in the US for several years and were believed to be legal immigrants, according to US government sources.

US government officials said the Tsarnaev brothers have not yet turned up in any databases as possible militants.

Investigators were looking for links to radical foreign groups or possible accomplices in the US.

A Russian language social networking site bearing Dzhokhar Tsarnaev's name paid tribute to Islamic websites and to those calling for Chechen independence. The author identified himself as a 2011 graduate of Cambridge Rindge and Latin School, a public school in Cambridge.

He said he went to primary school in Makhachkala, capital of Dagestan, a province in Russia that borders on Chechnya, and listed his languages as English, Russian and Chechen.

His "world view" was listed as "Islam" and his "personal priority" as "career and money".

He posted links to videos of fighters in Syria's civil war and to Islamic web pages with titles such as "Salamworld, my religion is Islam" and "there is no God but Allah, let that ring out in our hearts".

He also had links to pages calling for independence for Chechnya, a region of Russia that lost its bid for independence after two wars in the 1990s.