By Dana Hughes and Alex Marquardt

The designation of the Syrian rebel group al-Nusrah Front as a terrorist organization at the same time the United States is formally recognizing Syria's Opposition Coalition is not a coincidence. The Obama administration wants to send a clear a message that while it supports Syria's Opposition Coalition to lead Syria's democratic transition if or when the Assad regime falls, there is no place for extremism in the country's future.

In an exclusive interview with ABC's Barbara Walters, President Obama said that while the United States stands ready to fully acknowledge the group of Syria's rebels as the legitimate opposition to the Assad regime, groups with ties to al Qaeda like the al-Nurah front will not be tolerated.

"Not everybody who's participating on the ground in fighting Assad are people who we are comfortable with," Obama told Walters. "There are some who, I think, have adopted an extremist agenda, an anti-US agenda. And we are going to make clear to distinguish between those elements." On Tuesday State Department Spokesperson Victoria Nuland detailed the organization's crimes in a statement announcing the terror designation and sanctions on the group.

"Since November 2011, al-Nusrah Front has claimed nearly 600 attacks - ranging from more than 40 suicide attacks to small arms and improvised explosive device operations - in major city centers," said Nuland. "During these attacks numerous innocent Syrians have been killed. Through these attacks, al-Nusrah has sought to portray itself as part of the legitimate Syrian opposition while it is, in fact, an attempt by AQI to hijack the struggles of the Syrian people for its own malign purposes."

In a background briefing with reporters on the designation, senior Obama administration officials stressed that the designation of al Nusrah is not a reflection of the administration's policy on Syria's opposition, which the U.S. is expected to recognize following this week's Friends of Syria meeting in Morocco. "Al-Nusrah Front is one of many groups that are fighting the Syrian regime now. Its influence has grown over recent months, but it still represents a minority element within the broader armed opposition to the Assad regime," said the same official. "So I don't want to leave any kind of impressions that we are in any way acting against the broader Free Syrian Army, which is a much bigger organization."

Experts and officials say the strength and numbers of extremist groups in Syria like Jabhat-Nusra have grown as the conflict has dragged on. A year ago, Jabhat al-Nusra carried out the first suicide bombing and dozens have followed. Videos have surfaced online of the summary executions they have carried out, notably several weeks ago when pleading Syrian soldiers were piled onto the floor and shot. Administration officials did acknowledge they are concerned about the increasing influence radical Islamists are having on Syria's opposition movement.

"When we think about that political transition, extremist groups that are denouncing the government and attacking the government… have no role in that transition and in a future Syria," said one official who pointed out that the original protest movement in Syria, which began over a year ago, started out peacefully, demanding a tolerant and free Syria. "Nusrah Front rejects… a tolerant society, and insists that instead of elections there must be an Islamic state imposed upon Syria."

In practical terms the designation means that Syrian opposition leaders will not be able to work with al-Nusrah and still receive U.S. support. The administration's announcement also served to "out" the group to Syrians who may be sympathetic, said the officials. "It means that as al-Nusrah Front tries to wrap itself in the legitimacy of the opposition that does reflect the Syrian's people desires, we have called them out, and for those who are seeking to support the legitimate opposition of the Syrian people, we have drawn a bright line," said an official.

According to the administration, the group's roots are in Iraq, and the sanctions against the two top leaders of the Nusrah front, Maysar Ali Musa Abdallah al-Juburi and Anas Hasan Khattab, have close ties to Al Qaeda in Iraq. According to the officials, al-Juburi is the religious and military commander for the Nusrah Front in eastern Syria and came from Mosul, Iraq to Syria in late 2011. Khattab was involved with the formation of the Nusrah Front for AQI and has communicated with AQI leadership to coordinate the movement of funds and weapons for the Nusrah Front.

Today's announcement also included more sanctions on the Assad regime; specifically leaders of the Iranian-backed Shabiha militia, which has been accused of brutally targeting civilians and illegally procuring weapons. The officials said that it will be even-handed in condemning human rights violations and terrorism in Syria. "We will continue to target the thugs that have worked with the Assad militias, just as we will the terrorists who try to cloak themselves in the flag of the legitimate opposition," said another official.