Police charged Clark, 24, with murder on Thursday, arresting him at a motel a day after taking hair, fingernail and saliva samples to compare with evidence from the grisly crime scene.
Bond was set at $3 million for Clark, who kept his head down and said "Yes, your honor," when asked whether he understood his rights. He did not enter a plea.
The official, who spoke to The Associated Press on condition of anonymity because the investigation is ongoing and many details remain sealed, said Yale workers told police that Clark was a "control freak" who clashed with scientists and their proteges in the lab where they both worked at the Ivy League school.
Investigators haven't decided if the theory will ultimately lead to a motive, but don't believe that they'll need to establish one when Clark goes to trial because they have an abundance of strong forensic evidence, the official said.
Authorities are offering few details about the crime. They would not discuss a motive, largely because Clark will not talk to police, and would not disclose the DNA test results or how they connected Clark to the slaying.
Security guards continued their street patrols Friday morning and news crews set up for another day of staking out the college's medical complex. A makeshift memorial of candles and flowers was arranged at the entrance to a park across the street from the lab building, in an area of squat, utilitarian buildings about a mile from the majestic main campus.
Yale students are relieved that a suspect is in custody, yet shaken that the crime happened there.
"I think it's important to the community to know that something's been done and that somebody's actually being brought to justice," Juliana Biondo said Thursday.
But that doesn't bring full comfort to Doug Lindsay.
"Despite the fact that they found somebody ... it was still, to me, kind of scary," he said.
Le's work at the university involved experiments on mice that were part of research into enzymes that could have implications for treatment of cancer, diabetes and muscular dystrophy, while Clark's technician job involved cleaning floors and mouse cages.
At a news conference Thursday, New Haven Police Chief James Lewis called Le's death a case of workplace violence. He would not elaborate except to say reports that the two had a romantic relationship were untrue.
"It is important to note that this is not about urban crime, university crime, domestic crime but an issue of workplace violence, which is becoming a growing concern around the country," Lewis said, adding that he would not rule out additional charges.
The Rev. Dennis Smith, a Le family spokesman, said he was not authorized to comment on the arrest. Smith said he did not know whether Le had ever complained about Clark.
Clark appeared in court with two public defenders who were new to the case. A private-practice attorney who had represented him during the investigation did not attend the hearing and said Thursday he no longer represents Clark. The attorney declined to give a reason.
Public defender Joseph Lopez said he was still reviewing the case and declined to comment.
Two friends of Clark's since childhood, appearing on CNN's Larry King Live on Thursday night, said they were stunned by the murder allegations and could not reconcile them with the young man they've known for years.
"That's not the Raymond Clark I've talked to my whole entire life," Bobby Heslin said.
"I just can't picture him doing something like this," Maurice Perry said.
The New York Times reported that Clark at times grew angry if lab workers did not wear shoe covers. "He would make a big deal of it, instead of just requesting that they wear them," said a researcher who asked not to be identified.
ABC News reported that Clark sent a text message to Le on the day she vanished requesting a meeting to discuss the cleanliness of mouse cages in the research lab.
Reached at their homes after work Thursday, several of Le's co-workers at the lab declined to comment on her or Clark.
The Connecticut medical examiner said Wednesday that Le died of "traumatic asphyxiation," which could indicate a choke hold or some other form of suffocation caused by a hand or an object such as a pipe.
Investigators focused on Clark early in the investigation and searched his apartment Tuesday, when they labeled him a person of interest. He remained under constant surveillance after he was released early Wednesday and found a room at the Super 8 motel in Cromwell, Conn.
Clark was arrested about 8 a.m. Thursday. Details of the warrant remained sealed.
The New Haven Register printed a rare extra edition announcing Clark's arrest, wrapping it around Thursday's daily newspaper and selling it on the streets, editor Jack Kramer said.
Brian Garnett, a spokesman for the Connecticut Department of Correction, confirmed that Clark was being held Thursday night at the MacDougall-Walker Correctional Institution, a high-security facility in Suffield, about 20 miles north of Hartford.
Garnett said it was unclear whether Clark would remain there until his next scheduled court date Oct. 6.
Yale President Richard Levin released a statement shortly after the arrest, saying Clark's employment history raised no suspicions.
"This incident could have happened in any city, in any university, or in any workplace. It says more about the dark side of the human soul than it does about the extent of security measures," Levin said in a message sent to the Yale community.
Associated Press writers Colleen Long in New Haven and Matt Apuzzo in Washington, D.C., contributed to this report.