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 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 whether the theory will ultimately lead to a motive but don't believe 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.
"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 comfort 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.
New Haven Police Chief James Lewis has 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.
Clark appeared in court with two public defenders. Joseph Lopez, one of the defense attorneys, said he still was 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.
Clark was being held Thursday night at the MacDougall-Walker Correctional Institution, a high-security facility in Suffield, about 20 miles north of Hartford.
His next scheduled court date Oct. 6. Yale President Richard Levin said the killing "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."
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