BURLINGTON, Vt. (AP) – Brian Rooney said he didn’t do it.

For more than two weeks, police trying to link him to the disappearance of a 21-year-old University of Vermont senior searched for evidence, pleaded for the public’s help and charged him with unrelated crimes.

On Wednesday, they got their break: DNA analysis linked the 36-year-old construction worker to the young collegian he met when her cell phone wouldn’t work.

DNA in semen found on the body of Michelle Gardner-Quinn matched DNA from a blood stain on Rooney’s pants, according to a police affidavit that said he had cuts on his hands when he was interviewed by police.

Rooney, who is charged with aggravated murder, killed Gardner-Quinn during the course of a sexual assault after their chance Oct. 7 encounter on Main Street, which began when Rooney saw her having trouble with her cell phone and approached to offer her the use of his, according to the affidavit by police Detective Aljaray Nails, Jr.

Within two hours, she was dead.

An autopsy found she had been strangled and beaten, according to Police Chief Thomas Tremblay, although police still aren’t saying where the killing occurred.

Tremblay said the results of toxicology tests on Gardner-Quinn’s body were still pending.

“We feel confident that the preliminary results are strangulation and blunt-force trauma but we’re pending toxicology analysis,” Tremblay said.

The charging of Rooney drew an apparent close to a slayingmystery that rocked this college town on the shores of Lake Champlain, prompting women to think twice about walking anywhere alone.

The fact that Gardner-Quinn, 21, of Arlington, Va., vanished while walking along Main Street – between the city’s bustling downtown and the hilly campus above it – struck fear in many, whether they were young students or not.

“It was so horrible,” said Emily Libby, 19, a freshman from Topsfield, Mass. “Everyone’s parents were calling everyone, saying “Be careful,’ “Don’t walk alone.”‘

Rooney, who was seen walking with Gardner-Quinn on surveillance video shot from Perrywinkle’s Fine Jewelry’s exterior camera, was a prime suspect from the start, after her parents reported her missing when she failed to show up for a parents’ weekend dinner date.

Police interviewed him, searched his car and released photographs of it to the public in appeals for help but still couldn’t charge him.

When they did, it was for unrelated crimes – sex charges from the 1990s that were based on testimony elicited during the investigation into Gardner-Quinn’s disappearance. Last week, they tacked on more charges, accusing him of sexually assaulting a former girlfriend and soliciting someone to kill her.

Finally, on Wednesday, came the charges against him, which could put him in prison for life.

“We’re pleased with the results, but nobody can ever feel good about the tragedy that’s occurred in our community,” Tremblay said.

Rooney will be arraigned on the charge Thursday. His lawyer, David Sleigh, declined comment Wednesday.

Gardner-Quinn’s body was found Oct. 13 near a gorge about 13 miles east of Burlington, face down, her head wedged between a pair of rock outcroppings, according to the affidavit.

Tremblay said it wasn’t known where she was killed, but that it happened between when the surveillance video showed the two together at 2:34 a.m. and when he returned to his parents’ house in Richmond about 4:30 a.m.

Tremblay said it was too early to tell whether Gardner-Quinn willingly left Main Street with Rooney. Her hair, skin and fingerprints were found in his Jeep, according to the affidavit.

When asked by police if he was sure he didn’t offer her a ride, Rooney said: “I don’t believe so.”

Asked if he thought Gardner-Quinn was cute, he said: “Yeah … brunette,” according to Nails’ affidavit.

Gardner-Quinn’s family, which has yet to talk publicly about her disappearance save for an Internet video appealing for her safe return, were told about the arrest earlier Wednesday. They could not be reached for comment.

“They’re obviously still in grief, but very pleased with the efforts of all the men and women from local, state and federal agencies that worked this case,” Tremblay said.

At Perrywinkle’s, jeweler Winklette Taylor called the case her store helped to break “a sad situation.”

“We’re just grateful that our cameras could help,” she said.