Murad Musayev, a defense lawyer, said investigators had found a cigarette butt and a palm print, as well as hairs left on the gun. Experts have established that the DNA does not belong to Dzhabrail and Ibragim Makhmudov or Sergei Khadzhikurbanov, who have all been charged with involvement in the murder.
The man suspected of pulling the trigger, Rustam Makhmudov - the eldest of the three Makhmudov brothers - remains at large. A separate case has been launched against him.
Politkovskaya, who gained international recognition for her criticism of the Kremlin and reports of military atrocities against civilians in the troubled Caucasus republic of Chechnya, was gunned down in an elevator in her Moscow apartment building in October 2006, in what police described as a contract killing.
A former Federal Security Service (FSB) officer, Colonel Pavel Ryaguzov, has also been charged with telling the killers where Politkovskaya lived.
Meanwhile, a fourth juror in the trial of Politkovskaya was dismissed on Friday due to illness.
Last week, another juror asked to step down "due to family reasons." The trial will continue with a jury of 12 people and four reserve jurors.