Then came the arrest of billionaire Mikhail Khodorkovsky on a charge of tax fraud.
Putin did not say whether Khodorkovsky and Lebedev would be included in the amnesty.
Unlike Mikhail Khodorkovsky, a jailed tycoon, Mr Prokhorov has done well over the past decade.
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What changed this spring was Mr Khodorkovsky's decision to get deeply involved in Russian politics.
Putin only needed to jail one oligarch (Khodorkovsky) in order to intimidate all the rest.
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Khodorkovsky was 18 when his father was arrested on charges of fraud and tax evasion.
The most popular example: former Yukos oil boss Mikhail Khodorkovsky, once Russia's richest man.
Platon Lebedev, one of Mr Khodorkovsky's main partners, was arrested, and probes into Yukos were launched.
This is not to say that Mr Khodorkovsky or the other oligarchs are saints.
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Yukos founder Mikhail Khodorkovsky is currently in jail facing charges of fraud and tax evasion.
Unlike Mr Khodorkovsky, Mechel's owner, a former miner, steered clear of politics and shunned publicity.
Several companies, including France's Danone, reportedly put planned investments on hold after Mr Khodorkovsky's arrest.
Mr Khodorkovsky's verdict will take effect only after an appeal is heard by the Moscow City Court.
Viktor Pinchuk invoked the name of Mikhail Khodorkovsky in his struggle with the new government of Ukraine.
But Mr Khodorkovsky funded several political parties and rumours emerged that he fancied a tilt at the presidency.
Once this clash with Mr Khodorkovsky is resolved, will the same happen again?
No senior Russian officials will talk to him, so he relies mostly on Mr Khodorkovsky's family, friends and business associates.
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His harassment of Mr Khodorkovsky and other oligarchs has already seen a sharp resumption of capital flight out of Russia.
Russia's richest man, Yukos Oil boss Khodorkovsky, was marched off to prison on a conviction for tax evasion and fraud.
Khodorkovsky used similar maneuvers, but he sits in prison for tax evasion, while Abramovich roams the sidelines of Chelsea football games.
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His son Pavel Khodorkovsky, who lives in New York, told Forbes a couple of weeks ago that they needed a miracle.
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The downturn in Mr Khodorkovsky's fortunes became obvious in July 2003, when Platon Lebedev, his partner and now co-defendant, was arrested.
Last month's arrest of oil tycoon Mikhail Khodorkovsky on charges of fraud, theft and tax evasion has Russian businessmen biting their fingernails.
Not so lucky was another jailbird, Russian oil baron Mikhail Khodorkovsky .
Or he may just have thought that Mr Khodorkovsky would back down.
His latest decision to go after Mr Khodorkovsky only reinforces this picture.
Khodorkovsky has always maintained that his arrest was politically motivated, and at least one oligarch seems to have learned from his example.
The son of jailed Russian tycoon Mikhail Khodorkovsky issued an appeal to Davos participants to press the Russian delegation to eradicate corruption.
Then, seeing that the key to building a global business was foreign investment, Mr Khodorkovsky introduced unprecedented (for Russia, at least) transparency.
Three months later, Mr Khodorkovsky himself was nabbed on a Siberian runway.
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