You can use DNA-free™ Kit from (Invitrogen™) since this kit is used to digest DNA in extracted RNA and the DNA-free™ reagents effectively remove DNase and divalent cations from the reaction mixture.

If you only need the short DNA.. Make an Agarose gel and cut out the short sequences and reextract from the gel again...

DNase can be heat inactivated at 70 oC, 10 mins.

DNase is an enzyme, you can inactive it in 65C for 15 min (or 75 for 10 min). Also take a look at this link :

http://www.lifetechnologies.com/ir/en/home/references/ambion-tech-support/nuclease-enzymes/general-articles/dnase-i-demystified.html

My opinion is the less you rely on kits the better. I like Norbert's suggestion, assuming the fragments are of a somewhat homogeneous size and therefore will not run as a smear.

Two alternatives

1) Phenol-chloroform extract to remove the protein from your sample. Don't use something fancy... simple old water saturated phenol chloroform, neutral pH, no chaotropic salts or stabilizers or anti-foaming junk. Collect the aq phase, make sure the monovalent salt concentration is >= 200 mM and ethanol precipitate 2X. Take an absorbance spectra to be sure you did not bring any phenol over.

2) Depending on what 'DNAse' and what you want to do with the sample afterward.... All the DNAse enzymes I know of use a divalent cation cofactor and so can be inactivated by chelation.

I would probably go with 1.

If you don't want to heat your samples and want to minimize loss of low molecular weight fragments then add a reducing agent. The two disulfide bonds of DNase are reduced by mercaptoethanol and similar reagents in minutes at pH 7.2 and room temperature. The reduced protein is inactive.

J Biol Chem. 1969 Feb 10;244(3):929-32.

Effect of divalent cations on the reduction and re-formation of the disulfide bonds of deoxyribonuclease.