The recognition of the substrate by the DNAzyme is through base pairing. Because of this, the DNAzyme has affinity for the product ribonucleotides. This leads to pronounced product inhibition of the reaction. The longer the base-pairing recognition sequence, the greater the affinity of the DNAzyme for the products, the greater the product inhibition, and the slower the turnover.

Thank you so much for your great answer that can help me to understand.

And then, What about melting temperature (Tm), is there correlation??

Melting temperature of base-paired nucleic acids correlates with the number of hydrogen bonds in the base pairs (2 for each A-T and 3 for each G-C). The longer the base-paired sequence, the higher the melting temperature. For two sequences of the same length, the one with higher G-C content will have the higher melting temperature. Mismatches in the sequence lower the melting temperature. You can find on-line calculators for estimating melting temperature from sequence.

Thanks, Adam B Shapiro for the response, I have a related question and wonder for the reasoning of the phenomena. "I tried 8-17zyme sequence in HEPES buffer, followed with unmodified AuNPs. sometimes substrate and enzyme get cleaved even without the addition of target and induced salt concentration do not aggregate AuNPs. It is assumed that dissociated part of the substrate recognition adsorbs on the surface of AuNPs that protect them from getting aggregated". 

This is very strange, ideally, hybridized sequence should not dissociate in the identical parameters for which I found complete aggregation which is in accordance with the phenomena.

I really appreciate your comments and response, please.

Dear Abdul,

I am using DNAzyme "GR-5", but still not work.

There is problem in heating up and cooling down process.

I will be pleasured If you want to share with me.

Thanks