Is there any software can simulate RNA:DNA binding stability? Thanks!

Question

[wujy128]

There exist some mismatches. I need to get some stabilities value. I want to apply it into CRISPR/Cas9 design. Thanks!

Answer 1

[Charles Plessy]

Have you tried MELTING? It "computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA". Its version 4.3.1 (before it was rewritten in Java) and its GUI are available in Debian.

[wujy128]

Thank you for your answer!

I try to use it, My data contains different number of mismatches. The software shows some errors:

1. only one mismatch:

melting  -Hrnadna -N0.2 -P0.0001 -SGGTCAGTGAGTGTGTGCGTG -CCCACUCACUCACACACGCAC
  WARNING: The default mismatches parameters can efficiently
  account only for the DNA/DNA hybridisation. You can enter an
  alternative set of parameters with the option -M
  WARNING: The default inosine mismatches parameters can efficiently
  account only for the DNA/DNA hybridisation or RNA/RNA hybridization (however not completed yet). You can enter an
  alternative set of parameters with the option -M
  WARNING: The default mismatches parameters can efficiently
  account only for the DNA/DNA hybridisation. You can enter an
  alternative set of parameters with the option -M
  WARNING: The default inosine mismatches parameters can efficiently
  account only for the DNA/DNA hybridisation or RNA/RNA hybridization (however not completed yet). You can enter an
  alternative set of parameters with the option -M
  Enthalpy: -512050 J.mol-1
  Entropy: -1405.96 J.mol-1.K-1
  Melting temperature: 69.59 deg C

2. two mismatches:

melting  -Hrnadna -N0.2 -P0.0001 -SGCTCAGTGAGTGTGTGCGTG -CCCACUCACUCACACACGCAC
 The effect of mismatches (inosine mismatches included) located on the two extreme positions
 of a duplex are unpredictable (i.e. each case has to be
 considered separately).

[wujy128]

Do you know how to solve this problem?