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Sequence dependent interactions between Nucleic Acids

The sequence dependent pairing of ssDNA with ssDNA is well known; however, the Prentiss group has shown that dsDNA-dsDNA pairing can also be sequence dependent. https://www.pnas.org/content/106/47/19824.short

 

Pairing of homologous DNAs using the parallel single molecule, magnetic tweezers-based assay.
Pairing of homologous DNAs using the parallel single molecule, magnetic tweezers-based assay.
                 

 

Effect of sequence on DNA pairing.
Effect of sequence on DNA pairing.

 

https://royalsocietypublishing.org/doi/10.1098/rspa.2016.0186

In addition, the stringency of the pairing between long ssDNA molecules can be enhanced by inserted abasic sites into one of the ssDNA strands.

ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups (plos.org)

 

Measurements of the melting temperature, Tm.
Measurements of the melting temperature, Tm.

 

Finally, sequence dependent interactions between ssDNA and dsDNA can bring dsDNA molecules together

https://pubmed.ncbi.nlm.nih.gov/27580717/

 

 

  • Pairing of homologous DNAs using the parallel single molecule, magnetic tweezers-based assay.
  • Effect of sequence on DNA pairing.
  • Measurements of the melting temperature, Tm.