Unique properties of Purine/Pyrimidine asymmetric PNADNA duplexes:
Differential stabilization of PNADNA duplexes by purines in the PNA strand
Anjana Sen 1 and Peter E Nielsen 1*
1 University of Copenhagen
* To whom correspondence should be addressed. E-mail: pen{at}imbg.ku.dk.
Submitted on August 24, 2005
Revised on September 27, 2005
Accepted on 4 November 2005
 |
Abstract |
|---|
PNA•DNA duplexes are significantly stabilized by purine nucelobases in the PNA strand. In order to elucidate and understand the effect of switching backbone in a nucleic acid duplex, we now report a thermodynamics study along with solution conformations study of two purine/pyrimidine strand asymmetric duplexes and a strand symmetrical control by comparing the behaviour of all four possible PNA/DNA combinations. In essence we are comparing an identical base pair stack connected by either an aminoethyl glycine PNA or a deoxyribose DNA backbone. We show that the PNA•DNA duplexes containing purine-rich PNA strand are stabilized with regard to Tm and free energy as well as enthalpy (and concomitantly relatively less entropically disfavoured). Based on our data, we find it unlikely that differences in counter ion binding (identical ionic strength dependence was observed), hydration (identical and insignificant water release was observed) or single strand conformation can be responsible for the difference in duplex stability. The only consistent difference observed between the purine-rich PNA versus the pyrimidine-rich PNA in iso-sequential PNA•DNA duplexes is the significant increase in both binding enthalpy and entropy for the PNA•DNA duplexes containing pyrimidine-rich PNA in organic solvent, which would indicate that these duplexes are relatively enthalpically disfavored in water. Although our results so far do not allow us to identify the origin of the different stabilities of homopurine/homopyrimidine PNA•DNA duplexes, the evidence does point to a significant structural component, which involves enthalpic contributions both within the duplex structure and also from bound water molecules.
Key Words:
CD spectroscopy, DNA, PNA (peptide nucleic acid), duplex stability, sequence dependence, thermodynamics
