Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′-exo (north) and 3′-exo (south) ‘locked’ templates

The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers

Changes in the chemical shift of the imino protons between the -MCT- and -MCT- modified ODN species and the native DD at 5°C () and at 25°C ()

<p><b>Copyright information:</b></p><p>Taken from "Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′- (north) and 3′- (south) ‘locked’ templates"</p><p>Nucleic Acids Research 2007;35(6):1978-1991.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1895885.</p><p>© 2007 The Author(s)</p

1D NMR spectra of () T7 and () T7T8 imino regions at 200 μM strand concentration

<p><b>Copyright information:</b></p><p>Taken from "Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′- (north) and 3′- (south) ‘locked’ templates"</p><p>Nucleic Acids Research 2007;35(6):1978-1991.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1895885.</p><p>© 2007 The Author(s)</p> Additional peaks that were not observed in 1–2 mM solutions are indicated with arrows

NMR spectra of the imino H region of the -MCT modified oligos at various temperatures

<p><b>Copyright information:</b></p><p>Taken from "Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′- (north) and 3′- (south) ‘locked’ templates"</p><p>Nucleic Acids Research 2007;35(6):1978-1991.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1895885.</p><p>© 2007 The Author(s)</p> The assignments are as follows: filled diamond T8, filled square T7, filled triangle G2, filled circle G4, star G10 and double dagger, G12

Changes in the chemical shift of select non-exchangeable protons between the -MCT- () and -MCT- () modified ODN species and the native DD at 25°C

<p><b>Copyright information:</b></p><p>Taken from "Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2′- (north) and 3′- (south) ‘locked’ templates"</p><p>Nucleic Acids Research 2007;35(6):1978-1991.</p><p>Published online 6 Mar 2007</p><p>PMCID:PMC1895885.</p><p>© 2007 The Author(s)</p