Overall stability, stacking and base pairing contributions for DNA polymers at different temperatures () Temperature dependence of the stacking contributions to the stability of A•T- (red circles) and G•C- (blue circles) containing polymers

<p><b>Copyright information:</b></p><p>Taken from "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix"</p><p>Nucleic Acids Research 2006;34(2):564-574.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1360284.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Straight solid line of the same color gives the temperature dependence of the stability parameter of corresponding polymer calculated using and at [Na] = 15 mM. () Temperature dependence of A•T (red) and G•C (blue) base pairing parameters calculated as a difference between stability and stacking terms using data in (a). Horizontal broken lines correspond to mean values of kcal/mol and kcal/mol

Effect of ambient conditions—temperature () and ionic strength ()—on DNA stacking parameters for A•T- and G•C-containing contacts

<p><b>Copyright information:</b></p><p>Taken from "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix"</p><p>Nucleic Acids Research 2006;34(2):564-574.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1360284.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Dinucleotide stacks are shown at the top of each panel. Error bars represent the scatter range of the experimentally determined values of nicked stacks (see text). This data is tabulated in Supplementary Tables 2 and 3

Effect of phosphorylation state of 5′ nt at the nick site on stacked-unstacked equilibrium

<p><b>Copyright information:</b></p><p>Taken from "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix"</p><p>Nucleic Acids Research 2006;34(2):564-574.</p><p>Published online 31 Jan 2006</p><p>PMCID:PMC1360284.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () Stacking parameters measured in 1× TBE at 37°C of A•T-containing (top panel) and G•C-containing (bottom panel) nicked dinucleotide stacks before (circles) and after (triangles) dephosphorylation are compared. White and gray fills are used for fragments with the nick in the forward and reverse strand, respectively. Nicked dinucleotide stacks with a purine at a 5′-side of the nick are underscored (see text). () Salt dependence of Δ values of nicked contacts indicated to the right of each panel before (circles) and after (triangles) dephosphorylation. Total concentration of sodium assuming 1× TBE to be equivalent to 15 mM Na is indicated, see

End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes-0

<p><b>Copyright information:</b></p><p>Taken from "End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes"</p><p>Nucleic Acids Research 2005;33(19):6459-6459.</p><p>Published online 7 Nov 2005</p><p>PMCID:PMC1278943.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p