Intercalating nucleic acids (INAs) with insertion of N-(pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol. DNA (RNA) duplex and DNA three-way junction stabilities

N-(Pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol was synthesised from (3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol and (3R,4S)-4-[(1S)-1,2-dihydroxyethyl] pyrrolidin-3-ol using alkylation with 1-(chloromethyl)pyrene or reductive amination with pyrene-1-carbaldehyde and NaCNBH3. The incorporation of N-(pyren-1-ylmethyl)azasugar moiety into oligodeoxynucleotides (ODN) as a bulge to form an intercalating nucleic acid (INA) induced a slight destabilization of INA-DNA duplex, whereas the INA-RNA duplex was strongly destabilized and 9 degrees C difference per modification in thermal stability between INA-DNA over INA-RNA duplexes was observed. The stabilization of a DNA three way junction (TWJ) was improved when the intercalator moiety was inserted into the junction region as a bulge.     

Polymerization dynamics of double-stranded biopolymers: chemical kinetic approach

The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predictions of approximate multilayer models that consider only a finite number of the most relevant polymer configurations. Our theoretical approach is applied to analyze the experimental data on the growth and fluctuations dynamics of individual single actin filaments.