#Stacking factor coefficient free#

Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation. The Journal of Physical Chemistry B 2021, 125 Temperature-Responsive Peptide–Nucleotide Coacervates. HBsAg, Subviral Particles, and Their Clearance in Establishing a Functional Cure of Chronic Hepatitis B Virus Infection. Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine. Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi.This article is cited by 353 publications. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases such compounds may be useful in stabilizing designed DNA structures and complexes. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces) however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. The nonpolar analogues stack more strongly in general than the more polar natural bases. For the four natural bases, the order of stacking ability is A > G ≥ T = C. At 5 μM DNA concentration, T m values range from 41.7 ☌ (core sequence) to 64.1 ☌ (with dangling pyrene residues). Adding these dangling residues is found to stabilize the duplex by an additional −0.8 to −3.4 kcal We studied the effects of adding single dangling nucleosides (X) where the aromatic “base” is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. mol - 1 in a pH 7.0 buffer containing 1 M Na +.

#Stacking factor coefficient free#

Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 ☌) of −8.1 kcal We report the use of thermodynamic measurements in a self-complementary DNA duplex (5‘-dXCGCGCG) 2, where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA.