Sequence-dependent base pair opening in DNA double helix

Abstract

Preservation of genetic information in DNA relies on shielding the nucleobases from damage within the double helix. Thermal fluctuations lead to infrequent events of the Watson-Crick basepair opening, or DNA "breathing", thus making normally buried groups available for modification and interaction with proteins. Fluctuational basepair opening implies the disruption of hydrogen bonds between the complementary bases and flipping of the base out of the helical stack. Prediction of sequence-dependent basepair opening probabilities in DNA is based on separation of the two major contributions to the stability of the double helix: lateral pairing between the complementary bases and stacking of the pairs along the helical axis. The partition function calculates the basepair opening probability at every position based on the loss of two stacking interactions and one base-pairing. Our model also includes a term accounting for the unfavorable positioning of the exposed base, which proceeds through a formation of a highly constrained small loop, or a ring. Quantitatively, the ring factor is found as an adjustable parameter from the comparison of the theoretical basepair opening probabilities and the experimental data on short DNA duplexes measured by NMR spectroscopy. We find that these thermodynamic parameters suggest nonobvious sequence dependent basepair opening probabilities.

FIGURE 1

Fluctuational opening of one basepair in duplex DNA involves loss of pairing between complementary bases, disruption of stacking with neighboring pairs, and flipping the bases out of the helix leading to formation of a small highly constrained ring.

FIGURE 2

Comparison of the opening probabilities obtained in NMR experiments (bars with open or shaded fill for A·T or G·C pairs, respectively) with the results of theoretical calculations (bars with patterned fill) for duplexes I–III. The opening probabilities correspond to unique internal basepairs of palindromic sequences. Calculations were carried out with stacking and basepairing parameters corresponding to 15°C and 0.1 M [NaCl]. The ring factor ξ is indicated at each panel along with the least-square parameter 〈D〉 given by Eq. 10.

FIGURE 3

Comparison of the opening probabilities obtained in NMR experiments (bars with open or shaded fill for A·T or G·C pairs, respectively) with the results of theoretical calculations (bars with patterned fill) for duplexes IV–VII. The opening probabilities for four internal basepairs of palindromic sequences IV and V are shown. For duplexes VI and VII, experimental values are available only for basepairs that are underlined. Calculations were carried out with stacking and basepairing parameters corresponding to 20°C and 0.1 M [NaCl]. The ring factor ξ is indicated at each panel along with the least-square parameter 〈D〉 given by Eq. 10.

FIGURE 4

Experimental (circles) and theoretical (triangles) basepair opening probabilities of duplexes IV, V, and VI at different temperatures indicated at the top. In the case of duplex VI, experimental values are available only for basepairs that are underlined. The value of the ring factor are shown above each panel. Open and shaded fills indicate A·T and G·C pairs, respectively.

FIGURE 5

Schematic representation of possible open basepair configurations. (A) both bases are positioned extrahelically. (B) One base remains in the helical stack.