Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition

Abstract

Recent advancement in nucleic acid techniques inside cells demands the knowledge of the stability of nucleic acid structures in molecular crowding. The nearest-neighbor model has been successfully used to predict thermodynamic parameters for the formation of nucleic acid duplexes, with significant accuracy in a dilute solution. However, knowledge about the applicability of the model in molecular crowding is still limited. To determine and predict the stabilities of DNA duplexes in a cell-like crowded environment, we systematically investigated the validity of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding. The thermodynamic parameters for the duplex formation were measured in the presence of 40 wt% poly(ethylene glycol)200 for different self-complementary DNA oligonucleotides consisting of identical nearest-neighbors in a physiological buffer containing 0.1 M NaCl. The thermodynamic parameters as well as the melting temperatures (Tm) obtained from the UV melting studies revealed similar values for the oligonucleotides having identical nearest-neighbors, suggesting the validity of the nearest-neighbor model in the crowding condition. Linear relationships between the measured ΔG°37 and Tm in crowding condition and those predicted in dilute solutions allowed us to predict ΔG°37, Tm and nearest-neighbor parameters in molecular crowding using existing parameters in the dilute condition, which provides useful information about the thermostability of the self-complementary DNA duplexes in molecular crowding.

Figure 1.

Normalized UV melting curves of d(GATCCGGATC) (6a), d(GGATCGATCC) (6b), d(ATGAGCTCAT) (7a) and d(ATCAGCTGAT) (7b) in buffer containing 0.1 M NaCl, 10 mM Na₂HPO₄ (pH 7.0) and 1 mM Na₂EDTA in the presence of 40 wt% PEG 200. Oligonucleotide sequences are mentioned in the legends. The concentration of these oligonucleotides was 100 μM.

Figure 2.

T _m ⁻¹ versus ln (C_t) plots of d(GATCCGGATC) (6a), d(GGATCGATCC) (6b), d(ATGAGCTCAT) (7a) and d(ATCAGCTGAT) (7b).

Figure 3.

Relationship between the measured (A) ΔG°₃₇ and (B) T_m in the molecular crowding condition and those predicted in the absence of cosolute by the nearest-neighbor parameters. Least-square fits are shown as straight lines, and r² represents their correlation coefficients. White circles correspond to the sequences of pairs 1 and 8. In (B), the additional white circle corresponds to the T_m of oligonucleotide d(CGATCGGCCGATCG). White circles are not included in the fitted lines.

Figure 4.

Calculation by numeric approach of ΔG°₃₇ (crowding) to determine the nearest-neighbor parameters in the crowding condition from established nearest-neighbor parameters. (A) Schematic illustration of the analysis and (B) the best found correlation between the calculated and measured ΔG°₃₇ (crowding).