Probing the statistics of sequence-dependent DNA conformations in solution using SAXS

TL;DR

This study demonstrates that small-angle X-ray scattering (SAXS) data for four 60 bp DNA duplexes related to the GAGE6 promoter can be analyzed with a simple Kratky-Porod polymer model to extract the statistical distribution of local bending and twist in solution. By deriving the real-space pair-distance distribution $P_{exp}(r)$ and comparing it to ensembles generated by Monte Carlo simulations of a DNA with bending angles $\bftheta_n$ and dihedral angles $\bfvarphi_n$, the authors quantify sequence-dependent conformational propensities, including persistence length and torsional rigidity, while also introducing a method to orient conformations along the sequence for asymmetric samples. The results reveal that AT-rich domains are more flexible and tend to bend more, but the relationship between local sequence and global conformation exhibits cooperative, nonlocal effects; small sequence changes can dramatically shift bending domains, with potential implications for protein binding (e.g., SFPQ) and DNA recognition. The work underscores the value of real-space analysis for interpreting SAXS data on flexible polymers and highlights SAXS as a powerful, complementary tool to high-resolution structural methods for studying DNA conformations in solution.

Abstract

SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein binding. We show that the SAXS data can be analysed using a simple polymer model which nevertheless quantitatively describes the average persistence length and torsional rigidity of the DNA double helix to determine the statistical distribution of local conformations of the DNA in solution to a high accuracy. Although the SAXS data is averaged over time and all spatial orientations of the molecules, for sequences which have some asymmetry in the data we show that the conformations can be oriented with respect to the sequence. This allows specific features detected by the analysis to be precisely related to the DNA sequence, opening up new opportunities for SAXS to investigate the properties of DNA in solution. The biological implications of these results are discussed.

Figures (10)

• Figure 3: The DNA polymer model used in the analysis of the SAXS data.
• Figure 4: Statistics of the local bending angles $|\bftheta_n(i)|$ over the 1000 best saved conformations for the GAGE6 sample: the red full line shows $\overline{|\bftheta_n(i)|}$. The black line with circles shows the same average, limited to the bending angles which are above $\bftheta_0 = 5^{\circ}$, and the dashed blue curve shows the standard deviation of $|\bftheta_n(i)|$. The full brown vertical lines show the positions $n_1=36$, $n_2=48$ which have been used for the 'orientation' of the conformations and the dashed brown vertical lines show the mirror positions $n'_1=13$ and $n'_2=25$.
• Figure 9: Top panel: sequence GAGE6_2. Comparison of AutoGNOM-4-$P_{\mathrm{exp}}(r)$ (small circle points and thin black curve with error bars) and $P(r)$ given by the 1000 best conformations of the polymer model (thick red curve). The gray region for $r < 25\;$Å is the low-r domain in which the model cannot describe the internal structure of the double helix. Bottom panel: Upper part: Statistics of the absolute value of the local bending angles $|\bftheta_n(i)|$ over the 1000 best-saved conformations for the GAGE6 sample, after orientation of the conformations as discussed in the Materials and Methods section. The red full line shows the average over $i$ of $|\bftheta_n(i)|$ versus $n$. The black line with circles shows the same average, limited to the bending angles which are above $|\bftheta| = 5^{\circ}$, and the dashed blue curve shows the standard deviation of $|\bftheta_n(i)|$. Lower part: Statistics of the absolute values of the dihedral angles The red full line shows the average over $i$ of $|\bfvarphi_n(i)|$ versus $n$ and the the dashed blue curve shows their standard deviation. The vertical dashed lines show the boundaries of the domain where large bending was observed in the analysis of AutoGNOM-5-$P_{\mathrm{exp}}(r)$.
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