Conformational Space of Nucleic Acids

1. Conformational Space of Nucleic Acids • Bohdan Schneider • Institute of Organic Chemistry and Biochemistry AS Czech Republic • bohdan@uochb.cas.cz Supported by the grant LC512 from MŠ MT • to the Center for Biomolecules and Complex Molecular Systems

2. Motivation • Nucleic acids have key biological functions • Folding realized via the backbone conformational variability • Function might be connected to fold

4. Data for the Analysis • NA backbone analyzed across the NDB archive: • DNA: About Eight thousand nt units • RNA: About Four thousand nt units

5. Analysis of Multidimensional Space • One nucleotide has 7 torsion angles ~ 7D conformational space • Largest variability at the phosphodiester link • A minimal unit for analysis >>ribose-to-ribose<< • Analyze several 3D slices through the 14D space

6. Averaging of 3D distributions by Fourier averaging Point distribution Pseudoelectron representation

7. Fourier transforms of 3D torsion distributions • Calculated ~fifteen 3D maps • In all, fit peaks, assign residues to peaks • Sorted residues by lexicographical clustering: • 6 primary maps for clustering • 5 to monitor quality of proposed clusters • 6 more or less ignored in the analysis

11. Clustering by Peak Names

12. Protocol • Select structural data • Fourier-transform 3D distributions of torsions • Localize peak positions in all maps • Fit and name peaks • Name di-nts by nearby peaks • Cluster di-nts by their names • Check clusters by overlap in real 3D • Well overlapping dints form conformational family

13. DNA is conformationally compact

14. RNA is conformationally diverse