Visualizing single-stranded nucleic acids in solution

Transcription

1 1 SUPPLEMENTARY INFORMATION Visualizing single-stranded nucleic acids in solution Alex Plumridge 1, +, Steve P. Meisburger 2, + and Lois Pollack 1, * 1 School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA 2 Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States * To whom correspondence should be addressed. Tel: ; Fax: ; lp26@cornell.edu + The authors wish it to be known that, in their opinion, the first 2 authors should be regarded as joint First Authors.

2 2 The suite library Below, we provide supplementary Tables 1 and 2. Together, these tables define the suite libraries used for modelling the da and dt homopolymers explored in the manuscript. Table 1 provides the differing torsion angle sets, as defined in Figure 1b, while Table 2 provides the values specifying the base torsion (χ) and sugar pucker angles (δ) defined in Figure 1c. These suites are illustrated for both dt and da in Supplementary Figures 1 and 2 respectively. To further aid in visualizing the differences in these suites and their effects on chain geometries, we build 30-mers of poly dt defined by a single suite (e.g. 29 instances of suite B2 defining a half canonical B-form helix). For each pure suite chain, we give its structure and the theoretical Kratky plot derived from each conformation. These are illustrated in Supplementary Figure 3 and show the diversity of structural motifs available with our defined libraries. Mnemonic Derived ε ζ α β ϒ dt da Restrictions Note from on {δ(i-1), δ} A1p 5d,6d,6p None A1t 5j,5q,6j None A2p 4p,4d,7p,3d None P1p 9a,0b,0a None P3p 2a,2I,1I,1m None P3t 2h None S3p 1g,1z None S3t 1t None B1 BI {2,2} Canonical B-form. B2 BII {2,2} Non-canonical B-form. A1 AI {3,3} Canonical A-form. B2A BII-AI {3,2} Hybrid B-A form. Supplementary Table 1: Torsion angle library defining the route of the phosphate backbone, angles listed in degrees. For the non-stacked suites, the RNA rotamers each were derived from are listed corresponding to supplementary reference (1), while for the stacked suites we follow supplementary reference (2). Check marks show which torsion sets are included for each homopolymer library. The restrictions column defines which sugar puckers are modelled for each torsion angle set before removal of steric clashes. For example, the A-form A1 requires both sugar puckers to be C3 -endo {3,3}). Sugar-pucker δ Χ (anti, pyrimidines) Χ (anti, purines) Χ (syn, purines) C2 -endo C3 -endo Supplementary Table 2: Parameters used to define the sugar pucker (δ) and base torsion angles (χ) associated with the phosphate backbone (2), angles listed in degrees.

3 3 Supplementary Figure 1: Visualization of the dt torsion sets defined in Supplementary Table 1. We show the C2 -endo variants for all suites, except where the suite specifically requires otherwise (e.g. B2A and A1), these instances are listed in Supplementary Table 1. Supplementary Figure 2: Visualization of the da torsion sets defined in Supplementary Table 1. In accordance with the NMR derived sugar-pucker equilibrium constants for da dinucleotides (K3endo K2endo), all variants are C2 -endo sugar puckers (as described in the main text).

4 Supplementary Figure 3: To help visualize the suites listed in Table 1, we generated 30-mers of dt comprised of solely one suite type to exaggerate their effect on chain conformations. For example, B1 shows a half-canonical B-form helix of 30 dt bases (29 instances of suite B1). For additional insight into the nature of these suites, we show the theoretically derived Kratky plots for each 30-mer. Note that in some cases a 30-mer of a sole suite is dis-allowed by the sterics/adjacency matrix L4 (e.g. B2A and S3p), we leave these chains in for illustrative purposes only. 4

5 5 Additional experimental analysis Here we provide additional figures and analysis of the experimental examples that are not included in the main text. All data and models are available on SASBDB through codes: SASDBD6 and SASDBE6. Supplementary Figure 4 reproduces the Guinier and Kratky plots one will find under these listings. Additionally, we address the repeatability of the method through Supplementary Figures 5-7. Supplementary Figure 4: A reproduction of the Guinier fits (top panels) and Kratky plots (bottom panels) to the experimental SAXS data for a) dt30 and b) da30, as one will find in SASBDB entries: SASDBD6 and SASDBE6 respectively. Note that the rather featureless Kratky plot provides little insight into the conformations of these singe-strands, other than indicating they are unfolded and coil like. Supplementary Figure 5: Repetition of the algorithm three separate times starting from a completely unrefined pool for a) dt30 and b) da30. Each separate implementation yields the same Rg and R distributions, as well as the same conformational map.

6 6 Supplementary Figure 6: Repetition of the algorithm three separate times starting from a completely unrefined pool for dt30 (left) and da30 (right). Each separate implementation well reproduced the mean number of a given torsion set per structure. Supplementary Figure 7: Repetition of the algorithm three separate times starting from a completely unrefined pool for a) dt30 and b) da30.. Each separate implementation well reproduced the mean backbone shape of each homopolymer.

7 7 SUPPLEMENTARY REFERENCES 1. Richardson,J.S., Schneider,B., Murray,L.W., Kapral,G.J., Immormino,R.M., Headd,J.J., Richardson,D.C., Ham,D., Hershkovits,E., Williams,L.D., et al. (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA, 14, Svozil,D., Kalina,J., Omelka,M. and Schneider,B. (2008) DNA conformations and their sequence preferences. Nucleic Acids Res., 36,