Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2011 May 17;39(15):6813–6824. doi: 10.1093/nar/gkr369

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 4. — Affinity (ΔΔG) versus weight score (W_s) comparison validating the HS model. Traditional (open symbols) and Ψ-plots (closed symbols) for dyad (triangles) and dyad (+10)bend (circles and crosses) EcCrp/XD-DNA sequence-specific conformers. Substrate ΔΔG values relative to ΔG for ICAP were obtained from experiments performed by Lindemose et al. (34). PSSM #A was the scanning matrix for calculating all scores. The highest score fitting to PSSM #A (either strand orientation) is shown. (A) PSSM #A calculated W_s of dyad (open triangles) and dyad (+10)bend substrates (open circles). (B) PSSM #A calculated ψ-scores (W_ψs) of ψ_EcCrp/XD-DNA for dyad (closed triangles) and dyad (+10)bend substrates (closed circles and crosses). Each set of conformer-specific sequences scored (e.g. the circles) make up the input sequence background p_i for scoring that conformer. Specific ψ-sequences, ΔΔG values, and PSSM #A calculated ψ-scores are clearly listed in Supplementary Table S36. Outliers (crosses) are labeled vertically and not included in the R² value because they are distinct from a trendline. R² shown for trend lines (dotted) was obtained by fitting to y = y₀ + a_nlnx. ΔΔG is the same for any given substrate in each graph. The point for the highest affinity substrate is G8.85 = 85 and labels correspond to the G8.## clones as described (34). Note logarithmic scaling of the abscissa. For the XD-DNA shown, G = X and A = D. (C) The entire sequence distribution constituting the major binding mode illustrated as PSSM #A (25.7 bits). All 49 unique sequences of the SELEX system make up this logo. The EcCrp/XD-DNA complex affinities for 26 dsDNA substrates with these unique sequences were determined, leaving 23 sequences having unknown affinities. (D) The dyad (+10)bend conformer illustrated as PSSM #A1 (33.5 bits). The 14 sequences that contain (+10)CCCC make up this logo. A total of 12 affinities were determined (circles and crosses in A and B). (E) The dyad conformer illustrated as PSSM #A2 (31.2 bits). The seven sequences that contain ≤2 X/C bp's total in both (+ and −10)NNNN tracts make up this logo. A total of four affinities were determined (triangles in panels A and B). The reported bit values span between positions −16 and +16. The logos in C and D are not ψ-sequences. Base positions and arbitrary regions shaded in gray are labeled as in Figure 1A. Flanking flexible bend proximal primary kink associated positions +3, +5 and +7 (yellow bars) are where ψ-sequence changes were performed.