Structurally distributed surface sites tune allosteric regulation

  1. James W McCormick
  2. Marielle AX Russo
  3. Samuel Thompson
  4. Aubrie Blevins
  5. Kimberly A Reynolds  Is a corresponding author
  1. The Green Center for Systems Biology, University of Texas Southwestern Medical Center, United States
  2. Department of Biophysics, University of Texas Southwestern Medical Center, United States
  3. Department of Bioengineering, Stanford University, United States
8 figures, 1 table and 2 additional files

Figures

The DL121 DHFR/LOV2 fusion.

(A) Composite structures of the individual DHFR and LOV2 domains (PDB ID: 1R × 2 and 2V0U), indicating the LOV2 insertion site between positions 120 and 121 of DHFR (Sawaya and Kraut, 1997; Halavaty and Moffat, 2007). DHFR is in gray cartoon, NADP co-factor in green sticks, and folate substrate in yellow sticks. In LOV2 signaling, blue light triggers the formation of a covalent adduct between a cysteine residue (C450) and a flavin mononucleotide (FMN, yellow sticks) (Salomon et al., 2001; Crosson and Moffat, 2002; Swartz et al., 2002) and associated unfolding of the C-terminal Jα-helix (red cartoon); this order-to-disorder transition is used for regulation in several synthetic and natural systems (Pudasaini et al., 2015; Glantz et al., 2016). (B) DHFR loop conformational changes near the LOV2 insertion site. While the mechanism of DHFR regulation by LOV2 is currently unknown, inspecting the native DHFR structure provides some insight. The substrate-bound Michaelis complex of native DHFR is in the ‘closed’ conformation (gray cartoon), while the product ternary complex is in the ‘occluded’ state (purple cartoon). The βF-βG loop, where LOV2 is inserted, is highlighted in cyan. In native DHFR, hydrogen bonds between this loop (Asp122) and the Met20 loop (Gly15, Glu17) are thought to stabilize the closed conformation (Sawaya and Kraut, 1997; Schnell et al., 2004). Mutations to positions 121 and 122 reduce activity and cause the enzyme to prefer the occluded conformation (Cameron and Benkovic, 1997; Mhashal et al., 2018; Miller and Benkovic, 1998). (C) Steady state Michaelis Menten kinetics for the DL121 fusion under lit (blue) and dark (gray) conditions. The kcat of DHFR increases 28% in response to light; the difference in Km is statistically insignificant (Supplementary file 1a). Error bars represent standard deviation for three replicates. (D) Quantifying the allosteric effect of mutation. Allostery for the DL121 fusion is reported as the ratio between lit and dark velocity. The effect of a mutation on allostery is then computed as the ratio of mutant allostery to wt-DL121 allostery (bottom blue box).

A high-throughput, high-resolution assay for DHFR activity.

(A) The turbidostat. The instrument has 15 individual growth chambers (vials), positioned on a stir plate inside an incubator. Illumination was provided by blue LEDs in each vial holder. (B) Log-normalized relative allele frequency over time for 11 DHFR point mutations of known catalytic activity and the DL121 fusion. Allele frequency (colored circles) was determined by next-generation sequencing of mixed-population culture samples at each time point. All frequencies were normalized to t = 0 and WT DHFR (no LOV2 insertion). Error bars reflect standard error across four measurements, they are sometimes obscured by the marker. The slope for each line of best fit provides the growth rate of each mutant allele relative to WT DHFR. (C) Relative growth rate vs. log10(velocity) for the 11 DHFR mutants and DL121 as characterized in panel B. Color coding of mutations is matched to panel B. Error bars reflect standard error of the mean over four replicates. The dashed line was fit by linear regression to all mutants in the linear regime (M42F excluded).

Figure 3 with 6 supplements
The effect of DL121 DHFR mutations on growth rate.

(A-C) Representative relative growth rate trajectories for three mutations. (A) DL121 D27N was deleterious in both lit and dark conditions. (B) DL121 D122W was advantageous under both lit and dark conditions. (C) DL121 E154R was deleterious in the dark, and near neutral in the light. Solid lines were obtained by linear regression; the slope of these provides the difference in growth rate relative to the unmutated DL121 construct. Relative growth rates were measured in triplicate for each mutant under lit (blue) and dark (gray) conditions. (D) Distribution of relative growth rates under dark conditions. The distribution for all mutations with measurable growth rate effects is in gray (‘null data’ and ‘no data’ excluded); the distribution for sector mutations is in navy. The relative growth rate of DL121 D27N, a mutation that severely disrupts catalytic activity, is indicated with a cyan dashed line. (E) The fraction of DL121 mutations with measurable growth rates that can be categorized as: DHFR surface, core, sector, and evolutionarily conserved (see Materials and methods for definitions). The fraction is shown for both the complete library (gray bars), and the library after removing mutations with low growth (growth rate <= DL121 D27N). The absolute number of mutations is shown above each bar. A contingency table summarizes the overlap between mutations in the sector (at a p-value cutoff of 0.010), and the mutations that yield low growth (growth rate <= DL121 D27N). (F) Structural distribution of positions enriched for mutations with growth rates as low as or lower than DL121 D27N (red spheres). The DHFR backbone is in gray cartoon, the folate substrate in yellow sticks, and the NADP co-factor in green sticks. (G) Relationship of the sector (navy blue surface) to positions enriched for growth-rate disrupting mutations (red spheres, same as in F).

Figure 3—source data 1

Relative growth rates under lit and dark conditions for DL121 point mutations as determined by next-generation sequencing.

Column 1 is the mutation name, columns 2–4 are relative growth rates in the light (three replicates), column 5 is the average lit relative growth rate, and column 6 is the standard deviation across lit replicates. Columns 7–9 are relative growth rates in the dark (three replicates), column 10 is the average dark relative growth rate, and column 11 is the standard deviation across dark replicates. Relative growth rate values of −999 indicate mutations with insufficient counts to fit a reliable growth rate (‘null data’), values of −1000 indicate mutations missing from the library at t = 0 (‘no data’), respectively.

https://cdn.elifesciences.org/articles/68346/elife-68346-fig3-data1-v2.csv
Figure 3—figure supplement 1
Deep mutational scanning library completeness – heatmap of counts for all mutants.

Log10(counts) of all possible mutations in DHFR domain of DL121 chimeric protein library at time point zero. The y axis corresponds to positions on E. coli DHFR domain as numbered in PDB ID: 1R × 2. A red star indicates the location of the LOV2 domain insertion. The x axis corresponds to possible mutations. Wild-type residues are shown in gray; positions with no counts are shown in white.

Figure 3—figure supplement 2
Deep mutational scanning library completeness – distribution of counts for all mutants.

A histogram of the number of counts per mutant at time point zero. The median and mean number of counts is shown as a dashed and solid red line, respectively.

Figure 3—figure supplement 3
Reproducibility across biological replicates.

The relative growth rate (see Materials and methods) for each mutant is compared across all three lit (A-C) and dark (D-F) replicates. The line of best fit is indicated with a blue dashed line. The teal dashed lines represent the growth rate of DL121-D27N; mutants with a relative growth rate below this cutoff were considered near catalytically inactive and excluded from analysis of allostery.

Figure 3—figure supplement 4
Heatmaps of relative growth rates.

(A) Relative growth rate in the dark. (B) Relative growth rate in the light. Blue and red indicate mutations with deleterious and beneficial effects on growth rate respectively. White squares with black outlines mark the WT residue at each position. Mutations missing from the library (‘no data’) are colored gray, and mutations that did not have sufficient counts for at least three time points (‘null data’, no relative growth rate could be fit) are colored navy.

Figure 3—figure supplement 5
Growth rate measurements for DL121-D27N.

Comparison of growth rates as doublings per hour for three enzymes: nonchimeric E. coli DHFR with a D27N mutation (rendering it catalytically inactive), the unmutated fusion protein, DL121, and DL121 combined with the D27N mutation. All three mutants were grown in a 96-well plate in M9 media supplemented with either no thymidine, 1 μg/ml thymidine (the same media conditions as the experiments in this work), or 50 μg/ml thymidine at 30°C. Error bars represent standard deviation across six replicates.

Figure 3—figure supplement 6
Relationship between catalytically inactivating mutations and evolutionarily conserved positions.

(A) Structural distribution of positions enriched for mutations with growth rates as low as or lower than DL121 D27N (indicated with red spheres). The DHFR backbone is in gray cartoon, the folate substrate in yellow sticks, and the NADP co-factor in green sticks. (B) Relationship of evolutionarily conserved positions (light blue surface) to positions enriched for growth-rate disrupting mutations (red spheres, same as in A). (C) A contingency table summarizes the overlap between conserved positions, and the mutations that yield low growth (growth rate <= DL121 D27N).

Figure 4 with 6 supplements
The effect of DL121 DHFR mutations on allostery.

(A) Heatmap of mutational effects on allostery. Blue indicates allostery disrupting mutations, and red indicates allostery enhancing mutations. White squares with black outlines mark the WT residue at each position. Mutations missing from the library (‘no data’) are colored gray, and mutations that did not have sufficient sequencing counts for at least three time points (‘null data’) are colored navy. The LOV2 domain insertion site is indicated with a red star. (B) Volcano plot indicating the statistical significance of the light-dark growth rate difference (y-axis) as a function of relative growth rate difference (x-axis). p-Values were computed using a t-test across triplicate light and dark measurements. Individual points correspond to mutations; mutations on the left (yellow) side of the graph are allostery disrupting, while mutations on the right (blue) are allostery enhancing. Two cutoffs for statistical significance are indicated with dashed gray lines – both a standard value of p=0.05, and an adjusted p-value of 0.016, obtained by using Sequential Goodness of Fit (SGoF) to account for multiple hypothesis testing. Mutations selected for further in vitro experimental characterization are colored red and labeled. S148C and E154R did not yield sufficient quantities of active protein for further in vitro characterization. (C) Triplicate relative growth rate measurements under lit (blue) and dark (gray) conditions for all mutations with statistically significant allostery at the adjusted p-value (p<=0.016). The mutations are sorted by dark growth rate; mutations selected for in vitro characterization are marked with red asterisks. (D) Relationship between the allosteric effect as measured in vivo and in vitro. As we expect a log-linear relationship, we compare the ratio of velocity at 25 µM DHF (along x) to the exponent of the relative growth rate difference (along y). The relative growth rate difference under lit and dark conditions is the mean of triplicate measurements, error bars indicate SEM. All mutant effects on growth rate were measured in the same experiment (corresponding to a subset of the data in panel B) with the exception of DL121 C450S. The relative growth rate for this light-insensitive LOV2 mutant was measured in the ‘calibration curve’ experiment shown in Figure 2 (see also Materials and methods). The ratio between velocity in the light and velocity in the dark reflects the mean of triplicate measurements; error bars indicate SEM. The green line was fit by linear regression.

Figure 4—figure supplement 1
Distribution of mutational effects on allosteric regulation.

The allosteric effect of all viable mutants is shown in gray with the mean allosteric effect of 0.0017 shown as a red dotted line. The allosteric effect of viable mutants in the sector is shown overlaid in blue. The mean allosteric effect of sector positions is −0.0005. The cutoff for sector identity used is a p-value of 0.01 as calculated in Reynolds et al., 2011 (Rivoire et al., 2016).

Figure 4—figure supplement 2
Steady state kinetics measurements for select mutants in the light and dark.

Initial velocity vs. substrate (dihydrofolate) concentration for the purified DL121 chimeric protein, allosterically inactivated DL121-C450S and eight point mutations to the DHFR domain of DL121. Lit (blue) and dark (gray) conditions are shown with error bars representing standard deviation across three replicates. The kcat, KM, catalytic efficiency and associated error are reported in Supplementary file 1a.

Figure 4—figure supplement 3
Spectroscopic characterization of LOV2 activation for select DL121 mutants.

The absorbance of purified DL121 chimeric protein, allosterically inactivated DL121-C450S and eight point mutations to the DHFR domain of DL121. Lit state absorbance spectra (red line) were measured after illumination for at least 2 min by full spectrum 125 watt 6400K fluorescent lamp (Hydrofarm Inc). Dark conditions are taken under the same conditions but using opaque tubes when the sample was placed under the lamp. With the exception of the DL121-C450S mutant, all show a characteristic spectral shift upon light stimulation consistent with an active LOV2 domain. Formation of a covalent FMN-thiol adduct in the LOV2 domain upon light exposure causes the 447 nm peak in the dark state to shift to 390 nm in the light.

Figure 4—figure supplement 4
Relaxation rate of the LOV2 chromophore for select DL121 mutants.

The relaxation of the chromophore at 447 nm was observed for 5 min following illumination for at least 2 min by full spectrum 125 watt 6400K fluorescent lamp (Hydrofarm Inc). With the exception of the allosterically inactivated DL121-C450S all of the assayed LOV2 domains had exponential and reversible relaxation to the dark state near that of the unmutated DL121 (kFMN = 0.017 s−1), indicating an active light response in the protein.

Figure 4—figure supplement 5
Steady state kinetics parameters under lit and dark conditions for select mutants of the DL121 fusion.

(A) The KM values (B) enzyme velocity and (C) kcat values are shown for both lit (blue bar) and dark (gray bar) conditions, error bars represent standard error across three replicates. Above each pair of bars the lit:dark ratio of the relevant catalytic parameter is shown. The Michaelis-Menten kinetics values are reported in Supplementary file 1a.

Figure 4—figure supplement 6
Correlation between in vivo allostery and in vitro steady state kinetics parameters for mutants of the DL121 fusion.

The relationship between the relative growth rate difference (in vivo) and the ratio of (A) catalytic turnover (kcat) (B) catalytic efficiency (kcat/KM) or (C) the Michaelis constant (KM). As we expect a log-linear relationship, we compare the ratio of catalytic constants to the exponent of the relative growth rate difference. The green dashed line is the linear regression with the coefficient of correlation (R2) shown. The low coefficient of correlation in comparisons (B-C) indicates that there is little relationship between the allosteric growth rate difference and both catalytic efficiency and the Michaelis constant ratios. The error bars represent standard error.

Structural distribution of allosteric mutations.

(A) Sites of allostery disrupting mutations (orange spheres). DHFR backbone is in gray cartoon, folate substrate in yellow sticks, and NADP co-factor in green sticks. (B) Fraction of mutations that enhance (blue), disrupt (orange), or do not significantly influence allostery (gray) as a function of distance to the LOV2 insertion site at DHFR position 121. Solid and dashed lines indicate mutations at either the p=0.016 and p=0.05 significance cutoffs for allostery, respectively. (C) Sites of allostery enhancing mutations (light blue spheres). (D) Contingency table summarizing the overlap between allostery enhancing mutations and mutations on the DHFR solvent accessible surface (considered as >25% relative solvent accessibility in the 1R × 2 PDB). (E) Sites of allostery enhancing (light blue spheres) and disrupting mutations (orange spheres) in the context of the sector (dark blue surface). (F) Contingency table summarizing the relationship between allostery enhancing mutations and sector mutations (sector defined at a p-value cutoff of 0.010). No allostery enhancing mutations occur within the sector.

Figure 6 with 1 supplement
Combinatorial effect of allostery-enhancing mutations.

(A) Location of M16, D87, and H124 (blue spheres). The LOV2 insertion site, G121, is shown in red spheres. The DHFR backbone is in gray cartoon, the folate substrate in yellow sticks, and the NADP co-factor in green sticks. (B) The in vitro allosteric effect of the single, double and triple mutants. Included are the log-additive expectations (Expected) for the double and triple mutants given only the single mutation effects, and the experimentally measured effects (Observed). The ratio between velocity in the light and dark reflects the mean of triplicate measurements; error bars indicate SEM. There is not a statistically significant difference between the expected and observed allosteric effects (p=0.07 for M16A,H124Q, p=0.48 for M16A,D87A,H124Q; as computed by unpaired t-test). (C) Schematic whereby a novel domain insertion is iteratively optimized by surface residue variation.

Figure 6—figure supplement 1
Characterization of the DL121- M16A,H124Q and DL121- M16A, D87A, H124Q mutants.

(A-B) Steady state kinetics measurements in the light and dark. Initial velocity vs. substrate (dihydrofolate) concentration is plotted, Lit (blue) and dark (gray) conditions are shown with error bars representing standard deviation across three replicates. For both the double and triple mutant, the lit states were better fit by a substrate inhibition model than a standard Michaelis-Menten model (p<0.05). The kcat, KM, catalytic efficiency and associated error are reported in Supplementary file 1a. (C-D) Relaxation rate of the LOV2 chromophore. The relaxation of the chromophore at 447 nm was observed for 5 min following illumination for at least 2 min by full spectrum 125 watt 6400K fluorescent lamp (Hydrofarm Inc). (E-F) Spectroscopic characterization of LOV2 activation. Lit state absorbance spectra (red line) were measured after illumination for at least 2 min by full spectrum 125 watt 6400K fluorescent lamp (Hydrofarm Inc). Dark conditions are taken under the same conditions but using opaque tubes when the sample was placed under the lamp. Both mutants show a characteristic spectral shift upon light stimulation consistent with an active LOV2 domain.

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Tables

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional information
Gene (Escherichia coli)DHFR-LOV2 121Reynolds et al. Cell 2011 [20]Fusion of Escherichia coli DHFR and Avena sativa LOV2
Strain, strain background (Escherichia coli)BL21(DE3)New England BiolabsNEB #: C2527HCompetent cells
Strain, strain background (Escherichia coli)ER2566 ΔfolA ΔthyADr. Steven Benkovic, described in [20, 26]Competent cells
Strain, strain background (Escherichia coli)XL1-BlueAgilent TechnologiesCat. #:
200249
Competent cells
Recombinant DNA reagentpACYC-Duet_DL121_WTTS(plasmid)Reynolds et al. Cell 2011 [20]Addgene ID 171954Contains chimeric DL121 with TYMS (selection vector)
Recombinant DNA reagentpHIS8-3_DL121(plasmid)Reynolds et al. Cell 2011 [20]Addgene ID 171953Contains chimeric DL121 (expression vector)
Sequence-based reagentDL121_pos1_fwdThis PaperMutagenic PCR primerNNSATCAGTCTGATTGCGGCG
Sequence-based reagentDL121_pos2_fwdThis PaperMutagenic PCR primerNNSAGTCTGATTGCGGCGTTAG
Sequence-based reagentDL121_pos3_fwdThis PaperMutagenic PCR primerNNSCTGATTGCGGCGTTAGCG
Sequence-based reagentDL121_pos4_fwdThis PaperMutagenic PCR primerNNSATTGCGGCGTTAGCGGTA
Sequence-based reagentDL121_pos5_fwdThis PaperMutagenic PCR primerNNSGCGGCGTTAGCGGTAGAT
Sequence-based reagentDL121_pos6_fwdThis PaperMutagenic PCR primerNNSGCGTTAGCGGTAGATCGC
Sequence-based reagentDL121_pos7_fwdThis PaperMutagenic PCR primerNNSTTAGCGGTAGATCGCGTTATC
Sequence-based reagentDL121_pos8_fwdThis PaperMutagenic PCR primerNNSGCGGTAGATCGCGTTATCG
Sequence-based reagentDL121_pos9_fwdThis PaperMutagenic PCR primerNNSGTAGATCGCGTTATCGGCATG
Sequence-based reagentDL121_pos10_fwdThis PaperMutagenic PCR primerNNSGATCGCGTTATCGGCATGG
Sequence-based reagentDL121_pos11_fwdThis PaperMutagenic PCR primerNNSCGCGTTATCGGCATGGAAAA
Sequence-based reagentDL121_pos12_fwdThis PaperMutagenic PCR primerNNSGTTATCGGCATGGAAAACGC
Sequence-based reagentDL121_pos13_fwdThis PaperMutagenic PCR primerNNSATCGGCATGGAAAACGCC
Sequence-based reagentDL121_pos14_fwdThis PaperMutagenic PCR primerNNSGGCATGGAAAACGCCATG
Sequence-based reagentDL121_pos15_fwdThis PaperMutagenic PCR primerNNSATGGAAAACGCCATGCCG
Sequence-based reagentDL121_pos16_fwdThis PaperMutagenic PCR primerNNSGAAAACGCCATGCCGTGG
Sequence-based reagentDL121_pos17_fwdThis PaperMutagenic PCR primerNNSAACGCCATGCCGTGGAAC
Sequence-based reagentDL121_pos18_fwdThis PaperMutagenic PCR primerNNSGCCATGCCGTGGAACCTG
Sequence-based reagentDL121_pos19_fwdThis PaperMutagenic PCR primerNNSATGCCGTGGAACCTGCCT
Sequence-based reagentDL121_pos20_fwdThis PaperMutagenic PCR primerNNSCCGTGGAACCTGCCTGCC
Sequence-based reagentDL121_pos21_fwdThis PaperMutagenic PCR primerNNSTGGAACCTGCCTGCCGAT
Sequence-based reagentDL121_pos22_fwdThis PaperMutagenic PCR primerNNSAACCTGCCTGCCGATCTC
Sequence-based reagentDL121_pos23_fwdThis PaperMutagenic PCR primerNNSCTGCCTGCCGATCTCGCC
Sequence-based reagentDL121_pos24_fwdThis PaperMutagenic PCR primerNNSCCTGCCGATCTCGCCTGG
Sequence-based reagentDL121_pos25_fwdThis PaperMutagenic PCR primerNNSGCCGATCTCGCCTGGTTT
Sequence-based reagentDL121_pos26_fwdThis PaperMutagenic PCR primerNNSGATCTCGCCTGGTTTAAACGC
Sequence-based reagentDL121_pos27_fwdThis PaperMutagenic PCR primerNNSCTCGCCTGGTTTAAACGCAACA
Sequence-based reagentDL121_pos28_fwdThis PaperMutagenic PCR primerNNSGCCTGGTTTAAACGCAACAC
Sequence-based reagentDL121_pos29_fwdThis PaperMutagenic PCR primerNNSTGGTTTAAACGCAACACCTTAAATAAAC
Sequence-based reagentDL121_pos30_fwdThis PaperMutagenic PCR primerNNSTTTAAACGCAACACCTTAAATAAACCCG
Sequence-based reagentDL121_pos31_fwdThis PaperMutagenic PCR primerNNSAAACGCAACACCTTAAATAAACCCGTG
Sequence-based reagentDL121_pos32_fwdThis PaperMutagenic PCR primerNNSCGCAACACCTTAAATAAACCCGT
Sequence-based reagentDL121_pos33_fwdThis PaperMutagenic PCR primerNNSAACACCTTAAATAAACCCGTGATTATGG
Sequence-based reagentDL121_pos34_fwdThis PaperMutagenic PCR primerNNSACCTTAAATAAACCCGTGATTATGGG
Sequence-based reagentDL121_pos35_fwdThis PaperMutagenic PCR primerNNSTTAAATAAACCCGTGATTATGGGCC
Sequence-based reagentDL121_pos36_fwdThis PaperMutagenic PCR primerNNSAATAAACCCGTGATTATGGGCC
Sequence-based reagentDL121_pos37_fwdThis PaperMutagenic PCR primerNNSAAACCCGTGATTATGGGCC
Sequence-based reagentDL121_pos38_fwdThis PaperMutagenic PCR primerNNSCCCGTGATTATGGGCCGC
Sequence-based reagentDL121_pos39_fwdThis PaperMutagenic PCR primerNNSGTGATTATGGGCCGCCATAC
Sequence-based reagentDL121_pos40_fwdThis PaperMutagenic PCR primerNNSATTATGGGCCGCCATACCT
Sequence-based reagentDL121_pos41_fwdThis PaperMutagenic PCR primerNNSATGGGCCGCCATACCTGG
Sequence-based reagentDL121_pos42_fwdThis PaperMutagenic PCR primerNNSGGCCGCCATACCTGGGAA
Sequence-based reagentDL121_pos43_fwdThis PaperMutagenic PCR primerNNSCGCCATACCTGGGAATCG
Sequence-based reagentDL121_pos44_fwdThis PaperMutagenic PCR primerNNSCATACCTGGGAATCGATCGGT
Sequence-based reagentDL121_pos45_fwdThis PaperMutagenic PCR primerNNSACCTGGGAATCGATCGGT
Sequence-based reagentDL121_pos46_fwdThis PaperMutagenic PCR primerNNSTGGGAATCGATCGGTCGT
Sequence-based reagentDL121_pos47_fwdThis PaperMutagenic PCR primerNNSGAATCGATCGGTCGTCCG
Sequence-based reagentDL121_pos48_fwdThis PaperMutagenic PCR primerNNSTCGATCGGTCGTCCGTTG
Sequence-based reagentDL121_pos49_fwdThis PaperMutagenic PCR primerNNSATCGGTCGTCCGTTGCCA
Sequence-based reagentDL121_pos50_fwdThis PaperMutagenic PCR primerNNSGGTCGTCCGTTGCCAGGA
Sequence-based reagentDL121_pos51_fwdThis PaperMutagenic PCR primerNNSCGTCCGTTGCCAGGACGC
Sequence-based reagentDL121_pos52_fwdThis PaperMutagenic PCR primerNNSCCGTTGCCAGGACGCAAA
Sequence-based reagentDL121_pos53_fwdThis PaperMutagenic PCR primerNNSTTGCCAGGACGCAAAAATATTATCC
Sequence-based reagentDL121_pos54_fwdThis PaperMutagenic PCR primerNNSCCAGGACGCAAAAATATTATCCTGAG
Sequence-based reagentDL121_pos55_fwdThis PaperMutagenic PCR primerNNSGGACGCAAAAATATTATCCTGAGCTC
Sequence-based reagentDL121_pos56_fwdThis PaperMutagenic PCR primerNNSCGCAAAAATATTATCCTGAGCTCACAA
Sequence-based reagentDL121_pos57_fwdThis PaperMutagenic PCR primerNNSAAAAATATTATCCTGAGCTCACAACCGG
Sequence-based reagentDL121_pos58_fwdThis PaperMutagenic PCR primerNNSAATATTATCCTGAGCTCACAACCGGGTA
Sequence-based reagentDL121_pos59_fwdThis PaperMutagenic PCR primerNNSATTATCCTGAGCTCACAACCG
Sequence-based reagentDL121_pos60_fwdThis PaperMutagenic PCR primerNNSATCCTGAGCTCACAACCG
Sequence-based reagentDL121_pos61_fwdThis PaperMutagenic PCR primerNNSCTGAGCTCACAACCGGGT
Sequence-based reagentDL121_pos62_fwdThis PaperMutagenic PCR primerNNSAGCTCACAACCGGGTACG
Sequence-based reagentDL121_pos63_fwdThis PaperMutagenic PCR primerNNSTCACAACCGGGTACGGAC
Sequence-based reagentDL121_pos64_fwdThis PaperMutagenic PCR primerNNSCAACCGGGTACGGACGAT
Sequence-based reagentDL121_pos65_fwdThis PaperMutagenic PCR primerNNSCCGGGTACGGACGATCGC
Sequence-based reagentDL121_pos66_fwdThis PaperMutagenic PCR primerNNSGGTACGGACGATCGCGTA
Sequence-based reagentDL121_pos67_fwdThis PaperMutagenic PCR primerNNSACGGACGATCGCGTAACG
Sequence-based reagentDL121_pos68_fwdThis PaperMutagenic PCR primerNNSGACGATCGCGTAACGTGG
Sequence-based reagentDL121_pos69_fwdThis PaperMutagenic PCR primerNNSGATCGCGTAACGTGGGTG
Sequence-based reagentDL121_pos70_fwdThis PaperMutagenic PCR primerNNSCGCGTAACGTGGGTGAAG
Sequence-based reagentDL121_pos71_fwdThis PaperMutagenic PCR primerNNSGTAACGTGGGTGAAGTCGG
Sequence-based reagentDL121_pos72_fwdThis PaperMutagenic PCR primerNNSACGTGGGTGAAGTCGGTG
Sequence-based reagentDL121_pos73_fwdThis PaperMutagenic PCR primerNNSTGGGTGAAGTCGGTGGAT
Sequence-based reagentDL121_pos74_fwd2This PaperMutagenic PCR primerNNSGTGAAGTCGGTGGATGAAG
Sequence-based reagentDL121_pos75_fwdThis PaperMutagenic PCR primerNNSAAGTCGGTGGATGAAGCAATTG
Sequence-based reagentDL121_pos76_fwdThis PaperMutagenic PCR primerNNSTCGGTGGATGAAGCAATTGC
Sequence-based reagentDL121_pos77_fwdThis PaperMutagenic PCR primerNNSGTGGATGAAGCAATTGCGG
Sequence-based reagentDL121_pos78_fwdThis PaperMutagenic PCR primerNNSGATGAAGCAATTGCGGCG
Sequence-based reagentDL121_pos79_fwdThis PaperMutagenic PCR primerNNSGAAGCAATTGCGGCGTGT
Sequence-based reagentDL121_pos80_fwdThis PaperMutagenic PCR primerNNSGCAATTGCGGCGTGTGGT
Sequence-based reagentDL121_pos81_fwdThis PaperMutagenic PCR primerNNSATTGCGGCGTGTGGTGAC
Sequence-based reagentDL121_pos82_fwdThis PaperMutagenic PCR primerNNSGCGGCGTGTGGTGACGTAC
Sequence-based reagentDL121_pos83_fwdThis PaperMutagenic PCR primerNNSGCGTGTGGTGACGTACCA
Sequence-based reagentDL121_pos84_fwdThis PaperMutagenic PCR primerNNSTGTGGTGACGTACCAGAAATCAT
Sequence-based reagentDL121_pos85_fwdThis PaperMutagenic PCR primerNNSGGTGACGTACCAGAAATCATGG
Sequence-based reagentDL121_pos86_fwdThis PaperMutagenic PCR primerNNSGACGTACCAGAAATCATGGTGATTG
Sequence-based reagentDL121_pos87_fwdThis PaperMutagenic PCR primerNNSGTACCAGAAATCATGGTGATTGGC
Sequence-based reagentDL121_pos88_fwdThis PaperMutagenic PCR primerNNSCCAGAAATCATGGTGATTGGC
Sequence-based reagentDL121_pos89_fwdThis PaperMutagenic PCR primerNNSGAAATCATGGTGATTGGCGG
Sequence-based reagentDL121_pos90_fwdThis PaperMutagenic PCR primerNNSATCATGGTGATTGGCGGC
Sequence-based reagentDL121_pos91_fwdThis PaperMutagenic PCR primerNNSATGGTGATTGGCGGCGGC
Sequence-based reagentDL121_pos92_fwdThis PaperMutagenic PCR primerNNSGTGATTGGCGGCGGCCGC
Sequence-based reagentDL121_pos93_fwdThis PaperMutagenic PCR primerNNSATTGGCGGCGGCCGCGTT
Sequence-based reagentDL121_pos94_fwdThis PaperMutagenic PCR primerNNSGGCGGCGGCCGCGTTTAT
Sequence-based reagentDL121_pos95_fwdThis PaperMutagenic PCR primerNNSGGCGGCCGCGTTTATGAA
Sequence-based reagentDL121_pos96_fwdThis PaperMutagenic PCR primerNNSGGCCGCGTTTATGAACAGTT
Sequence-based reagentDL121_pos97_fwdThis PaperMutagenic PCR primerNNSCGCGTTTATGAACAGTTCTTGC
Sequence-based reagentDL121_pos98_fwdThis PaperMutagenic PCR primerNNSGTTTATGAACAGTTCTTGCCAAAAGCGC
Sequence-based reagentDL121_pos99_fwdThis PaperMutagenic PCR primerNNSTATGAACAGTTCTTGCCAAAAGCGCAAA
Sequence-based reagentDL121_pos100_fwdThis PaperMutagenic PCR primerNNSGAACAGTTCTTGCCAAAAGCGCAAAAGC
Sequence-based reagentDL121_pos101_fwdThis PaperMutagenic PCR primerNNSCAGTTCTTGCCAAAAGCGCAAAAGCTTT
Sequence-based reagentDL121_pos102_fwdThis PaperMutagenic PCR primerNNSTTCTTGCCAAAAGCGCAAAAG
Sequence-based reagentDL121_pos103_fwdThis PaperMutagenic PCR primerNNSTTGCCAAAAGCGCAAAAGC
Sequence-based reagentDL121_pos104_fwdThis PaperMutagenic PCR primerNNSCCAAAAGCGCAAAAGCTTTATCTG
Sequence-based reagentDL121_pos105_fwdThis PaperMutagenic PCR primerNNSAAAGCGCAAAAGCTTTATCTGACG
Sequence-based reagentDL121_pos106_fwdThis PaperMutagenic PCR primerNNSGCGCAAAAGCTTTATCTGACG
Sequence-based reagentDL121_pos107_fwdThis PaperMutagenic PCR primerNNSCAAAAGCTTTATCTGACGCATATCGAC
Sequence-based reagentDL121_pos108_fwdThis PaperMutagenic PCR primerNNSAAGCTTTATCTGACGCATATCGAC
Sequence-based reagentDL121_pos109_fwdThis PaperMutagenic PCR primerNNSCTTTATCTGACGCATATCGACGC
Sequence-based reagentDL121_pos110_fwdThis PaperMutagenic PCR primerNNSTATCTGACGCATATCGACGCA
Sequence-based reagentDL121_pos111_fwdThis PaperMutagenic PCR primerNNSCTGACGCATATCGACGCAG
Sequence-based reagentDL121_pos112_fwdThis PaperMutagenic PCR primerNNSACGCATATCGACGCAGAAGT
Sequence-based reagentDL121_pos113_fwdThis PaperMutagenic PCR primerNNSCATATCGACGCAGAAGTGGAAC
Sequence-based reagentDL121_pos114_fwdThis PaperMutagenic PCR primerNNSATCGACGCAGAAGTGGAACT
Sequence-based reagentDL121_pos115_fwdThis PaperMutagenic PCR primerNNSGACGCAGAAGTGGAACTGG
Sequence-based reagentDL121_pos116_fwdThis PaperMutagenic PCR primerNNSGCAGAAGTGGAACTGGCC
Sequence-based reagentDL121_pos117_fwdThis PaperMutagenic PCR primerNNSGAAGTGGAACTGGCCACC
Sequence-based reagentDL121_pos118_fwdThis PaperMutagenic PCR primerNNSGTGGAACTGGCCACCACT
Sequence-based reagentDL121_pos119_fwdThis PaperMutagenic PCR primerNNSGAACTGGCCACCACTCTAGA
Sequence-based reagentDL121_pos120_fwdThis PaperMutagenic PCR primerNNSCTGGCCACCACTCTAGAG
Sequence-based reagentDL121_pos121_fwdThis PaperMutagenic PCR primerNNSGACACCCATTTCCCGGATTAC
Sequence-based reagentDL121_pos122_fwdThis PaperMutagenic PCR primerNNSACCCATTTCCCGGATTACGA
Sequence-based reagentDL121_pos123_fwdThis PaperMutagenic PCR primerNNSCATTTCCCGGATTACGAGCC
Sequence-based reagentDL121_pos124_fwdThis PaperMutagenic PCR primerNNSTTCCCGGATTACGAGCCG
Sequence-based reagentDL121_pos125_fwdThis PaperMutagenic PCR primerNNSCCGGATTACGAGCCGGAT
Sequence-based reagentDL121_pos126_fwdThis PaperMutagenic PCR primerNNSGATTACGAGCCGGATGACTG
Sequence-based reagentDL121_pos127_fwdThis PaperMutagenic PCR primerNNSTACGAGCCGGATGACTGG
Sequence-based reagentDL121_pos128_fwdThis PaperMutagenic PCR primerNNSGAGCCGGATGACTGGGAA
Sequence-based reagentDL121_pos129_fwdThis PaperMutagenic PCR primerNNSCCGGATGACTGGGAATCG
Sequence-based reagentDL121_pos130_fwdThis PaperMutagenic PCR primerNNSGATGACTGGGAATCGGTATTCAG
Sequence-based reagentDL121_pos131_fwdThis PaperMutagenic PCR primerNNSGACTGGGAATCGGTATTCAGC
Sequence-based reagentDL121_pos132_fwdThis PaperMutagenic PCR primerNNSTGGGAATCGGTATTCAGCGAATT
Sequence-based reagentDL121_pos133_fwdThis PaperMutagenic PCR primerNNSGAATCGGTATTCAGCGAATTCCAC
Sequence-based reagentDL121_pos134_fwdThis PaperMutagenic PCR primerNNSTCGGTATTCAGCGAATTCCAC
Sequence-based reagentDL121_pos135_fwdThis PaperMutagenic PCR primerNNSGTATTCAGCGAATTCCACGATG
Sequence-based reagentDL121_pos136_fwdThis PaperMutagenic PCR primerNNSTTCAGCGAATTCCACGATGC
Sequence-based reagentDL121_pos137_fwdThis PaperMutagenic PCR primerNNSAGCGAATTCCACGATGCTG
Sequence-based reagentDL121_pos138_fwdThis PaperMutagenic PCR primerNNSGAATTCCACGATGCTGATGC
Sequence-based reagentDL121_pos139_fwdThis PaperMutagenic PCR primerNNSTTCCACGATGCTGATGCG
Sequence-based reagentDL121_pos140_fwdThis PaperMutagenic PCR primerNNSCACGATGCTGATGCGCAG
Sequence-based reagentDL121_pos141_fwdThis PaperMutagenic PCR primerNNSGATGCTGATGCGCAGAACT
Sequence-based reagentDL121_pos142_fwdThis PaperMutagenic PCR primerNNSGCTGATGCGCAGAACTCTC
Sequence-based reagentDL121_pos143_fwdThis PaperMutagenic PCR primerNNSGATGCGCAGAACTCTCACAG
Sequence-based reagentDL121_pos144_fwdThis PaperMutagenic PCR primerNNSGCGCAGAACTCTCACAGC
Sequence-based reagentDL121_pos145_fwdThis PaperMutagenic PCR primerNNSCAGAACTCTCACAGCTATTGCTTTG
Sequence-based reagentDL121_pos146_fwdThis PaperMutagenic PCR primerNNSAACTCTCACAGCTATTGCTTTGAGATT
Sequence-based reagentDL121_pos147_fwdThis PaperMutagenic PCR primerNNSTCTCACAGCTATTGCTTTGAGATTCT
Sequence-based reagentDL121_pos148_fwdThis PaperMutagenic PCR primerNNSCACAGCTATTGCTTTGAGATTCTGG
Sequence-based reagentDL121_pos149_fwdThis PaperMutagenic PCR primerNNSAGCTATTGCTTTGAGATTCTGGAG
Sequence-based reagentDL121_pos150_fwdThis PaperMutagenic PCR primerNNSTATTGCTTTGAGATTCTGGAGCG
Sequence-based reagentDL121_pos151_fwdThis PaperMutagenic PCR primerNNSTGCTTTGAGATTCTGGAGCG
Sequence-based reagentDL121_pos152_fwdThis PaperMutagenic PCR primerNNSTTTGAGATTCTGGAGCGGC
Sequence-based reagentDL121_pos153_fwdThis PaperMutagenic PCR primerNNSGAGATTCTGGAGCGGCGG
Sequence-based reagentDL121_pos154_fwdThis PaperMutagenic PCR primerNNSATTCTGGAGCGGCGGTAA
Sequence-based reagentDL121_pos155_fwdThis PaperMutagenic PCR primerNNSCTGGAGCGGCGGTAACAT
Sequence-based reagentDL121_pos156_fwdThis PaperMutagenic PCR primerNNSGAGCGGCGGTAACATCCG
Sequence-based reagentDL121_pos157_fwdThis PaperMutagenic PCR primerNNSCGGCGGTAACATCCGTCG
Sequence-based reagentDL121_pos158_fwdThis PaperMutagenic PCR primerNNSCGGTAACATCCGTCGACAAG
Sequence-based reagentDL121_pos159_fwdThis PaperMutagenic PCR primerNNSTAACATCCGTCGACAAGCTTG
Sequence-based reagentDL121_pos1_revThis PaperMutagenic PCR primerCGGATCCTGGCTGTGGTG
Sequence-based reagentDL121_pos2_revThis PaperMutagenic PCR primerCATCGGATCCTGGCTGTG
Sequence-based reagentDL121_pos3_revThis PaperMutagenic PCR primerGATCATCGGATCCTGGCTG
Sequence-based reagentDL121_pos4_revThis PaperMutagenic PCR primerACTGATCATCGGATCCTGG
Sequence-based reagentDL121_pos5_revThis PaperMutagenic PCR primerCAGACTGATCATCGGATCCTG
Sequence-based reagentDL121_pos6_revThis PaperMutagenic PCR primerAATCAGACTGATCATCGGATCCTG
Sequence-based reagentDL121_pos7_revThis PaperMutagenic PCR primerCGCAATCAGACTGATCATCGG
Sequence-based reagentDL121_pos8_revThis PaperMutagenic PCR primerCGCCGCAATCAGACTGATC
Sequence-based reagentDL121_pos9_revThis PaperMutagenic PCR primerTAACGCCGCAATCAGACTGA
Sequence-based reagentDL121_pos10_revThis PaperMutagenic PCR primerCGCTAACGCCGCAATCAG
Sequence-based reagentDL121_pos11_revThis PaperMutagenic PCR primerTACCGCTAACGCCGCAAT
Sequence-based reagentDL121_pos12_revThis PaperMutagenic PCR primerATCTACCGCTAACGCCGC
Sequence-based reagentDL121_pos13_revThis PaperMutagenic PCR primerGCGATCTACCGCTAACGC
Sequence-based reagentDL121_pos14_revThis PaperMutagenic PCR primerAACGCGATCTACCGCTAAC
Sequence-based reagentDL121_pos15_revThis PaperMutagenic PCR primerGATAACGCGATCTACCGCTAAC
Sequence-based reagentDL121_pos16_revThis PaperMutagenic PCR primerGCCGATAACGCGATCTACC
Sequence-based reagentDL121_pos17_revThis PaperMutagenic PCR primerCATGCCGATAACGCGATCTAC
Sequence-based reagentDL121_pos18_revThis PaperMutagenic PCR primerTTCCATGCCGATAACGCG
Sequence-based reagentDL121_pos19_revThis PaperMutagenic PCR primerGTTTTCCATGCCGATAACGC
Sequence-based reagentDL121_pos20_revThis PaperMutagenic PCR primerGGCGTTTTCCATGCCGATAACG
Sequence-based reagentDL121_pos21_revThis PaperMutagenic PCR primerCATGGCGTTTTCCATGCC
Sequence-based reagentDL121_pos22_revThis PaperMutagenic PCR primerCGGCATGGCGTTTTCCAT
Sequence-based reagentDL121_pos23_revThis PaperMutagenic PCR primerCCACGGCATGGCGTTTTC
Sequence-based reagentDL121_pos24_revThis PaperMutagenic PCR primerGTTCCACGGCATGGCGTT
Sequence-based reagentDL121_pos25_revThis PaperMutagenic PCR primerCAGGTTCCACGGCATGGC
Sequence-based reagentDL121_pos26_revThis PaperMutagenic PCR primerAGGCAGGTTCCACGGCAT
Sequence-based reagentDL121_pos27_revThis PaperMutagenic PCR primerGGCAGGCAGGTTCCACGG
Sequence-based reagentDL121_pos28_revThis PaperMutagenic PCR primerATCGGCAGGCAGGTTCCA
Sequence-based reagentDL121_pos29_revThis PaperMutagenic PCR primerGAGATCGGCAGGCAGGTT
Sequence-based reagentDL121_pos30_revThis PaperMutagenic PCR primerGGCGAGATCGGCAGGCAG
Sequence-based reagentDL121_pos31_revThis PaperMutagenic PCR primerCCAGGCGAGATCGGCAGG
Sequence-based reagentDL121_pos32_revThis PaperMutagenic PCR primerAAACCAGGCGAGATCGGC
Sequence-based reagentDL121_pos33_revThis PaperMutagenic PCR primerTTTAAACCAGGCGAGATCGG
Sequence-based reagentDL121_pos34_revThis PaperMutagenic PCR primerGCGTTTAAACCAGGCGAGAT
Sequence-based reagentDL121_pos35_revThis PaperMutagenic PCR primerGTTGCGTTTAAACCAGGCGA
Sequence-based reagentDL121_pos36_revThis PaperMutagenic PCR primerGGTGTTGCGTTTAAACCAGG
Sequence-based reagentDL121_pos37_revThis PaperMutagenic PCR primerTAAGGTGTTGCGTTTAAACCAGG
Sequence-based reagentDL121_pos38_revThis PaperMutagenic PCR primerATTTAAGGTGTTGCGTTTAAACCAGG
Sequence-based reagentDL121_pos39_revThis PaperMutagenic PCR primerTTTATTTAAGGTGTTGCGTTTAAACCAG
Sequence-based reagentDL121_pos40_revThis PaperMutagenic PCR primerGGGTTTATTTAAGGTGTTGCGTTTAAAC
Sequence-based reagentDL121_pos41_revThis PaperMutagenic PCR primerCACGGGTTTATTTAAGGTGTTGCGT
Sequence-based reagentDL121_pos42_revThis PaperMutagenic PCR primerAATCACGGGTTTATTTAAGGTGTTGC
Sequence-based reagentDL121_pos43_revThis PaperMutagenic PCR primerCATAATCACGGGTTTATTTAAGGTGTTG
Sequence-based reagentDL121_pos44_revThis PaperMutagenic PCR primerGCCCATAATCACGGGTTTATTTAAGG
Sequence-based reagentDL121_pos45_revThis PaperMutagenic PCR primerGCGGCCCATAATCACGGG
Sequence-based reagentDL121_pos46_revThis PaperMutagenic PCR primerATGGCGGCCCATAATCAC
Sequence-based reagentDL121_pos47_revThis PaperMutagenic PCR primerGGTATGGCGGCCCATAATC
Sequence-based reagentDL121_pos48_revThis PaperMutagenic PCR primerCCAGGTATGGCGGCCCATA
Sequence-based reagentDL121_pos49_revThis PaperMutagenic PCR primerTTCCCAGGTATGGCGGCC
Sequence-based reagentDL121_pos50_revThis PaperMutagenic PCR primerCGATTCCCAGGTATGGCG
Sequence-based reagentDL121_pos51_revThis PaperMutagenic PCR primerGATCGATTCCCAGGTATGGCG
Sequence-based reagentDL121_pos52_revThis PaperMutagenic PCR primerACCGATCGATTCCCAGGTATG
Sequence-based reagentDL121_pos53_revThis PaperMutagenic PCR primerACGACCGATCGATTCCCA
Sequence-based reagentDL121_pos54_revThis PaperMutagenic PCR primerCGGACGACCGATCGATTC
Sequence-based reagentDL121_pos55_revThis PaperMutagenic PCR primerCAACGGACGACCGATCGA
Sequence-based reagentDL121_pos56_revThis PaperMutagenic PCR primerTGGCAACGGACGACCGAT
Sequence-based reagentDL121_pos57_revThis PaperMutagenic PCR primerTCCTGGCAACGGACGACC
Sequence-based reagentDL121_pos58_revThis PaperMutagenic PCR primerGCGTCCTGGCAACGGACG
Sequence-based reagentDL121_pos59_revThis PaperMutagenic PCR primerTTTGCGTCCTGGCAACGG
Sequence-based reagentDL121_pos60_revThis PaperMutagenic PCR primerATTTTTGCGTCCTGGCAAC
Sequence-based reagentDL121_pos61_revThis PaperMutagenic PCR primerAATATTTTTGCGTCCTGGCAAC
Sequence-based reagentDL121_pos62_revThis PaperMutagenic PCR primerGATAATATTTTTGCGTCCTGGCAAC
Sequence-based reagentDL121_pos63_revThis PaperMutagenic PCR primerCAGGATAATATTTTTGCGTCCTGGC
Sequence-based reagentDL121_pos64_revThis PaperMutagenic PCR primerGCTCAGGATAATATTTTTGCGTCCTG
Sequence-based reagentDL121_pos65_revThis PaperMutagenic PCR primerTGAGCTCAGGATAATATTTTTGCGTCCT
Sequence-based reagentDL121_pos66_revThis PaperMutagenic PCR primerTTGTGAGCTCAGGATAATATTTTTGCG
Sequence-based reagentDL121_pos67_revThis PaperMutagenic PCR primerCGGTTGTGAGCTCAGGATAATATTTTTG
Sequence-based reagentDL121_pos68_revThis PaperMutagenic PCR primerACCCGGTTGTGAGCTCAG
Sequence-based reagentDL121_pos69_revThis PaperMutagenic PCR primerCGTACCCGGTTGTGAGCT
Sequence-based reagentDL121_pos70_revThis PaperMutagenic PCR primerGTCCGTACCCGGTTGTGA
Sequence-based reagentDL121_pos71_revThis PaperMutagenic PCR primerATCGTCCGTACCCGGTTG
Sequence-based reagentDL121_pos72_revThis PaperMutagenic PCR primerGCGATCGTCCGTACCCGG
Sequence-based reagentDL121_pos73_revThis PaperMutagenic PCR primerTACGCGATCGTCCGTACC
Sequence-based reagentDL121_pos74_rev2This PaperMutagenic PCR primerCGTTACGCGATCGTCC
Sequence-based reagentDL121_pos75_revThis PaperMutagenic PCR primerCCACGTTACGCGATCGTC
Sequence-based reagentDL121_pos76_revThis PaperMutagenic PCR primerCACCCACGTTACGCGATC
Sequence-based reagentDL121_pos77_revThis PaperMutagenic PCR primerCTTCACCCACGTTACGCG
Sequence-based reagentDL121_pos78_revThis PaperMutagenic PCR primerCGACTTCACCCACGTTACG
Sequence-based reagentDL121_pos79_revThis PaperMutagenic PCR primerCACCGACTTCACCCACGT
Sequence-based reagentDL121_pos80_revThis PaperMutagenic PCR primerATCCACCGACTTCACCCA
Sequence-based reagentDL121_pos81_revThis PaperMutagenic PCR primerTTCATCCACCGACTTCACC
Sequence-based reagentDL121_pos82_revThis PaperMutagenic PCR primerTGCTTCATCCACCGACTTCACC
Sequence-based reagentDL121_pos83_revThis PaperMutagenic PCR primerAATTGCTTCATCCACCGACTTC
Sequence-based reagentDL121_pos84_revThis PaperMutagenic PCR primerCGCAATTGCTTCATCCACC
Sequence-based reagentDL121_pos85_revThis PaperMutagenic PCR primerCGCCGCAATTGCTTCATC
Sequence-based reagentDL121_pos86_revThis PaperMutagenic PCR primerACACGCCGCAATTGCTTC
Sequence-based reagentDL121_pos87_revThis PaperMutagenic PCR primerACCACACGCCGCAATTGC
Sequence-based reagentDL121_pos88_revThis PaperMutagenic PCR primerGTCACCACACGCCGCAAT
Sequence-based reagentDL121_pos89_rev2This PaperMutagenic PCR primerTACGTCACCACACGCC
Sequence-based reagentDL121_pos90_revThis PaperMutagenic PCR primerTGGTACGTCACCACACGC
Sequence-based reagentDL121_pos91_revThis PaperMutagenic PCR primerTTCTGGTACGTCACCACACGC
Sequence-based reagentDL121_pos92_revThis PaperMutagenic PCR primerGATTTCTGGTACGTCACCACACGCC
Sequence-based reagentDL121_pos93_revThis PaperMutagenic PCR primerCATGATTTCTGGTACGTCACCACACGC
Sequence-based reagentDL121_pos94_revThis PaperMutagenic PCR primerCACCATGATTTCTGGTACGTCACCACA
Sequence-based reagentDL121_pos95_revThis PaperMutagenic PCR primerAATCACCATGATTTCTGGTACGTCA
Sequence-based reagentDL121_pos96_revThis PaperMutagenic PCR primerGCCAATCACCATGATTTCTGGTAC
Sequence-based reagentDL121_pos97_revThis PaperMutagenic PCR primerGCCGCCAATCACCATGATTT
Sequence-based reagentDL121_pos98_revThis PaperMutagenic PCR primerGCCGCCGCCAATCACCATG
Sequence-based reagentDL121_pos99_revThis PaperMutagenic PCR primerGCGGCCGCCGCCAATCAC
Sequence-based reagentDL121_pos100_revThis PaperMutagenic PCR primerAACGCGGCCGCCGCCAAT
Sequence-based reagentDL121_pos101_revThis PaperMutagenic PCR primerATAAACGCGGCCGCCGCC
Sequence-based reagentDL121_pos102_revThis PaperMutagenic PCR primerTTCATAAACGCGGCCGCC
Sequence-based reagentDL121_pos103_revThis PaperMutagenic PCR primerCTGTTCATAAACGCGGCC
Sequence-based reagentDL121_pos104_revThis PaperMutagenic PCR primerGAACTGTTCATAAACGCGGC
Sequence-based reagentDL121_pos105_revThis PaperMutagenic PCR primerCAAGAACTGTTCATAAACGCGG
Sequence-based reagentDL121_pos106_revThis PaperMutagenic PCR primerTGGCAAGAACTGTTCATAAACGC
Sequence-based reagentDL121_pos107_revThis PaperMutagenic PCR primerTTTTGGCAAGAACTGTTCATAAACG
Sequence-based reagentDL121_pos108_revThis PaperMutagenic PCR primerCGCTTTTGGCAAGAACTGTTCATAAA
Sequence-based reagentDL121_pos109_revThis PaperMutagenic PCR primerTTGCGCTTTTGGCAAGAACT
Sequence-based reagentDL121_pos110_revThis PaperMutagenic PCR primerCTTTTGCGCTTTTGGCAAGAAC
Sequence-based reagentDL121_pos111_revThis PaperMutagenic PCR primerAAGCTTTTGCGCTTTTGGC
Sequence-based reagentDL121_pos112_revThis PaperMutagenic PCR primerATAAAGCTTTTGCGCTTTTGGCA
Sequence-based reagentDL121_pos113_revThis PaperMutagenic PCR primerCAGATAAAGCTTTTGCGCTTTTGG
Sequence-based reagentDL121_pos114_revThis PaperMutagenic PCR primerCGTCAGATAAAGCTTTTGCGCTTT
Sequence-based reagentDL121_pos115_revThis PaperMutagenic PCR primerATGCGTCAGATAAAGCTTTTGCG
Sequence-based reagentDL121_pos116_revThis PaperMutagenic PCR primerGATATGCGTCAGATAAAGCTTTTGC
Sequence-based reagentDL121_pos117_revThis PaperMutagenic PCR primerGTCGATATGCGTCAGATAAAGCTTTTG
Sequence-based reagentDL121_pos118_revThis PaperMutagenic PCR primerTGCGTCGATATGCGTCAGATAAA
Sequence-based reagentDL121_pos119_revThis PaperMutagenic PCR primerTTCTGCGTCGATATGCGTCA
Sequence-based reagentDL121_pos120_revThis PaperMutagenic PCR primerCACTTCTGCGTCGATATGCG
Sequence-based reagentDL121_pos121_revThis PaperMutagenic PCR primerGTCGATGTTCTCGGCGGT
Sequence-based reagentDL121_pos122_revThis PaperMutagenic PCR primerGCCGTCGATGTTCTCGGC
Sequence-based reagentDL121_pos123_revThis PaperMutagenic PCR primerGTCGCCGTCGATGTTCTC
Sequence-based reagentDL121_pos124_revThis PaperMutagenic PCR primerGGTGTCGCCGTCGATGTT
Sequence-based reagentDL121_pos125_revThis PaperMutagenic PCR primerATGGGTGTCGCCGTCGAT
Sequence-based reagentDL121_pos126_revThis PaperMutagenic PCR primerGAAATGGGTGTCGCCGTC
Sequence-based reagentDL121_pos127_revThis PaperMutagenic PCR primerCGGGAAATGGGTGTCGCC
Sequence-based reagentDL121_pos128_revThis PaperMutagenic PCR primerATCCGGGAAATGGGTGTC
Sequence-based reagentDL121_pos129_revThis PaperMutagenic PCR primerGTAATCCGGGAAATGGGTGTC
Sequence-based reagentDL121_pos130_revThis PaperMutagenic PCR primerCTCGTAATCCGGGAAATGGG
Sequence-based reagentDL121_pos131_revThis PaperMutagenic PCR primerCGGCTCGTAATCCGGGAA
Sequence-based reagentDL121_pos132_revThis PaperMutagenic PCR primerATCCGGCTCGTAATCCGG
Sequence-based reagentDL121_pos133_revThis PaperMutagenic PCR primerGTCATCCGGCTCGTAATCC
Sequence-based reagentDL121_pos134_revThis PaperMutagenic PCR primerCCAGTCATCCGGCTCGTA
Sequence-based reagentDL121_pos135_revThis PaperMutagenic PCR primerTTCCCAGTCATCCGGCTC
Sequence-based reagentDL121_pos136_revThis PaperMutagenic PCR primerCGATTCCCAGTCATCCGG
Sequence-based reagentDL121_pos137_revThis PaperMutagenic PCR primerTACCGATTCCCAGTCATCCG
Sequence-based reagentDL121_pos138_revThis PaperMutagenic PCR primerGAATACCGATTCCCAGTCATCC
Sequence-based reagentDL121_pos139_revThis PaperMutagenic PCR primerGCTGAATACCGATTCCCAGTC
Sequence-based reagentDL121_pos140_revThis PaperMutagenic PCR primerTTCGCTGAATACCGATTCCCA
Sequence-based reagentDL121_pos141_revThis PaperMutagenic PCR primerGAATTCGCTGAATACCGATTCCC
Sequence-based reagentDL121_pos142_revThis PaperMutagenic PCR primerGTGGAATTCGCTGAATACCGATTC
Sequence-based reagentDL121_pos143_revThis PaperMutagenic PCR primerATCGTGGAATTCGCTGAATACC
Sequence-based reagentDL121_pos144_revThis PaperMutagenic PCR primerAGCATCGTGGAATTCGCTG
Sequence-based reagentDL121_pos145_revThis PaperMutagenic PCR primerATCAGCATCGTGGAATTCGC
Sequence-based reagentDL121_pos146_revThis PaperMutagenic PCR primerCGCATCAGCATCGTGGAATT
Sequence-based reagentDL121_pos147_revThis PaperMutagenic PCR primerCTGCGCATCAGCATCGTG
Sequence-based reagentDL121_pos148_revThis PaperMutagenic PCR primerGTTCTGCGCATCAGCATC
Sequence-based reagentDL121_pos149_revThis PaperMutagenic PCR primerAGAGTTCTGCGCATCAGC
Sequence-based reagentDL121_pos150_revThis PaperMutagenic PCR primerGTGAGAGTTCTGCGCATCAG
Sequence-based reagentDL121_pos151_revThis PaperMutagenic PCR primerGCTGTGAGAGTTCTGCGC
Sequence-based reagentDL121_pos152_revThis PaperMutagenic PCR primerATAGCTGTGAGAGTTCTGCG
Sequence-based reagentDL121_pos153_revThis PaperMutagenic PCR primerGCAATAGCTGTGAGAGTTCTGC
Sequence-based reagentDL121_pos154_revThis PaperMutagenic PCR primerAAAGCAATAGCTGTGAGAGTTCTG
Sequence-based reagentDL121_pos155_revThis PaperMutagenic PCR primerCTCAAAGCAATAGCTGTGAGAGTTC
Sequence-based reagentDL121_pos156_revThis PaperMutagenic PCR primerAATCTCAAAGCAATAGCTGTGAGAGTT
Sequence-based reagentDL121_pos157_revThis PaperMutagenic PCR primerCAGAATCTCAAAGCAATAGCTGTGAG
Sequence-based reagentDL121_pos158_revThis PaperMutagenic PCR primerCTCCAGAATCTCAAAGCAATAGCTG
Sequence-based reagentDL121_pos159_revThis PaperMutagenic PCR primerCCGCTCCAGAATCTCAAAGC
Sequence-based reagentDL121_E154R_FThis PaperMutagenic PCR primerctctcacagctattgctttaggattctggagcggcggtaa
Sequence-based reagentDL121_E154R_RThis PaperMutagenic PCR primerttaccgccgctccagaatcctaaagcaatagctgtgagag
Sequence-based reagentDL121_D122W_FThis PaperMutagenic PCR primergtaatccgggaaatgggtccagccgtcgatgttctcggc
Sequence-based reagentDL121_D122W_RThis PaperMutagenic PCR primergccgagaacatcgacggctggacccatttcccggattac
Sequence-based reagentDL121_D127W_FThis PaperMutagenic PCR primercagtcatccggctcgtaccacgggaaatgggtgtcgc
Sequence-based reagentDL121_D127W_RThis PaperMutagenic PCR primergcgacacccatttcccgtggtacgagccggatgactg
Sequence-based reagentDL121_M16A_FThis PaperMutagenic PCR primercggcatggcgttttccgcgccgataacgcgatct
Sequence-based reagentDL121_M16A_RThis PaperMutagenic PCR primeragatcgcgttatcggcgcggaaaacgccatgccg
Sequence-based reagentDL121_A9N_FThis PaperMutagenic PCR primercatgccgataacgcgatctacatttaacgccgcaatcagactgatc
Sequence-based reagentDL121_A9N_RThis PaperMutagenic PCR primergatcagtctgattgcggcgttaaatgtagatcgcgttatcggcatg
Sequence-based reagentDL121_R52K_FThis PaperMutagenic PCR primertcctggcaacggcttaccgatcgattcccaggtatggc
Sequence-based reagentDL121_R52K_RThis PaperMutagenic PCR primergccatacctgggaatcgatcggtaagccgttgccagga
Sequence-based reagentDL121_E120P_FThis PaperMutagenic PCR primerctagagtggtggccagtggcacttctgcgtcgatat
Sequence-based reagentDL121_E120P_RThis PaperMutagenic PCR primeratatcgacgcagaagtgccactggccaccactctag
Sequence-based reagentDL121_S148C_FThis PaperMutagenic PCR primeraagcaatagctgtgacagttctgcgcatcagcatc
Sequence-based reagentDL121_S148C_RThis PaperMutagenic PCR primergatgctgatgcgcagaactgtcacagctattgctt
Sequence-based reagentDL121_H124Q_FThis PaperMutagenic PCR primertcgtaatccgggaactgggtgtcgccgtc
Sequence-based reagentDL121_H12RQ_RThis PaperMutagenic PCR primergacggcgacacccagttcccggattacga
Sequence-based reagentDL121_D27N_FThis PaperMutagenic PCR primeraaaccaggcgagattggcaggcaggttcc
Sequence-based reagentDL121_D27N_RThis PaperMutagenic PCR primerggaacctgcctgccaatctcgcctggttt
Sequence-based reagentDL121_D87A_FThis PaperMutagenic PCR primercatgatttctggtacggcaccacacgccgcaat
Sequence-based reagentDL121_D87A_RThis PaperMutagenic PCR primerattgcggcgtgtggtgccgtaccagaaatcatg
Sequence-based reagentThrombin_to_TEV_FThis PaperMutagenic PCR primercttccagggtcatgggatgatgatcagtctgattgc
Sequence-based reagentThrombin_to_TEV_RThis PaperMutagenic PCR primertacaggttctcaccaccgtggtggtggtg
Sequence-based reagentDL121_SL1V2_FThis PaperRound one Amplicon PCR primercactctttccctacacgacgctcttccgatctnnnnatcaccatcatcaccacagc
Sequence-based reagentDL121_SL1V2_RThis PaperRound one Amplicon PCR primertgactggagttcagacgtgtgctcttccgatctnnnnaccgatcgattcccaggta
Sequence-based reagentDL121_SL2V2_FThis PaperRound one Amplicon PCR primercactctttccctacacgacgctcttccgatctnnnngcaacaccttaaataaacccg
Sequence-based reagentDL121_SL2V2_RThis PaperRound one Amplicon PCR primertgactggagttcagacgtgtgctcttccgatctnnnngatttctggtacgtcaccaca
Sequence-based reagentDL121_SL3V2_FThis PaperRound one Amplicon PCR primercactctttccctacacgacgctcttccgatctnnnngtaacgtgggtgaagtcg
Sequence-based reagentDL121_SL3V2_RThis PaperRound one Amplicon PCR primertgactggagttcagacgtgtgctcttccgatctnnnnctcgatgcgctctagagtg
Sequence-based reagentDL121_SL4V2_FThis PaperRound one Amplicon PCR primercactctttccctacacgacgctcttccgatctnnnnaagaagaccgccgagaacat
Sequence-based reagentDL121_SL4V2_RThis PaperRound one Amplicon PCR primertgactggagttcagacgtgtgctcttccgatctnnnncttaagcattatgcggccg
Sequence-based reagentDL121_CLV3_FThis PaperRound one Amplicon PCR primercactctttccctacacgacgctcttccgatctnnnngacacccatttcccggattacgagc
Sequence-based reagentDL_WTTS_R3This PaperRound one Amplicon PCR primertgactggagttcagacgtgtgctcttccgatctnnnngccgtgtacaatacgattactttctg
Sequence-based reagentD501Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacactatagcctacactctttccctacacgac
Sequence-based reagentD502Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacacatagaggcacactctttccctacacgac
Sequence-based reagentD503Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacaccctatcctacactctttccctacacgac
Sequence-based reagentD504Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacacggctctgaacactctttccctacacgac
Sequence-based reagentD505Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacacaggcgaagacactctttccctacacgac
Sequence-based reagentD506Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacactaatcttaacactctttccctacacgac
Sequence-based reagentD507Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacaccaggacgtacactctttccctacacgac
Sequence-based reagentD508Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primeraatgatacggcgaccaccgagatctacacgtactgacacactctttccctacacgac
Sequence-based reagentD701Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatcgagtaatgtgactggagttcagacgtg
Sequence-based reagentD702Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagattctccggagtgactggagttcagacgtg
Sequence-based reagentD703Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagataatgagcggtgactggagttcagacgtg
Sequence-based reagentD704Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatggaatctcgtgactggagttcagacgtg
Sequence-based reagentD705Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatttctgaatgtgactggagttcagacgtg
Sequence-based reagentD706Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatacgaattcgtgactggagttcagacgtg
Sequence-based reagentD707Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatagcttcaggtgactggagttcagacgtg
Sequence-based reagentD708Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatgcgcattagtgactggagttcagacgtg
Sequence-based reagentD709Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatcatagccggtgactggagttcagacgtg
Sequence-based reagentD710Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatttcgcggagtgactggagttcagacgtg
Sequence-based reagentD711Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatgcgcgagagtgactggagttcagacgtg
Sequence-based reagentD712Illumina/Reynolds et al. Cell 2011 [20]Round two Amplicon PCR primercaagcagaagacggcatacgagatctatcgctgtgactggagttcagacgtg
Commercial assay or kitQuikChange II site-directed mutagenesis kitAgilentCat. #: 200523
Software, algorithmusearch v11.0.667Edgar Bioinformatics 2010 (PMID:20709691)Merge read pairshttps://www.drive5.com/usearch/

Additional files

Supplementary file 1

Supplementary tables.

(a) Steady state kinetic parameters for select point mutants of the DL121 fusion. The parameter kcat is reported in units of s−1, Km is in units of µM. Error is calculated as standard error of the mean over three replicates. Related to Figure 4 of the main text. (b) Fisher Exact Test p-values for the null hypothesis that the sector and inactivating mutants are independent properties. Inactivating mutations are defined as those that yield relative growth rates at or below the growth rate for DL121-D27N. Over a range of sector definitions, the null hypothesis is rejected at a confidence level of 0.05 or better, shown in red. Sector definitions were taken from Reynolds et al., 2011 (Rivoire et al., 2016). (c) Fisher Exact Test p-values for the null hypothesis that conserved positions and inactivating mutants are independent. Calculations were made over a range of conservation definitions chosen to result in an equal number positions as the sector positions in Supplementary file 1b 23, 36, 40, and 49 positions respectively. In all cases, the null hypothesis is rejected at a confidence level of 0.05 or better (red), and inactivating mutations are enriched at conserved positions beyond expectation due to random chance. Conservation values are calculated as in Reynolds et al., 2011 (Rivoire et al., 2016), and reflect the Kullback-Leibler relative entropy of amino acid frequencies at each DHFR position. (d) Fisher Exact Test p-values for the null hypothesis that the sector and allosteric mutations are independent. We compared over four sector cutoffs (as defined in Rivoire et al., 2016) and at two cutoffs for allostery significance (a standard p-value of 0.05, and an adjusted p-value of 0.016). The multiple hypothesis testing adjusted p-value was obtained by Sequential Goodness of Fit (SGoF, Carvajal-Rodriguez and de Uña-Alvarez, 2011). The top table shows the association between sector positions and allostery enhancing mutations; the bottom table computes the associate between sector positions and allostery disrupting mutations. In nearly all cases, the null hypothesis is rejected at a confidence level of 0.05 or better, shown in red. (e) Fisher Exact Test p-values for the null hypothesis that the solvent accessible DHFR surface and allosteric mutations are independent. At two cutoffs for allostery (a standard p-value of 0.05, and an adjusted p-value of 0.016), the null hypothesis is rejected at a confidence level of 0.05 or better, shown in red. (f) Statistical association of allosteric mutations and surface positions that are either within or contacting the sector. Contacting was defined as two atoms within the sum of their Pauling radii plus 20%. A surface site contacts the sector if the peptide bond atoms of the surface site contact any atoms in the sector position. P-values were computed by Fisher exact test with the null hypothesis that the sector and allosteric mutations are independent. Cutoffs for sector definition as defined in Rivoire et al., 2016 are shown as well as mutants determined to effect allostery either at a 95% confidence interval (p<0.05) or at the multiple hypothesis testing adjusted p-value (p<0.016). The null hypothesis that there is no relationship between allosteric mutations and sector or sector contacting positions on the surface of DHFR of the DL121 chimera is rejected at a confidence level of 0.05 or better over a range of cutoffs, shown in red. Allostery enhancing mutations are depleted from sector connected surface sites, while allostery disrupting mutations are enriched (in comparison with random expectation). (g) Statistical association of allosteric mutations and surface positions that are contacting the sector. In contrast to Supplementary file 1f, surface positions within the sector are excluded. Fisher Exact Test p-values were calculated for the null hypothesis that the sector and allosteric mutations are independent. Cutoffs for sector definition as defined in Rivoire et al., 2016 are shown as well as mutants determined to effect allostery either at a 95% confidence interval (p<0.05) or at the multiple hypothesis testing adjusted p-value (p<0.016). At most cutoff combinations, there is not a statistically significant association between sector connected surface sites and either mutations that enhance (top panel) or disrupt allostery (bottom panel).

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  1. James W McCormick
  2. Marielle AX Russo
  3. Samuel Thompson
  4. Aubrie Blevins
  5. Kimberly A Reynolds
(2021)
Structurally distributed surface sites tune allosteric regulation
eLife 10:e68346.
https://doi.org/10.7554/eLife.68346