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@@ -134,7 +134,7 @@ in complex with an attached piece of DNA. Finally, we assess the effects of one
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<a class="sidenav-text nav-link sidenav-link unactive" href="#StructurePrediction">
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- <span class="fw-medium">Static</span>
+ <span class="fw-medium">Static Predictions</span>
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@@ -152,7 +152,7 @@ in complex with an attached piece of DNA. Finally, we assess the effects of one
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<a class="sidenav-text nav-link sidenav-link" href="#Discussion">
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- <span class="fw-medium">Discussion & <br> road ahead</span>
+ <span class="fw-medium">Discussion & <br> Road Ahead</span>
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@@ -258,7 +258,7 @@ Performing this initial setup laid a solid foundation for all upcoming simulatio
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<p class="fw-semi-bold">Comparing macroscopic conditions</p>
<p></p>To test the influence of simulation temperature on PICasSO, we simulated a range of reaction temperatures from 275 K to 315 K over a time span of 1 ns. The resulting trajectories were compared using the <b> Hausdorff- and the Frechét metrics </b> (Seyler et al., 2015). The range and specific simulation temperatures were optimized using the design of experiment theory developed by Plackett and Burman and implemented within the pyDOE package (Baudin & Christopoulou, 2018; PLACKETT & BURMAN, 1946). For this we developed, and implemented the plan, of how to set up experiments, using an optimal number of experiments. We generated data for those experiments but were not able to process it, as we generated more than 2 TB of data, whose alignment of trajectories did not finish running. </p>
- <h4 class="fs-h4 fw-semi-bold mt-5">Coarse-grained molecular dynamics</h4>
+ <h4 class="fs-h4 fw-semi-bold mt-5">Coarse-grained Molecular Dynamics</h4>
<p>To model full-length DNA strands, all-atom molecular dynamics proved insufficient as its memory requirements scale with O(T N log N), where T is the number of time-steps and N is the number of simulated atoms. To simulate long-range DNA dynamics, we therefore decided to run simulations at <b> lower resolution based on oxDNA </b> - a coarse-grain molecular dynamics approach specialized in DNA-DNA interactions that is used to model large DNA assemblies (Rovigatti et al., 2015). It is particularly effective for investigating B-DNA interactions and mechanical properties like bond and angular forces, as well as base stacking effects. By representing each nucleotide as a single particle, oxDNA significantly reduces complexity compared to all-atom approaches, enabling us to study large DNA systems while retaining the DNA-dependent behavior critical to our analysis. Even though oxDNA is mostly used to accurately simulate the self-assembly processes in DNA origami, we leveraged its precision in determining whether DNA strands remain bound to the Cas staples and to one another. Very importantly, taking into account the exerted forces, we also examined if our staples could cause unintended DNA double-strand breaks.
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oxDNA models DNA interactions by <b> only considering Watson-Crick base pairings </b>, which allows <b>large-scale analysis while staying computationally efficient</b>. The three possible interaction types for DNA implemented in oxDNA are similar to each other while having slight differences regarding nucleotide orientation, strength of interactions, and availability of screened electrostatic interactions (Sengar et al., 2021).
@@ -338,19 +338,19 @@ Performing this initial setup laid a solid foundation for all upcoming simulatio
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<p>Before simulating our Cas staples, we needed to explore and subsequently optimize the configurations of the fgRNA, which is key to connecting the Cas proteins into the staple complex. Selecting the appropriate fgRNA linker, i.e. the nucleic acid sequence connecting the Cas12a and Cas9 parts of the fgRNA, is crucial, as the linker length and composition determines the proximity and steric arrangement of the stapled DNA sequences, ultimately impacting functionality. <br><br>
- <b>We experimented with varying linker lengths</b>, focusing on a poly-CA configuration to minimize secondary structure formation. Without a connecting linker (i.e. direct fusion of Cas12a crRNA to Cas9 gRNA), we observed steric hindrance between the two Cas proteins upon fgRNA binding, leading to a loss of staple functionality (see <b>fig. 1</b>). However, by <b>using a longer 40-nucleotide linker RNA</b>, we were able to resolve this issue and could confirm functionality of the <i class="italic">in silico</i> optimized Cas-staple in our wet lab experiments.
+ <b>We experimented with varying linker lengths</b>, focusing on a poly-CA configuration to minimize secondary structure formation. Without a connecting linker (i.e. direct fusion of Cas12a crRNA to Cas9 gRNA), we observed steric hindrance between the two Cas proteins upon fgRNA binding, leading to a loss of staple functionality (see <b>fig. 1</b>). However, by <b>using a longer 40-nucleotide linker RNA</b>, we were able to resolve this issue and could confirm functionality of the <i class="italic">in silico</i> optimized Cas staple in our wet lab experiments.
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<p class="figcaption"><b>Figure 1:</b>
- Cas Staples comprising dCas12 (left protein, in grey) and dCas9 (right protein, in grey) with fused guide RNA (fgRNA) without (left figure panel) or with (right figure panel) 40 nt linker. Each Cas staple is attached to two dsDNA strands. Proteins are derived from Part <a class="underline--magical" href="https://parts.igem.org/Part:BBa_K5237000" target="_blank">BBa_K5237000</a>
+ <b>Cas Staples comprising dCas12 (left protein, in grey) and dCas9 (right protein, in grey) with fused guide RNA (fgRNA) without (left figure panel) or with (right figure panel) 40 nt linker.</b> Each Cas staple is attached to two dsDNA strands. Proteins are derived from Part <a class="underline--magical" href="https://parts.igem.org/Part:BBa_K5237000" target="_blank">BBa_K5237000</a>
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<p>For the fgRNA without a linker <b> we observed restricted movement of the dCas12 subunit</b>, which aligns with the wet lab results showing this staple is non-functional<i class="italic"> in vivo</i> or <i class="italic">in vitro</i>. The added linker allowed for greater freedom of movement of the Cas moieties, enabling successful stapling, which we could confirm in wet lab experiments. <br><br>
Relying solely on the fgRNA to connect our Cas staple limits its overall functionality. So we next looked into a fusion Cas approach: <b>connecting the two Cas proteins with an additional peptide linker</b> can improve the stability of the staple complex while allowing for functional flexibility by using the fgRNA to precisely program the DNA residue pairs to be tethered. <br><br>
- When selecting a suitable peptide linker, both the linker length and rigidity are important parameters to consider. Similar to the fgRNA linker, these parameters are essential for optimal functionality of a Cas-staple construct. We selected seven peptide linkers from the literature to cover a broad range of biophysical properties (Chen et al., 2013). We tested these linkers first on our Mini staples consisting of simple and small DNA binding domains (GCN4 leucine-zipper-based, TetR-based, Oct1-based), which allowed for quicker and easier experimental assessment before moving to the more complex Cas staples. A detailed description of these Mini staples can be found in the <a class="underline--magical" href="https://2024.igem.wiki/heidelberg/results#ReadoutSystems" target="_blank">proximity assay section</a> of our wet lab results page and on the registry
+ When selecting a suitable peptide linker, both the linker length and rigidity are important parameters to consider. Similar to the fgRNA linker, these parameters are essential for optimal functionality of a Cas staple construct. We selected seven peptide linkers from the literature to cover a broad range of biophysical properties (Chen et al., 2013). We tested these linkers first on our Mini staples consisting of simple and small DNA binding domains (GCN4 leucine-zipper-based, TetR-based, Oct1-based), which allowed for quicker and easier experimental assessment before moving to the more complex Cas staples. A detailed description of these Mini staples can be found in the <a class="underline--magical" href="https://2024.igem.wiki/heidelberg/results#ReadoutSystems" target="_blank">proximity assay section</a> of our wet lab results page and on the registry
<a class="underline--magical" href="https://parts.igem.org/Part:BBa_K5237009" target="_blank">BBa_K5237009</a>.
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