Diverse small molecules can be covalently attached to DNA assemblies. In most cases, a flexible linker connects the small molecule to a specific atom of the DNA assembly so that the small molecule can freely sample conformationally any point in a sterically accessible volume (AV) around the DNA attachment site. We have implemented the AV algorithm [19-20] as a MATLAB function that computes this AV as a point cloud using three input parameters: linker length, linker width, and radius of the attached molecule. The script is available here.
Users of this tool are kindly requested to cite the following reference:
- Pan, K., Boulais, E., Yang, L., Bathe, M. Structure-based model for light-harvesting properties of nucleic acid nanostructures. Nucleic Acids Research, 42: 2159–2170 (2014). [ PubMed Article ]
Step 1. Add the directory in the downloaded ZIP package to the MATLAB path.
>> addpath AV_v2.0
Step 2. Set the path to the atomic model.
>> pdbFilename = ‘example_4way_junction.pdb’;
Step 3. Set the attachment point to Chain 1, Residue 1, Atom O5′ as an example.
>> attAtom.chainSerNo = 1;
>> attAtom.resSeq = 1;
>> attAtom.AtomName = ‘O5”’;
Step 4. Set the linker length, linker width, and radius of the molecule to 16, 2.5, and 3.5 Angstroms, respectively, as an example.
>> linkerGeometry(1).L_link = 16;
>> linkerGeometry(1).w_link = 2.5;
>> linkerGeometry(1).R_dye = 3.5;
Step 5. Read the atomic model into MATLAB.
>> pdbStruct = pdb2struct_multimodel(pdbFilename);
Step 6. Compute the AV. The variable AV_point contains all the points in the AV, and the variable posGrid gives a 3D grid for the AV computation. The result AV_point can be downloaded as a MATLAB .mat file here.
>> [posGrid, AV_point] = AV(pdbStruct, attAtom, linkerGeometry);