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 ]

Example: Application of the AV algorithm to a DNA four-way junction

Here we use the atomic model of a four-way junction to demonstrate the use of the AV calculator. The atomic model of this junction consists of four DNA strands, which are stored as four models in the PDB file format.

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);