Using a new set of reduced coordinates developed for describing regular and unusual nucleic acid structures, we have revised our nucleic acid modeling tool NAMOT2. NAMOT2 is general in terms of modeling different nucleic acid structures. A set of modifiable libraries allows users to customize their modeling environment. With this set of libraries, NAMOT2 can be used to model non-canonical structures such as parallel-stranded, triple-stranded and quadruple-stranded nucleic acid molecules. For modeling irregular structures (junctions, hairpin loops, etc.), we introduce a structural recipe approach. The complete procedure using NAMOT2 to construct the structure of a specific molecule is treated as the recipe for that structural motif. The existing recipes can be modified to generate new recipes for different structural motifs. Several examples of nucleic acids with non-canonical structures were modeled using NAMOT2. These examples include a DNA-drug complex, a DNA cube, a six-arm junction and a curved DNA molecule.

The helical nature of the molecule (almost all of the DNA and a significant portion of the RNA) makes the modeling of nucleic acids a unique task. Unlike other biopolymers (proteins, lipids, etc.), the integrity the structure of a nucleic acid molecule depends strongly on the maintenance of the base pairing within the molecule. Structural alterations (bending, stretching, compressing, etc.), in general, should not disturb the base pairings. A custom-made molecular modeling tool is developed taking into consideration this specific property of the molecule. Instead of Cartesian coordinates, the modeling is carried out on a set of reduced coordinates developed here in our laboratory. One of the advantages using this set of reduced coordinates is the readiness of maintaining the base pairings while altering the structure. A graphic routine is incorporated into the package to display the image of the molecule while the modeling work is being executed. The program is written in C using XView tool kit with Xlib routines to ensure portability to different workstations.