Best Approach To Store Node Coordinate Data

I have a question on the best way to store model data for my app. My app will basically be drawing a bunch of elements (lines) connected to a node at each end. Im trying to decide how im going to store my node data (as well as element data). The node data im trying to store will consist of the node XYZ coordinates and some other info about the node. The element data will consist of the node numbers at each end plus additional info about the element. There a number of ways i've been thinking i can do this. They are:

1) Store my node/element data as a Dictionary object, where the key represents the node/element, and the value would be an array of the information i want to store.

2) Create a "Node" structure and an "Element" structure to store the info i want. Im a bit worried here as my model could potentially have thousands of nodes and elements.

3) Create a "Node" datatable and an "Element" datatable, and store my info in those instead. I can see some advantages in this in regards to displaying information to the user in datagridview etc. But then again i can easily pull the required data from a method i mentioned above, and generate the datatable when required.

Not quite sure what the best approach is. Either way i do it, i will be serializing whatever object i use to save the data to disk.