We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are central to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Practical aptamer optimization often requires higher accuracy predictions for only a small subset of sequences suggested e.g., by SELEX experiments, but in the absence of a streamlined procedure this task is extremely time and expertise intensive. We address this gap by introducing E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands, and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy. As a case study we simulate a DNA-UTP (uridine triphosphate) complex in water using AMOEBA force field. https://github.com/InfluenceFunctional/E2EDNA.