1. A system for preparing a chimeric oligonucleotide, comprising at least two instruments and program code which, when executed, configures the system to: (a) synthesize a first nucleic acid (NA) oligonucleotide and a second peptide nucleic acid (PNA) oligonucleotide, thereby providing a first sample of the first oligonucleotide and a second sample of the second oligonucleotide; (b) determine the volume of each sample, the concentration of the oligonucleotide in each sample and whether each oligonucleotide has a secondary structure; (c) subject each oligonucleotide to chromatography under conditions suitable for disrupting the secondary structure of the oligonucleotide if the oligonucleotide has a secondary structure, and achieving single base-resolution for each oligonucleotide, wherein the conditions are a function of the volume and/or concentration measured in step (b); (d) collect each oligonucleotide from the chromatography; and (e) conjugate the first oligonucleotide to the second oligonucleotide to form a chimeric oligonucleotide.