Abstract: Nucleic acids (DNA and RNA) provide a versatile platform for engineering synthetic biology in a variety of technology areas including medicine, science, agriculture, and energy. In many settings, degradation of nucleic acid molecules poses a significant engineering challenge as the molecules do not function if they have been degraded. In some embodiments, nucleic acid protective elements (PELs) are used to protect chemically synthesized or expressed nucleic acid molecules from degradation. PELs may be derived from all or part of a viral xrRNA sequence and/or structural motif, PELs may include rationally designed sequences and/or structural motifs, PELs may be engineered using directed evolution, and in some embodiments, PELs comprise a mixture of biologically derived, rationally designed sequence and/or structural motifs, and/or sequences and/or structural motifs that are engineered by directed evolution.