The mammalian cell nucleus is a membrane-bounded compartment filled with self-organizing, interconnected, nanometer-scale machines. These machines carry out essential processes of DNA replication, RNA synthesis, pre-mRNA processing, early ribosome biogenesis, RNA transport, and DNA repair [1
]. We refer to the general class of machines that are made primarily of proteins and act on nucleic acid substrates as “nucleoprotein machines.” They are complex: synthesis of a typical human mRNA, for example, requires precise interaction of hundreds of protein and RNA components, including initiation, capping, elongation, splicing, polyadenylation and termination factors.
Nucleoprotein machines are quite dynamic and do not have a fixed composition. For example, the nonhomologous end joining (NHEJ) machine that repairs DNA double strand breaks (DSBs) requires a different constellation of ancillary factors depending on the complexity of the DNA damage [2
]. NHEJ also occurs within domains of modified chromatin containing roughly 2 million base pairs of DNA [3
] and must be able to join ends of virtually any nucleotide sequence. The uniqueness of individual repair complexes exemplifies why it is essential to study the behavior of single nucleoprotein complexes, rather than population averages, in order to obtain insights into their design principles.
Elucidation of these principles involves understanding: (1) the role of each component in a nanomachine, (2) the pathway by which the machine assembles and disassembles, and (3) the signalling and control mechanism within and between nanomachines. Nucleoprotein machines work with a common set of raw materials (nucleotides and polynucleotides), carry out similar elementary steps (nucleotidyl and phosphoryl group transfer), and often have interchangeable components. TFIIH, for example, participates in both RNA transcription and nucleotide excision repair [4
], and Ku and DNA-PKcs participate in both NHEJ and in telomere maintenance [5
]. If each of these components works by the same mechanism in different processes, then it is likely that study of different machines will reveal common, and generalizable, engineering principles.
A long-term goal is to adapt and redesign nucleoprotein machines to carry out novel functions, including precise modification of the information stored in DNA (or RNA) to provide genetic cures for common human diseases. Consistent with this goal, we focus here on the NHEJ machine that repairs DNA DSBs. This machine has an intrinsic ability to add, delete, and rejoin DNA sequences at the break sites. Adapting this machine to directly manipulate the information encoded in DNA on the nanoscale in a directed fashion would provide a broad and powerful approach to medicine that potentially transcends limitations of present-day pharmaceutical technology.