Satellite DNA are non-coding tandem-repetitive nucleotide sequences. Historically considered “junk” DNA, satellite DNA is now predicted to play an important role in maintaining stability of DNA in the centromere and modulating gene expression. Due to its repetitive nature, satellite sequences can often fold into non-canonical DNA secondary structures. Depending on physiological context, these structures can be beneficial or deleterious to the cell and body and are implicated in human diseases and cancer. Satellite III is one of the most abundant satellite DNAs, composed of perfect d(ATGGA)n repeats. The secondary structure of Satellite III without a complementary strand is well-studied in mutated variants, and includes hairpin, loop-stem-loop, duplex, and other structures. However, the X-ray structure of a multi-repeat native sequence has not yet been reported. Here I will present our recent characterization of a four-repeat sequence (ATGGA)4 using biophysical and X-ray structural methods. Biophysical results show that the sequence forms a monomeric structure in diluted solution, likely a hairpin. The crystal structure was solved in space group P212121 to resolution 1.57 Å using molecular replacement. The asymmetric unit contains three self-complementary duplexes truncated to five nucleotides (AATGG), which are extended infinitely through symmetry. The strands in duplex interact via two canonical A-T base pairs, two sheared A-G base pairs, and unpaired guanines which intercalate leading to G-G-G-G stack. These unique structural features and the conformational difference between the biophysical to crystal results inform our understanding of Satellite III’s behavior in biologically relevant settings.

Elucidating the structure of a four-repeat Satellite III DNA sequence

ACS Spring Meeting 2021

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