In negative-sense MVM genomes, the left-end hairpin is 121 nucleotides in length and exists in a single flip sequence orientation. This telomere is Y-shaped and contains small internal palindromes that fold into the "ears" of the Y, a duplex stem region 43 nucleotides in length that is interrupted by an asymmetric thymidine residue, and a mismatched "bubble" sequence in which the 5′-GAA-3′ sequence on the inboard arm is opposite of 5′-GA-3′ in the outboard strand. Sequences in this hairpin are involved in both replication and regulation of transcription. The elements involved in these two functions separate the two arms of the hairpin.
The left-end telomere of MVM, and likely of all heterotelomeric parvoviruses, cannot function as a replication origin in its hairpin configuration. Instead, a single origin on the lower strand is created when the hairpin is unfolded, extended, and copied to form a duplex basepaired sequence that spans adjacent genomes in the dimer RF. Within this structure, the sequence from the outboard arm that surrounds a GA/TC dinucleotide serves as an origin, OriL. The equivalent GAA/TTC sequence on the inboard arm that contains the bubble trinucleotide, called OriL, does not serve as an origin. The inboard arm and hairpin configuration of the terminus instead appear to function as upstream control elements for the viral transcriptional promoter P4. Additionally, the ability to segregate one arm from nicking appears essential for replication.
The minimal linear left-end origin is about 50 basepairs long and extends from two 5′-ACGT-3′ motifs, spaced five nucleotides apart at one end, to a position seven basepairs beyond the nick site. The bubble's GA sequence itself is relatively unimportant, but the space that it occupies is necessary for the origin to function. Within the origin, there are three recognition sequences: an NS1-binding site that orients the NS1 complex over the nick site 5′-CTWWTCA-3′, which is located 17 nucleotides downstream (toward the 3′-end), and the two ACGT motifs. These motifs bind a heterodimeric cellular factor called either parvovirus initiation factor (PIF) or glucocorticoid modulating element-binding protein (GMEB).
PIF is a site-specific DNA-binding heterodimeric complex that contains two subunits, p96 and p79, and functions as a transcription modulator in the host cell. It binds DNA via a KDWK fold and recognizes two ACGT half-sites. The spacing between these sites can vary significantly for PIF, from one to nine nucleotides, with an optimal spacing of six. PIF stabilizes the binding of NS1 on the active form of the left-end origin, OriL, but not on the inactive form, OriL, because the two complexes are able to establish contact over the bubble binucleotide. The left-end hairpin of all other species in the Protoparvovirus genus, of which MVM belongs, have bubble asymmetries and PIF-binding sites, though with slight variation in spacing. This suggests that they all share a similar origin segregation mechanism.