| Full-length Epstein-Barr virus nuclear antigen-1 binding to viral DNA
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Epstein-Barr virus is maintained and replicated in widely occurring latent infections of human B lymphocytes and in tumor cells. Specific binding of the Epstein-Barr Virus Nuclear Antigen-1 (EBNA-1) in viral DNA elements is required. View Details
EBNA-1 experiments were done with Dr. Janet Hearing, Stony Brook University.
EBNA-1 Binding to A High Affinity Site
EBNA-1 (641 amino acids) exists as a 140 kDa dimer. One dimer binds per 16-bp DNA binding site. Binding reactions are viewed hydrated in buffer.
DNA fragments have a single high affinity binding site (16 bp) located off-center. Arms are 136 and 94 bp in length.
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Single EBNA-1 dimers are observed on single DNAs (arrows point to a few).
Aggregates of several EBNA-1 proteins and DNAs are common also. They arise because EBNA-1 has two linking domains that are able to join dimers bound to different DNAs.
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Resolution variation
Resolution varies due to tip contamination from small competitor oligonucleotides present in EBNA-1/DNA reactions.
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The tip scanning this complex in a dilute reaction is not contaminated. DNA image width is 6 to 7 nm, expected after adding 4- 5 nm for the tip diameter to the 2 nm native DNA width. |
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An equivalent binding reaction has not been diluted and the equivalent tip gets contaminated. DNA image width is 15-20 nm.
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