5' cap contains which unusual linkage?
Eukaryotic five prime cap harbors highly unusual five prime to five prime linkage instead of canonical three prime to five prime phosphodiester found in RNA backbone. After RNA triphosphatase generates diphosphate RNA, guanylyltransferase hydrolyzes GTP to GMP and catalyzes attack of diphosphate RNA on alpha phosphate forming Gp pppN triphosphate bridge linking guanine five prime to first nucleotide five prime. Three phosphate groups create 5'-5' connection. Subsequent methylation at N7 of guanine and ribose 2' O positions generate cap zero, cap one, cap two structures resistant to decapping and exonuclease attack.
Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: 5'-5' triphosphate cap linkage; Lodish 9th ed., Mechanism of guanylyltransferase forms unusual linkage