Structure of Long Human Telomeric RNA (TERRA): G-Quadruplexes Formed by Four and Eight UUAGGG Repeats Are Stable Building Blocks

摘要

The discovery of long RNA transcripts of telomeric repeats (TERRA) andntheir potential to form G-quadruplexes stimulated studies on the possible arrangements ofnG-quadruplexes along TERRA. Here we performed ribonuclease protection assay toninvestigate the structures formed by long human TERRA. We found that G-quadruplexesncomprising four and eight UUAGGG repeats were most resistant to RNase T1 digestion,npresumably with the former adopting an all-parallel-stranded propeller-type conformationnand the latter forming a structure with two tandemly stacked G-quadruplex subunits eachncontaining three G-tetrad layers. Molecular dynamics simulations of eight-repeat humannTERRA sequences consisting of different stacking interfaces between the two G-quadruplexnsubunits, i.e., 50u000150, 30u000130, 30u000150, and50 u000130, demonstrated stacking feasibility for all but then50u000130 arrangement. A continuous stacking of the loop bases from one G-quadruplex subunitnto the next was observed for the 50u000150 stacking conformation. We also put forward othernpossible stacking arrangements that involve more than one linker connecting the twonG-quadruplex subunits. On the basis of these results, we propose a “beads-on-a-string”-like arrangement along human TERRA,nwhereby each bead ismade up of either four or eightUUAGGGrepeats in a one- or two-blockG-quadruplex arrangement, respectively.