TY - JOUR
T1 - Revealing the distinct folding phases of an RNA three-helix junction
AU - Plumridge, Alex
AU - Katz, Andrea M.
AU - Calvey, George D.
AU - Elber, Ron
AU - Kirmizialtin, Serdal
AU - Pollack, Lois
N1 - Publisher Copyright:
© The Author(s) 2018.
PY - 2018/8/21
Y1 - 2018/8/21
N2 - Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass throughmultiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Ourmeasurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
AB - Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass throughmultiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Ourmeasurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
UR - http://www.scopus.com/inward/record.url?scp=85055112436&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85055112436&partnerID=8YFLogxK
U2 - 10.1093/nar/gky363
DO - 10.1093/nar/gky363
M3 - Article
C2 - 29762712
AN - SCOPUS:85055112436
SN - 0305-1048
VL - 46
SP - 7354
EP - 7365
JO - Nucleic acids research
JF - Nucleic acids research
IS - 14
ER -