Single-molecule studies of DNA and RNA four-way junctions.
Branched helical junctions are common in nucleic acids. In DNA, the four-way junction (Holliday junction) is an essential intermediate in homologous recombination and is a highly dynamic structure, capable of stacking conformer transitions and branch migration. Our single-molecule fluorescence studies provide unique insight into the energy landscape of Holliday junctions by visualizing these processes directly. In the hairpin ribozyme, an RNA four-way junction is an important structural element that enhances active-site formation by several orders of magnitude. Our single-molecule studies suggest a plausible mechanism for how the junction achieves this remarkable feat; the structural dynamics of the four-way junction bring about frequent contacts between the loops that are needed to form the active site. The most definitive evidence for this is the observation of three-state folding in single-hairpin ribozymes, the intermediate state of which is populated due to the intrinsic properties of the junction.
McKinney
S A
SA
Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.
Tan
E
E
Wilson
T J
TJ
Nahas
M K
MK
Déclais
A-C
AC
Clegg
R M
RM
Lilley
D M J
DM
Ha
T
T
D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D045566:DNA, Cruciform / Q000737:chemistry / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D008274:Magnesium / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D045566:DNA, Cruciform; D016337:RNA, Catalytic; D012313:RNA; D004247:DNA; D008274:Magnesium