Structure, dynamics, and branch migration of a DNA Holliday junction

A single-molecule fluorescence and modeling study

Mikhail A. Karymov, Mathivanan Chinnaraj, Aleksey Bogdanov, Annankoil R. Srinivasan, Guohui Zheng, Wilma K. Olson, Yuri L Lyubchenko

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

The Holliday junction (HJ) is a central intermediate of various genetic processes, including homologous and site-specific DNA recombination and DNA replication. Elucidating the structure and dynamics of HJs provides the basis for understanding the molecular mechanisms of these genetic processes. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. These data led us to the conclusion that one hop can be more than 1 basepair (bp); moreover, we hypothesized that continuous runs over the entire sequence homology (5 bp) can occur. Direct measurements of the dependence of the fluorescence resonance energy transfer (FRET) value on the donor-acceptor (D-A) distance are required to justify this model and are the major goal of this article. To accomplish this goal, we performed single-molecule FRET experiments with a set of six immobile HJ molecules with varying numbers of bps between fluorescent dyes placed on opposite arms. The designs were made in such a way that the distances between the donor and acceptor were equal to the distances between the dyes formed upon 1-bp migration hops of a HJ having 10-bp homology. Using these designs, we confirmed our previous hypothesis that the migration of the junction can be measured with bp accuracy. Moreover, the FRET values determined for each acceptor-donor separation corresponded very well to the values for the steps on the FRET time trajectories, suggesting that each step corresponds to the migration of the branch at a defined depth. We used the dependence of the FRET value on the D-A distance to measure directly the size for each step on the FRET time trajectories. These data showed that one hop is not necessarily 1 bp. The junction is able to migrate over several bps, detected as one hop and confirming our model. The D-A distances extracted from the FRET properties of the immobile junctions formed the basis for modeling the HJ structures. The composite data fit a partially opened, side-by-side model with adjacent double-helical arms slightly kinked at the four-way junction and the junction as a whole adopting a global X-shaped form that mimics the coaxially stacked-X structure implicated in previous solution studies.

Original languageEnglish (US)
Pages (from-to)4372-4383
Number of pages12
JournalBiophysical journal
Volume95
Issue number9
DOIs
StatePublished - Nov 1 2008

Fingerprint

Cruciform DNA
Fluorescence Resonance Energy Transfer
Fluorescence
Humulus
Genetic Phenomena
Sequence Homology
DNA Replication
Fluorescent Dyes
Genetic Recombination
Molecular Biology
Coloring Agents
DNA

ASJC Scopus subject areas

  • Biophysics

Cite this

Structure, dynamics, and branch migration of a DNA Holliday junction : A single-molecule fluorescence and modeling study. / Karymov, Mikhail A.; Chinnaraj, Mathivanan; Bogdanov, Aleksey; Srinivasan, Annankoil R.; Zheng, Guohui; Olson, Wilma K.; Lyubchenko, Yuri L.

In: Biophysical journal, Vol. 95, No. 9, 01.11.2008, p. 4372-4383.

Research output: Contribution to journalArticle

Karymov, Mikhail A. ; Chinnaraj, Mathivanan ; Bogdanov, Aleksey ; Srinivasan, Annankoil R. ; Zheng, Guohui ; Olson, Wilma K. ; Lyubchenko, Yuri L. / Structure, dynamics, and branch migration of a DNA Holliday junction : A single-molecule fluorescence and modeling study. In: Biophysical journal. 2008 ; Vol. 95, No. 9. pp. 4372-4383.
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AU - Srinivasan, Annankoil R.

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