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Branch migration is movement of the strand-exchange point in a Holliday junction. Successive changes in base pairing shift the junction along homologous DNA without requiring a new break in each phosphodiester backbone. Moving the boundary changes the extent of heteroduplex DNA, where strands from different parental DNA molecules pair together.

An illuminating experiment built two double-stranded DNA substrates with complementary single-stranded tails. Pairing the tails formed a four-stranded junction at one end. Complete branch migration to the opposite end produced two strand-exchanged duplex products, giving an observable endpoint for a process otherwise occurring along a molecular junction.^[ref]

The spontaneous reaction depended strongly on the surrounding ions: under the reported conditions, removing magnesium made it roughly a thousand times faster. This is not a universal speed for DNA exchange inside a cell; the experiment isolated a spontaneous process whose kinetics depend on junction structure and solution conditions.^[ref]

I. G. Panyutin studied the physical chemistry of DNA strand exchange. In 1994, work with P. Hsieh measured spontaneous branch migration, the motion of an exchange junction along homologous double-stranded DNA.^[ref]

The experiments varied temperature and ions while using defined DNA substrates. Removing magnesium accelerated the reported process by roughly a thousandfold. The comparison illustrates why an observed reaction rate is not a property of the DNA sequence alone: solution conditions can alter junction geometry and therefore how readily exchange proceeds.^[ref]

P. Hsieh investigated DNA reactions involved in genetic recombination. A 1994 study with I. G. Panyutin isolated spontaneous branch migration of a Holliday junction for kinetic measurement.^[ref]

Complementary single-stranded ends joined two double-stranded DNA substrates into a four-stranded junction. Movement to the far end produced strand-exchanged products. Measuring that conversion under different solution conditions showed that the surrounding ions, especially magnesium, strongly changed the rate. This separated a physical DNA reaction from the additional regulation supplied by cellular proteins.^[ref]