The nat­u­rally occur­ring antibi­otic Actin­o­mycin D (ActD) was approved by the Food and Drug Admin­is­tra­tion as a chemotherapy drug in 1964 and has been widely used for nearly 50 years to treat a variety of tumor types. Since then, sci­en­tists have dis­cov­ered that ActD works by blocking DNA tran­scrip­tion, the process that tran­scribes DNA into RNA, a macro­mol­e­cule that codes for the pro­teins nec­es­sary for cell survival.

Inhi­bi­tion by ActD is a good thing in rapidly dividing and tran­scribing cancer cells, but healthy cells are also sus­cep­tible to ActD, which makes it toxic, like many forms of chemotherapy.

Despite its long his­tory, the mol­e­c­ular details of ActD’s func­tion remained a mys­tery — until now.

If you don’t know how it works, then you can’t design a new mol­e­cule that has the same char­ac­ter­is­tics [but less tox­i­city],” said Mark Williams, a physics pro­fessor in the Col­lege of Sci­ence at North­eastern Uni­ver­sity. “This is why we decided to study it.”

Williams and his exper­i­mental bio­physics team used “optical tweezers” to probe the mol­e­cule and its inter­ac­tion with DNA to deter­mine the under­lying mech­a­nism by which ActD pre­vents transcription.

The find­ings were pub­lished on Feb. 10 in the journal Nucleic Acids Research.

Optical tweezers, researchers noted, fix a single DNA mol­e­cule in place using the force of tightly focused laser beams. “Once trapped, DNA may be stretched along its length,” said Micah McCauley, a senior research sci­en­tist in Williams’ lab. “Using our instru­ment, vari­able ten­sion may be applied down to picoNewton precision.”

In the cell there are forces exerted all the time,” Williams said. The pro­tein RNA poly­merase, for example, dis­rupts DNA’s double helix in order to copy its sequence into RNA. In the exper­i­mental set­ting, Williams’ lab uses lasers to achieve this destabilization.

Once the DNA is desta­bi­lized, ActD finds its way inside the double helix. In the body’s cells, the DNA zips back up after the poly­merase moves away, leaving ActD securely in place and thus pre­venting future tran­scrip­tion. In the lab, the lasers simply relax their force on the DNA.

By mim­ic­king the in vivo activity through this kind of manip­u­la­tion, Williams’ team could pre­cisely quan­tify changes in the DNA struc­ture during its inter­ac­tion with ActD. “We’re taking a dynamic pic­ture of what’s hap­pening,” he said. “We show how much it has to change dynam­i­cally in order for the binding to occur.”

With this infor­ma­tion, the team can then pro­vide a model that explains the drug’s observed action in cells.

Meriem Bahira, an under­grad­uate researcher in Williams’ lab, is per­forming follow-​​up studies that apply the same strategy to a sim­ilar syn­thetic mol­e­cule that could one day be used as a cancer drug itself. “Our tech­nique is spe­cial in the sense that it is a single mol­e­cule tech­nique so we can get really small details from it,” Bahira said. “Bulk exper­i­ments are useful in that they give you aver­ages. This gives you details about the process.”