USC Scientists Find DNA Replication Begins When the Double Helix Melts

 12/12/2016 – For years, scientists have puzzled over what prompts the

intertwined double-helix DNA to open its two strands and then start

replication. Knowing this could be the key to understanding how organisms —

from healthy cells to cancerous tumors — replicate and multiply for their

survival. 

USC scientists believe they have solved the mystery. Replication

is prompted by a ring of proteins that bond with the DNA at a special location

known as “origin DNA.” The ring tightens around the strands and melts them to

open up the DNA, initiating replication.  

This all takes place at a nano level that is impossible to see

with the naked eye. A strand of DNA is only about one nanometer in size — not

even close to the width of a human hair which is roughly equivalent to 100,000

DNA strands. 

The researchers made their discovery by studying SV40, a

cancerous virus. The virus hijacked the DNA replication process with a ring of

proteins called a “helicase” that mimicked the rings of proteins that prompt

genetic replication in healthy cells. 

The findings were published on Dec. 6 in the journal eLife. 

“Understanding the mechanisms of origin DNA opening or melting

allows us to learn this fundamental process of genetic duplication,” said

corresponding author Xiaojiang Chen, a professor of biological sciences and

chemistry at the USC Dornsife College of Letters, Arts and Sciences and

director of the college’s Center of Excellence in NanoBiophysics. “The knowledge

we have gained may be applicable for future intervention of this process to

block the replication of viral pathogens and cancer cells.” 

Xerox copies 

When the origin DNA melts, the double helix divides into

separate strands, Chen explained. Those DNA strands then become the template

for faithful duplication of other strands — a Xerox copy of their parental DNA.

As soon as replication is complete, one double helix DNA now becomes two exact

copies of the same double helix. 

“DNA replication is critical for heredity and survival,” said

Chen, who also is affiliated with the Norris Comprehensive Cancer Center at the

Keck School of Medicine at USC. “The origin DNA’s opening is an essential step

for DNA replication in our cells and for some tumor viral pathogens to

replicate and spread.” 

Prime location 

Why is origin DNA so special? Regular DNA sequences contain the

A, T, G and C nucleotides, more or less in equal ratio. But origin DNA

sequences contain more A and T nucleotides than usual. 

To prompt replication, the scientists used a helicase from a

“Large Tumor Antigen” or Large T. The antigen comes from the SV40 virus linked

to human cancers such as brain and bone cancers, mesothelioma and lymphoma. The

six proteins from Large T comprise a “helicase” that mimics the structure of

the healthy cells’ helicases. 

The scientists obtained a 3-D view of the atomic structure of

the helicase using X-ray crystallography, a technique for examining

nano-biomolecules and their structures at the atomic level that has been

refined over centuries. Chen said the images revealed that the proteins

surrounding the DNA had attached to it, then tightened like a vice until the

bonds between the two strands of the double helix broke — or melted — the

origin DNA. 

Although the scientists used a cancerous virus to study

replication, healthy cells replicate in a similar way, Chen said. 

Other co-authors were Dahai Gai, also of USC Dornsife, Damian

Wang of the Keck School of Medicine at USC and Shu-Xing Li of USC Dornsife’s

Center for Excellence in NanoBiophysics. 

The study was funded by a National Institutes of Health grant

(A1055926). 

[Image

caption: This ribbon diagram depicts a magnified view of genetic

replication in the making, as a group of proteins surround the DNA strands.

Each of the six proteins is in distinct color, with origin DNA in the center.

Credit: Xiaojiang Chen, USC.]