Molecular alternatives to DNA, RNA offer new insight into life's origins


April 19, 2012

Living systems owe their existence to a pair of information-carrying molecules: DNA and RNA. These fundamental chemical forms possess two features essential for life: they display heredity – meaning they can encode and pass on genetic information, and they can adapt over time, through processes of Darwinian evolution. 

A long-debated question is whether heredity and evolution could be performed by molecules other than DNA and RNA.  Download Full Image

John Chaput, a researcher at ASU’s Biodesign Institute, who recently published an article in Nature Chemistry describing the evolution of threose nucleic acids, joined a multidisciplinary team of scientists from England, Belgium and Denmark to extend these properties to other so-called Xenonucleic acids or XNAs. 

The group demonstrates for the first time that six of these unnatural nucleic acid polymers are capable of sharing information with DNA. One of these XNAs, a molecule referred to as anhydrohexitol nucleic acid or HNA was capable of undergoing directed evolution and folding into biologically useful forms.

Their results appear in the current issue of Science. 

The work sheds new light on questions concerning the origins of life and provides a range of practical applications for molecular medicine that were not previously available. 

Nucleic acid aptamers, which have been engineered through in vitro selection to bind with various molecules, act in a manner similar to antibodies – latching onto their targets with high affinity and specificity. “This could be great for building new types of diagnostics and new types of biosensors,” Chaput says, pointing out that XNAs are heartier molecules, not recognized by the natural enzymes that tend to degrade DNA and RNA. New therapeutics may also arise from experimental Xenobiology. 

Both RNA and DNA embed data in their sequences of four nucleotides – information vital for conferring hereditary traits and for supplying the coded recipe essential for building proteins from the 20 naturally occurring amino acids. Exactly how (and when) this system got its start however, remains one of the most intriguing and hotly contested areas of biology. 

According to one hypothesis, the simpler RNA molecule preceded DNA as the original informational conduit. The RNA world hypothesis proposes that the earliest examples of life were based on RNA and simple proteins. Because of RNA’s great versatility – it is not only capable of carrying genetic information but also of catalyzing chemical reactions like an enzyme – it is believed by many to have supported pre-cellular life. 

Nevertheless, the spontaneous arrival of RNA through a sequence of purely random mixing events of primitive chemicals was at the very least, an unlikely occurrence. “This is a big question,” Chaput says. “If the RNA world existed, how did it come into existence? Was it spontaneously produced, or was it the product of something that was even simpler than RNA?” 

This pre-RNA world hypothesis has been gaining ground, largely through investigations into XNAs, which provide plausible alternatives to the current biological regime and could have acted as chemical stepping-stones to the eventual emergence of life. The current research strengthens the case that something like this may have taken place. 

Threose nucleic acid or TNA for example, is one candidate for this critical intermediary role. “TNA does some interesting things,” Chaput says, noting the molecule’s capacity to bind with RNA through antiparallel Watson-Crick base pairing. “This property provides a model for how XNAs could have transferred information from the pre-RNA world to the RNA world.” 

Nucleic acid molecules, including DNA and RNA consist of 3 chemical components: a sugar group, a triphosphate backbone and combinations of the four nucleic acids. By tinkering with these structural elements, researchers can engineer XNA molecules with unique properties. However, in order for any of these exotic molecules to have acted as a precursor to RNA in the pre-biotic epoch, they would need to have been able to transfer and recover their information from RNA. To do this, specialized enzymes, known as polymerases are required. 

Nature has made DNA and RNA polymerases, capable of reading, transcribing and reverse transcribing normal nucleic acid sequences. For XNA molecules, however; no naturally occurring polymerases exist. So the group, led by Phil Holliger at the MRC in England, painstakingly evolved synthetic polymerases that could copy DNA into XNA and other polymerases that could copy XNA back into DNA. In the end, polymerases were discovered that transcribe and reverse-transcribe six different genetic systems: HNA, CeNA, LNA, ANA, FANA and TNA. The experiments demonstrated that these unnatural DNA sequences could be rendered into various XNAs when the polymerases were fed the appropriate XNA substrates. 

Using these enzymes as tools for molecular evolution, the team evolved the first example of an HNA aptamer through iterative rounds of selection and amplification. Starting from a large pool of DNA sequences, a synthetic polymerase was used to copy the DNA library into HNA. The pool of HNA molecules was then incubated with an arbitrary target. The small fraction of molecules that bound the target were separated from the unbound pool, reverse transcribed back into DNA with a second synthetic enzyme and amplified by PCR. After many repeated rounds, HNAs were generated that bound  HIV trans-activating response RNA (TAR) and hen egg lysosome (HEL), which were used as binding targets.) “This is a synthetic Darwinian process,” Chaput says. “The same thing happens inside our cells, but this is done in vitro.”

The method for producing XNA polymerases draws on the path-breaking work of Holliger, one of the lead authors of the current study. The elegant technique uses cell-like synthetic compartments of water/oil emulsion to conduct directed evolution of enzymes, particularly polymerases. By isolating self-replication reactions from each other, the process greatly improves the accuracy and efficiency of polymerase evolution and replication. “What nobody had really done before,” Chaput says,  “is to take those technologies and apply them to unnatural nucleic acids. ”

Chaput also underlines the importance of an international collaboration for carrying out this type of research, particularly for the laborious effort of assembling the triphosphate substrates needed for each of the 6 XNA systems used in the study:  

“What happened here is that a community of scientists came together and organized around this idea that we could find polymerases that could be used to open up biology to unnatural polymers. It would have been a tour de force for any lab to try to synthesize all the triphosphates, as none of these reagents are commercially available.” 

The study advances the case for a pre-RNA world, while revealing a new class of XNA aptamers capable of fulfilling myriad useful roles. Although many questions surrounding the origins of life persist, Chaput is optimistic that solutions are coming into view: “Further down the road, through research like this, I think we’ll have enough information to begin to put the pieces of the puzzle together.” 

The research group consisted of investigators from the Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, led by Philipp Holliger; the Institute, Katholieke Universiteit Leuven, Belgium, led by Piet Herdewijn; the Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, led by Jesper Wengel; and the Biodesign Institute at Arizona State University, led by John Chaput. 

In addition to his appointment at the Biodesign Institute, John Chaput is an associate professor in the Department of Chemistry and Biochemistry, in the College of Liberal Arts & Sciences.

Richard Harth

Science writer, Biodesign Institute at ASU

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Track and field heads west for Mt. SAC Relays


April 19, 2012

ASU Notes - Mt. SAC Relays Get Acrobat Reader

The Arizona State University track and field team will hit the road for the first time this season as the squad heads to Walnut, Calif., for the annual Mt. SAC Relays hosted by Mt. San Antonio College.  The pretigious event features some of the elite competition from across the world, collegiately or post-collegiately.  The Sun Devils will send members from the majority of the team, including the jumps. distance and women’s sprints.  The men enter the weekend ranked 8th in the country while the women sit 16th.  This will be the first time this season the Sun Devils have travelled as a team away from home after hosting four home meets to start the 2012 outdoor campaign.  Download Full Image

OUT OF THE BLOCKS

•  The Sun Devil men are coming off a trophy-earning fourth-place finish at the NCAA Indoor Championships in Boise earlier in March.  The men saw two national champions crowned in Jordan Clarke in the shot put and Mason McHenry at 800 meters.

•  The Sun Devil women return two first team outdoor All-Americans this season in Anna Jelmini (discus) and Christabel Nettey (long jump).

• Head coach Greg Kraft is in his 16th season at Arizona State, the third-longest tenure of any of ASU’s current sports coaches.

• Junior Jordan Clarke is currently ranked in the NCAA top-15 in three throwing events (1st in the shot put, 9th in the hammer and 19th in the discus)

Jordan Clarke is the NCAA”s returning shot put champion outdoors and will be the returning champion when the team reaches the 2013 indoor season as well after his performance in Boise earlier this year. 

• The Sun Devil men currently rank 8th nationally while the women sit 16th

• The Sun Devil men and women have combined for 23 marks in the top 25 in the nation (12 men, 11 women) heading into the weekend and the ASU men have both relays ranked in the top 10 nationally.

IN THE RANKINGS: USTFCCCA TOP 25

After a relatively down weekend on the track last weekend, the Sun Devil men and women each dropped one position in the USTFCCCA computer rankings released earlier this week.  The men sit 8th entering the weekend while the women are ranked 16th. 

IN THE RANKINGS: USTFCCCA WEST REGION

The ASU men still maintain the top stop in the West Regional rankings, holding an advantage of nearly thirty points over Oregon with 717.49 points to the Ducks’ 689.24.  The ASU women remain third in the West region with 616.83 points behind Oregon and Stanford.

FOLLOW LIVE

There will be live results available from the Mt. SAC Relays at http://www.mtsacrelays.com/results.html.

THROWING THEIR WEIGHT

Over the past 10 years, David Dumble has continued to bring in top talent and build the throws program at Arizona State, which has collected 13 total national titles, including the shiny new trophy earned by Jordan Clarke at the NCAA Indoor Championships just two weeks ago.  With Clarke the defending indoor AND outdoor national champion and Anna Jelmini the top returning discus thrower in the nation, the ASU throws team looks to continue their perennial dominance of the event into the outdoor season.

NETTEY POT

Christabel Nettey looked up to snuff with her outdoor long jumping self that earned first-team All-America honors last season as she soared 6.58m (21-07.25) in the team’s season opener at the Baldy Castillo Invitational for a new career best and improved her second-place hold on ASU’s all-time list in the event.  Nettey also moved into second all-time at ASU in the triple jump with her leap of 12.80m (42-00.00) at the ASU Invite.  Both marks rank in the top 20 nationally this season.

RUNNING RELAY FAST

The ASU men’s relay teams strutted their stuff at the Sun Angel Classic with the men’s 4x100m of Daniel Auberry, Chris Burrows, Rashad Ross and Ryan Milus clocking a time of 39.12 that ranks fourth in the country thus far.  The 4x400m team of Kelsey Caesar, Chris Burrows, John Kline and Will Henry currently sits seventh as well with their season opening time of 3:05.29.  

I’VE GOT A HINCH

Before the 2012 season even got underway, head coach Greg Kraft said that Derick Hinch, a junior college pole vault transfer out of Cuesta College in California, would be one of the team’s dark horse as it fights for Pac-12 dominance this year.  Hinch looked to be playing the part at the ASU Invite as he soared 5.50m (18-00.50) for the second-best jump in school history and the current third-best pole vault in the nation. 

PINNICK BASKET

Keeping track of Keia Pinnick at a track meet isn’t always an easy task.  The junior does just about everything for the Sun Devils and showed it at the Jim Click Combined Events in Tucson as she set a career best in the heptathlon with a score of 5,622.  That score sits fourth in the nation in 2012 and would have been good for fifth at the NCAA Championships in 2011.  Not only that, but it moves Pinnick to third on ASU’s all-time descending order list in the event.

RUNNING FOR MILUS AND MILES

If there is such a thing as a sophomore slump, Ryan Milus is showing no symptoms of it early in the 2012 outdoor season.  The second-year runner broke the meet record at the ASU invite with a career-best time of 10.21 in the 100-meter dash and followed it up with a career-best 20.86 in the 200-meter dash later in the event.  Milus currently sits ninth in the nation at 100 meters and 17th at 200 meters. 

GRAND MASON

Another student-athlete not looking at any dropoff is Mason McHenry at 800 meters.  After winning the 2012 NCAA Indoor Championship in the event, McHenry clocked a new outdoor best of 1:47.60 at the ASU Invite for the fifth-fastest time in the country and second-fastest in school history. 

SHELBY GT800

Freshman Shelby Houlihan is fast becoming one of the top middle-distance runners to ever come through Tempe and she’s only competed in just a handful of races.  Competing against several potential Olympians at the Sun Angel Classic, Houlihan clocked a freshman record and the fifth-fastest time in the country in 2:03.85 for the third-best time in school history in just her second outdoor 800-meter run.  

A MAN OF MANY DIFFERENT HATS

Jordan Clarke has wasted little time establishing himself as one of the top all-around throwers in the country with his recent performances.  Clarke ranks in the top 15 in three events currently, sitting first in the shot put, ninth in the hammer and 19th in the discus throw.  Clarke is the only thrower in the nation that can lay claim to such a feat and also finds himself ranked in the top-10 on ASU’s all-time lists in each of the three events as well. 

EVERYTHING IS JEL-ING

Clarke isn’t the only Sun Devil turning it on in the throws.  Sophomore Anna Jelmini finds herself ranked second in the discus and seventh in the shot put events early this season.  Jelmini has also already set a career-best in the hammer throw this season and she, too, finds herself ranked in ASU’s top-10 in all three events.

FLYING HIGH

Bryan McBride has come on strong in his sophomore campaign and finds himself fast rising the ASU all-time ranks in the process.  McBride currently ranks ninth in the nation with his career outdoor best of 2.20m (7-02.50) in both oudoor contests he has competed in this year, good for seventh on ASU’s all-time list.  In addition, McBride is becoming a solid addition in the triple jump as well, setting a career best at the Sun Angel Classic with a leap of 15.38m.

TRIPLE THE EXCITEMENT

Chris Benard is another one fast making his mark in the ASU record books.  Benard soared 16.38m at the Sun Angel Classic for the second-best mark in the nation this far in 2012 and the third-best jump in school history for the ASU All-American.  Benard also set a new career best in the long jump with a leap of 7.75m to move right on the cusps of ASU’s all-time top-10 list in the process.

IN THE TOP 10 ALL-TIME - OUTDOORS

The Sun Devils are starting to get into the swing of things and, as such, the record book is starting to need some re-writing.  Thus far in 2012, four student-athletes have etched their names in the record books for the first time while 10 athletes in 11 events have all improved upon prior record book marks. Derick Hinch, Andrea Crook, Chris Benard and Shelby Houlihan are the newest additions to the list, with Hinch moving to second all-time in the pole vault, Crook seventh in the triple jump, Benard third in the triple jump and Houlihan ninth in the 1,500-meter run and third in the 800m.   Christabel Nettey is pacing the way for the returners, as she has improved to second in both the long jump and triple jump. Ryan Milus (100m), Mason McHenry (800m), Bryan McBride (high jump), Shaylah Simpson (pole vault), Linda Kuenzi (pole vault), Jordan Clarke (hammer), Ashley Lampley (hammer) Anna Jelmini (hammer) and Keia Pinnick (heptathlon) have all also improved upon marks they already held within the top 10.