Volume 40 , March 27 , 2007

Please see our “Did You Know?” section toward the end of this issue.  

Topic: Stability of mRNA/DNA and DNA/DNA duplexes modulates mRNA transcription 

For events and conferences please go to the end of the newsletter. If there are any events you would like for us to mention, please send me the name and dates with a website link for further details.

In the news, Washington State has started the Stranger Rape DNA Project that will allow for faster results on DNA tests in cases of rape by strangers. Samples will be sent to a private lab in Dallas, Texas, as part of a new federally funded program.

In Vermont, the Attorney General questions a DNA proposal that would permanently preserve DNA evidence collected in serious crimes like rape, kidnapping, and murder. Supporters of the proposal argue that this law has been enacted in other states where people were cleared by DNA after having been wrongfully convicted. Attorney General Bill Sorrell feels that this is unnecessary in Vermont, as claims of innocence are rare in this state.

Following these stories we are including a number of new and ongoing cases involving the use of DNA evidence.

Stranger Rape DNA Project will speed police work — and already has

The Washington Association of Sheriffs and Police Chiefs have started the Stranger Rape DNA Project, a program that will speed the investigation of stranger-rape cases.

Now when a medical worker examines a rape victim after an attack, the DNA evidence will be sent to a laboratory in Dallas. The evidence will be tested quickly, and the results will be released within 30 days, according to WASPC.

In the past, it could take years for DNA evidence in stranger rapes to be tested in Washington because of a backlog at the State Patrol's crime laboratory, said Aaron Toso of Gordon Thomas Honeywell, a public affairs agency that represents the Washington Association of Sheriffs and Police Chiefs. About 200 stranger rapes occur in Washington state each year, Toso said.

The test results in Dallas will be compared to known suspects and given to the Washington State Patrol so it can be compared to state and national DNA databases, Toso said.

The stranger-rape project has already been put to use.

Last month, an 11-year-old girl was raped at her Olympia home. DNA evidence was flown to Dallas and the results were available in two weeks. Those results exonerated a 23-year-old man arrested in connection with the rape.

David Lynch had been arrested Feb. 6, the day after the rape. He had been living in an elaborate underground bunker a few blocks from her home. Lynch is now at Western State Hospital under a civil commitment that is separate from the criminal case.

Police have since arrested Peter Inouye, 24, who has been charged with rape of a child.

Thurston County Chief Deputy Prosecutor Jon Tunheim said that had it not been for the Stranger Rape DNA Project, it is likely Lynch would still be locked up.

"All the other kinds of evidence pointed pretty strongly at him," Tunheim said. "The DNA was clearly not his. We knew at that point it was time refocus the investigation."

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref01.html 

AG Questions Necessity of DNA Law 

Vermont's Attorney General and a key state lawmaker are squaring off over a proposal that would mandate preservation of DNA evidence in case it could later be used to clear innocent people wrongfully convicted of serious crimes.

Key lawmakers say the DNA Innocence law has been enacted in other states where innocent people were wrongfully convicted and then cleared years later by DNA evidence that was often suppressed by the police, prosecutors, and even judges.

Attorney General Bill Sorrell says that law may be needed in other states, but not in Vermont.

"This is a solution in search of a problem," said Sorrell, who believes the DNA proposal that would permanently preserve DNA evidence collected in serious crimes like rape, kidnapping, and murder is unnecessary.

"I don't want to see innocent people convicted," said Sorrell, who acknowledges that in other states innocent people have been convicted and cleared years later by DNA that was suppressed by authorities.

But he says it can't happen in Vermont, because police and prosecutors must share all evidence with defendants before trial and the record shows that about 95% of people charged with crimes of all types, even murder, end up pleading guilty. So claims of innocence are rare in Vermont.

I'm disappointed to hear the Attorney General comment that way about a senate bill that was a priority for the senate judiciary committee," said Senator Dick Sears, Chair of Judiciary Committee that drafted and strongly supports the DNA innocence proposal. He says Sorrell obviously forgot about the case of former Burlington cop Paul Lawrence, who framed more than 70 innocent people for drug dealing in the seventies and eighties.

"And if somebody's locked up for 20 years for a crime they didn't commit, and can prove their innocence, they deserve to be out, but so that also means the guilty party is not in," said Sears.

In response, Attorney General Sorrell says that the Paul Lawrence drug-frame scandal supports his criticism of the proposed DNA innocence law. Sorrell points out that it was other police officers who caught Lawrence. He was convicted, imprisoned, and every one of the framed innocents, more than 70 of them, was pardoned. Sorrell says the Lawrence case proves the system worked to protect the innocent just as designed, and a DNA innocence law would be unnecessary in Vermont.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref02.html 

New and ongoing stories involving the use of DNA evidence include:

New York - On Jan. 31, 1982, her mother found the body of 19-year-old Michele Mika facedown in bed with an eight-inch carving knife stuck in her back. After she was killed, the police had said, Ms. Mika was sexually assaulted for several hours.

Investigators questioned hundreds of people, and took blood samples from people who had attended a party with Ms. Mika that evening, the Bergen County prosecutor said.

On Wednesday, after more than 25 years, the Bergen police arrested a recovering drug addict in the case, two weeks after being notified of a DNA match. At the time, the search had concentrated on Ms. Mika’s boyfriends, said John L. Molinelli, the county prosecutor, but ultimately, semen left at the scene was traced to her former neighbor, Angelo Speziale, now 45. They had lived on opposite sides of the same duplex on Teaneck Avenue here with their mothers, but were not known to have been romantically involved, Mr. Molinelli said on Thursday.

Mr. Speziale pleaded not guilty to felony murder in Bergen County Superior Court on Thursday and is being held in $2 million bail.

Mr. Molinelli said Hackensack police obtained DNA samples from Mr. Speziale after he was arrested in a shoplifting case in 2005. It was sent to a State Police laboratory to be checked, but because of a large backlog at the lab, Mr. Molinelli said, the Bergen County police were not notified until March 7.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref03.html

Nevada - A registered sex offender in Arkansas has been linked by his DNA to the murder of a woman in Las Vegas in 1985.

Charles Conner, 58, was arrested Tuesday at the probation office in Bentonville after Las Vegas authorities notified police in Arkansas of the match.

Conner was sought for the June 1985 slaying of Beth Lynn Jardine, 23, who was stationed at Nellis Air Force Base. She was raped and beaten to death in her apartment, police said.

Conner was arrested in 1994 in Rogers for rape, kidnapping and burglary. The Crime Lab later obtained a DNA sample from Conner. Last month, Las Vegas police who work in a cold-case unit submitted the DNA evidence, and the match was made.

Conner is being held in the Benton County Jail pending transfer to Las Vegas.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref04.html

Pennsylvania - The DNA of accused killer Jauquin Jaron Byrd matched "touch" DNA found on a hammer and scissors used in last year's murder of Upper Merion resident and Marple Newtown High School graduate Sarah Boone at the Ardmore catering company where she was employed.

Ken Mayberry, a forensic scientist in the Pennsylvania State Police's DNA laboratory, testified Wednesday that there was better than a 99 percent chance the DNA mixture found on the handle of a hammer and pair of scissors found at the murder scene was a combination of DNA matching that of both Boone and Byrd.

Byrd, who was arrested on Feb. 15, 2006, repeatedly has denied the allegations against him, claiming he was not in the Ardmore area on the day of the murder.  
 
However, the prosecution has presented an eyewitness who did business with Byrd earlier that afternoon in Ardmore. 

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref05.html 

Pennsylvania - A DNA sample from a Fayette County man already jailed on other charges led police to issue warrants alleging his involvement in a year-old church burglary.

Robert M. Oros Jr., 28, of Yauger Hollow Road, Lemont Furnace, will be charged with burglarizing St. Cecilia Catholic Church and the Lemont Sportsmen's Club, both in North Union Township, on Nov. 9, 2005.

He is accused of breaking a window in the sportsmen's club, entering and setting off an alarm system. He fled to the nearby St. Cecilia, smashed a window to enter, then damaged the alarm panel, state police at Uniontown said.

Blood samples were recovered from both scenes.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref06.html 

California - After more than 15 years, investigators believe they have identified the killer of 14-year-old Jessica McHenry of Livermore.

At a press conference this afternoon, Alameda County Sheriff's investigators said a DNA match identified former Livermore resident Derick Moncada, 35, as the killer. Investigators believe he may also be connected to another 1991 murder with similar circumstances.

The press conference to announce Moncada's name occurred at 1 p.m. in San Leandro — minutes after a funeral for Moncada concluded in Livermore. According to investigators, Moncada hung himself in his jail cell at Kern Valley Prison in Delano. He died about 2 a.m. on March 13, just hours after Alameda County investigators spoke to him about the McHenry case.

Jessica disappeared from Granada High School on June 11, 1991. Her burnt, partially nude body was found later that day in a turnout on Tesla Road in an unincorporated area of Livermore. Alameda County Sheriff's investigators said she had been raped and strangled.

John Van Rensselaer, supervising deputy for the Kern County coroner's office, said Moncada was found by prison staff about 12:45 a.m. March 13. He had tied a bedsheet around his neck, feet and the bed frame and rolled off the top bunk.

At the press conference, Sgt. Scott Dudek said investigators believe Moncada may be connected to another 1991 murder, in which the burnt, dead body of an unidentified woman was found on Palomares Canyon Road near Castro Valley.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref07.html 
 

Texas - Daniel Ray Gallow, 35 (dob 7/22/61), was sentenced today (3/19/07) to a term of fifty (50) years in the state penitentiary in connection with a 2001 aggravated sexual assault. The sentence resulted from a jury trial in February (2/8/07) in Jefferson County’s first trial based solely on DNA identification of the defendant.  
 
On February 22, 2001, a then 29 year-old Beaumont woman was asleep on the couch of her home in the 3100 block of Grand Street when she was awakened by someone covering her head and face with a cloth jacket. She quickly realized that an unknown attacker whom she described as speaking with a “Cajun” accent had broken into the house. She later came to the conclusion that a second invader was also present.  
 
Late in 2001 results from the DPS Crime Laboratory in Houston indicated that foreign DNA samples were found among the evidence taken from the victim. The genetic fingerprint from the unknown attacker was placed into the C.O.D.I.S. (Combined D.N.A. Index System) database.

When Gallow (a native of Lafayette, Louisiana) was taken into custody to serve a sentence for Indecency with a Child on August 12, 2002, a sample of DNA was taken from him as part of the C.O.D.I.S. inmate sample collection program. It was matched to the “unknown” sample already in the database and was reported to the Beaumont Police Department, where Detective Phillip Gouthier then sought a search warrant for Gallow’s blood. Confirming tests resulted in an indictment for Gallow being handed up by a Jefferson County Grand Jury in April of 2004, while he was still in custody for the Indecency with a Child case.  
 
Gallow also has previous felony convictions for Injury to a Child and Possession of a Controlled Substance in 1994. He must serve twenty-five (25) years of his sentence before he can be considered for parole.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref08.html

Ohio - A forensic scientist said the DNA found on Lindsey Bruce's genitals could have come from the girl he's accused of murdering and, at most, 17 other people among the nearly 1.1 million people in Franklin County.

Improved analysis has halved the number of potential contributors of the DNA since 2005, when Bruce was convicted of kidnapping 5-year-old Emily Rimel from her Madison Township bedroom.

Max Larijani, of the Ohio Bureau of Criminal Identification and Investigation, analyzed three teeth taken from a child's skull found along Big Walnut Creek last May. In Common Pleas Court today, he testified that the DNA was consistent with Emily Rimel's.

He said the DNA was also consistent with the DNA taken from Bruce's genitals shortly after Emily's disappearance. Using a statistical formula, he said that 1-in-61,390 people could be the source of the DNA found on Bruce. That would amount to about 18 people in Franklin County, including Emily, who could have been the source.

Emily disappeared Dec. 7, 2004. Bruce was charged with kidnapping her and raping her. In that case, a state forensic scientist said that 1-in-26,930 people could have been the source of the DNA. That amounts to about 40 people, including Emily.

Bruce was acquitted of rape but sentenced last year to 10 years in prison for kidnapping her.

After the skull was found and teeth analyzed, Bruce was charged with aggravated murder and tampering with evidence.

Bruce, a family friend, was at Emily's apartment early the morning she went missing. In this trial, four men who had been in jail or prison with Bruce have testified that he told them he killed Emily.

Bruce's attorneys are expected to begin their case next week. Bruce faces the death penalty if convicted.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref09.html

California - A Costa Mesa man who was one of 125 men who voluntarily provided samples of their DNA after two women were sexually assaulted in his apartment complex was convicted of both assaults Thursday, and now faces a life term in state prison.

Jose Fernandez Lopez, 34, was arrested in July 2005 after his DNA was matched with evidence from the sexual assaults of two women inside their homes at Newport Village Apartments on West Baker Street.

Costa Mesa detectives spent four nights in June 2005 canvassing the 276-unit apartment complex, informing women of the incidents and asking men to allow a swab to be taken of their inner cheek cells. Only two of the men refused. Lopez was among the 125 men who agreed to provide the swab.

He was living at the apartment complex when the women were attacked in September 2004 and May 2005 but was in the process of moving to Merced after submitting his DNA when police took him into custody.

The victims – ages 67 and 45 – could not identify Lopez as the attacker. But the DNA evidence helped convince a jury after only an hour of deliberations following a four-day trial, said Deputy District Attorney Heather Brown.

Lopez now faces a 125-years-to-life term in state prison at his sentencing April 20 by Superior Court Judge Richard Toohey.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref10.html

Ohio - Three teenage boys arrested after DNA evidence led police to them have admitted to vandalizing school buses.

The boys, two age 15 and one 16, on Wednesday pleaded the juvenile equivalent of guilty to seven counts of felony vandalism. They broke about 140 windows in seven Jackson Local School District buses on New Year's Eve.

DNA was collected from beer cans left at the scene and a bloody strip of gauze.

School officials estimated the damage at $10,000.

Stark County Family Court Judge Jim D. James put the boys on probation and ordered them to complete 200 hours of community service at a recycling center.

The teens also were ordered to pay about $580 each in restitution to the school district, have a drug and alcohol assessment and take victim awareness classes.

One of the boys who had a record was also sentenced to 30 days of juvenile detention.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref11.html 

Utah - A 26-year-old cloud of suspicion over Steven Strom lifted this week as Woods Cross police arrested another man in the 1980 strangling of his wife, Karin Strom.

 
A friend woke Strom early Thursday to tell him that DNA tests linked a former co-worker of his to the crime scene and he was no longer a suspect.  

Earlier this week, a DNA match came back linking 56-year-old Edward Owens to the DNA evidence found under Karin Strom's fingernails, said Woods Cross police Sgt. Brad Benson  

Owens was arrested Wednesday and booked into Davis County jail.  

But questions remain, including the motive for the killing.  

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref12.html

Florida - Police in Jacksonville say DNA evidence connects a jailed inmate with a series of attacks. Investigators have re-arrested 29-year-old Tracy Newton
 
According to police, they traced blood found on a box cutter found in his car, to the DNA of a prostitute critically hurt earlier this year. Police believe Newton could be responsible for attacks on prostitutes and homeless women dating back six years.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref13.html

New Jersey - Police used DNA from a speck of blood to find a man suspected of taking $82,000 worth of jewelry from an Englewood Cliffs home.

On Wednesday, police arrested Pedro Cruz, 38, at his Haledon home and charged him with burglary and theft.

Cruz then confessed to the May 20 break-in, said Deputy Police Chief Michael Cioffi.

Police believe Cruz cut himself while smashing through the sliding doors of the home on Sara Hill Lane, or while jimmying open a small safe in the master bedroom.

A spot of blood on the safe was sent to the state for analysis. A DNA match with Cruz came back.

Cruz allegedly took $1,200 in cash from the safe.

He was transferred to the Bergen County Jail, and bail was set at $125,000.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref14.html 

California - DNA of a gang member accused of killing a sheriff's deputy was found on what is believed to be the murder weapon, according to expert witness testimony on Wednesday.

The jury in the trial of Jose Luis Orozco, a Hawaiian Gardens gang member accused of gunning down Los Angeles County Sheriff's Deputy Jerry Ortiz in 2005, was given a lengthy introduction to basic forensic science Wednesday.

Prosecutors called two sheriff's crime lab experts, who testified about a number of items found at the murder scene, on the victim, on the defendant and on a witness that were tested for DNA.

Several DNA samples were found on the .38-caliber revolver allegedly used by Orozco to shoot Ortiz.

Most of the samples - lifted from the gun's muzzle, trigger, hammer, interior handle and exterior handle - matched Orozco's, said senior criminalist Gregory Wong. The probability that those same DNA samples could match another person, he calculated, were 20 quadrillion to one.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref15.html

Missouri - Prosecutors say that while Lorenzo Gilyard was escaping detection as a serial killer for two decades, advances in DNA testing were being made that would eventually link him to seven women who were killed in Kansas City in 1986 and 1987.

"The defendant wasn’t counting on the fact that science would catch up with him, but it did," said Ted Hunt, chief trial assistant, during closing arguments in the murder trial. "Twenty years later, a part of his own body is pointing a finger back at him."

Six other murder counts, including one stemming from the death of an Austrian national, were dropped last week as the trial got under way, although prosecutors could refile those charges later.

Gilyard, a former trash company supervisor, would face life in prison if convicted of any of the slayings. His fate is being decided by Jackson County District Judge John O’Malley.

Prosecutors made DNA evidence linking Gilyard to all seven women the centerpiece of their presentation. The cases were connected in April 2004 when the police department’s crime lab tested evidence from unsolved homicides using a federal grant.

Gilyard’s semen or seminal fluid was found on six of the women, and his hair was found on the seventh victim. All of the victims were left in sexually compromising positions.

But defense attorney Susan Elliott said the lifestyles of the victims - all but one of whom were prostitutes - suggested it was not only probable but likely that they had sexual contact with other men.

The defense went through each of the cases suggesting alternatives, including that one victim was killed as retaliation for talking to the FBI about a drug supplier and that another had been threatened by a boyfriend before her death.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref16.html

Minnesota - A Red Wing man has been charged with sexually assaulting a woman nearly five years ago, after recent DNA tests identified him as a suspect.

Wilmer Eliel Lopez, 27, was charged last month in Goodhue District Court with two counts of first-degree burglary and one count each of second-degree burglary, third-degree criminal sexual conduct, fourth-degree criminal sexual conduct and fifth-degree criminal sexual conduct. Bail was set at $250,000 without conditions and $75,000 with conditions.

The investigation of the sexual assault began April 21, 2002, when a 26-year-old Red Wing woman told police she'd been assaulted at her home by a man she didn't know, according to a criminal complaint.

Although DNA tests were done using evidence collected from the sexual assault, the case remain unsolved.

On Jan. 30, 2007, the Minnesota Bureau of Criminal Apprehension told a Red Wing police investigator that the profile of the DNA sample from the sexual assault case matched Lopez's DNA profile. On Feb. 1, the alleged victim identified Lopez from a photographic line-up as the man who assaulted her.

When questioned about the case last month, Lopez allegedly told police he was living in Red Wing in 2002 and was doing drugs and having sex with a lot of women then. He did not admit to breaking into the woman's home and sexually assaulting her, according to the complaint.

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref17.html 

Massachusetts - One week before the 15-year statute of limitations ran out on a Dewey Street rape investigation, a former city man with an extensive criminal history was charged in the case, based on a DNA record.  
 
Tyrone Garden, 42, with a last-known address in Boston, was arraigned on a charge of aggravated rape last week in Central District Court in connection with the September 1991 rape of a 33-year-old woman in her Dewey Street apartment. The arraignment came after he finished a jail sentence in an unrelated case.  
 
Mr. Garden was held on $50,000 cash bail and his case was continued to April 5.

 
 
In September, with the 15-year statute of limitations nearing, the court issued a criminal complaint against Mr. Garden.  
 
According to court records and police Sgt. Michael A. Cappabianca of the Special Crimes Division, Mr. Garden’s DNA profile on file with the state led to his arrest.  
 
Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref18.html

New York - It took almost 10 years. 
 
But, as the result of a hit in a DNA databank, a Long Island man has been sentenced to 23 years in prison for a knife-point rape in Queens Village that occurred in 1997. 
 
Gregory Stovall, 38, of 32 Gray Ave., Medford, was sentenced on first-degree rape charges Monday by Justice Robert C. Kohm in Queens Supreme Court. Stovall pleaded guilty on Feb. 5, after his DNA profile had been entered into the National DNA Databank by law enforcement authorities in Virginia. 
 
"The sentence imposed today severely punishes the defendant for his brutal sexual assault and removes him from stepping foot on our streets for many years to come," Queens District Attorney Richard Brown said in a prepared statement released Monday. "The defendant was ultimately done in by his own DNA." 
 
According to the charges, Stovall entered the Queens Village home of the then-34-year-old victim between 6 and 7 p.m. on Dec. 11, 1997, then waited for her to come home from work. 
 
When she entered the home, Stovall, wearing a mask, lunged at her, held a knife to her throat and told her: "Don't do anything stupid. ... You want me to cut your head off?" 
 
When the woman tried to escape, authorities said, Stovall tackled her in the driveway, dragged her back inside the house, then took her to the basement, blindfolded her, bound her feet, cut off her clothing and raped her. 
 
He fled the scene with her car and other items -- including a mink coat, a VCR, a fax machine and even some of her Christmas presents. 
 
For years after the attack, the DNA collected in a sexual assault evidence kit led police nowhere. Then Stovall was charged in a burglary in Virginia in September 2005, authorities said. When his DNA sample was entered into the national databank, officials found a match to the rape evidence in Queens. 

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref19.html 
 

New York - DNA has helped to thaw a cold case for MTA police. 
 
The technology was used to arrest a Connecticut man in a 2002 sexual assault at the Metro-North station in Bridgeport. 
 
46-year-old Jose Benet of Bridgeport, was arrested and arraigned on March 8, MTA police said. 
 
He's charged with aggravated sexual assault in the first degree and is being held on $500,000 bail. 
 
On March 28, 2002, authorities say a woman was walking to the Port Jefferson Ferry terminal from a nearby parking garage when she was abducted at knife point under the walkway entrance to the Bridgeport Train Station. She was then sexually assaulted underneath the station on the banks of the Bridgeport Harbor. The assailant's DNA was recovered during the sexual assault examination routinely performed by hospitals. 
 
MTA and Bridgeport Detectives investigated the case for months without any leads. At the time, the DNA from the sexual assault kit did not match any law enforcement databases. 
 
Police say the case went cold until Monday, March 5. During the investigation of an unrelated case a new search was made of the Connecticut Convicted Offenders DNA Database, and a DNA match was made. 

Source: http://www.dnalabsinternational.com/email_newsletter/vol_40_mar_07/vol40_ref20.html

Did You Know?

Topic: Stability of mRNA/DNA and DNA/DNA duplexes modulates mRNA transcription

The distribution of the four nucleotides along the DNA sequence encodes the genetic information in living systems. However, do nucleic acids possess other attributes that contribute to their biological functions? Recent work of a team led by Stoyno Stoynov, working at the Bulgarian Academy of Sciences, suggests that thermodynamic stability of DNA/DNA and RNA/DNA duplexes influences mRNA transcription. The manuscript appears in the March 14 issue of the international, peer-reviewed, open-access online journal PLoS ONE.

"These findings challenge the way we look at DNA," says Stoynov. "Until now we have pretty much simplified our view of DNA helix as a Lego combination of four different pieces, which encodes genetic information and contain patterns, recognized by DNA binding proteins. However, nucleic acids are real molecules with defined physical characteristics, which can influence their biological functions."

In this work the authors present a calculation of the thermodynamic stability of DNA/DNA and mRNA/DNA duplexes across the genomes of four species in the genus Saccharomyces. The researchers found that genes of these organisms are more stable than intergenic regions near their 3’-end. In addition, introns (internal non-coding regions in genes) are significantly less stable than exons (coding sequences in genes), suggesting that stable sense duplexes are characteristic of the coding sequences.

Next, the authors showed a relationship between the pattern of thermodynamic stability and the mRNA level of genes. There is a general trend of increased mRNA level with increasing thermodynamic stability of the respective gene. Positive correlation was observed between the mRNA level and the stability of DNA/DNA and mRNA/DNA duplexes of both exons and introns. In contrast, an inverse relationship exists between mRNA levels and stability of the region near 3’-end of genes. mRNA levels increase with decreasing thermodynamic stability of this region. "The observed correlations are impressive, given that several other factors like promoter effectiveness, promoter regulation, and mRNA half-life directly influence mRNA level, as well," says Stoynov.

The researchers also observed that, in contrast to intergenic regions, genes have more stable sense RNA/DNA duplexes than potential antisense RNA/DNA duplexes. "The difference between stability of sense and antisense mRNA/DNA is a property that can aid gene discovery," explains Stoynov.

"Thermodynamic stability of nucleic acid duplexes depends primarily on thermodynamic properties of nearest-neighbor nucleotide interactions. Therefore, the stability of DNA/DNA and RNA/DNA duplexes is determined by the distribution of the ten possible DNA/DNA nucleotide duplets (dAA/dTT, dGC/dCG, etc.) and the sixteen possible RNA/DNA duplets (rAA/dTT, rUA/dAT, etc.). Such duplet code does not carry any genetic information but seems to modulate the level of RNA expression. It is amazing that the same nucleotide sequence can simultaneously encode its respective protein and modulate its level of expression." says Stoynov.

The mechanism of how DNA/DNA and mRNA/DNA duplex stability influences mRNA level remains unclear. The authors propose two models, but further work is needed to understand how thermodynamic stability modulates mRNA level.

Source: http://www.eurekalert.org/pub_releases/2007-03/plos-som031207.php 
 

Events and conferences for 2007 that may of interest to you include: 

18th International Symposium on Human Identification - October 1-4, 2007

Renaissance Hollywood Hotel - Hollywood, California

Web site: www.promega.com/geneticsymp18/ 

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