Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Stability of mRNA/DNA and DNA/DNA Duplexes modulates mRNA Transcription

14.03.2007
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.

The study was funded by Alexander von Humboldt Foundation Return Fellowship and NATO Grant EAP.RIG.981642.

The work was conducted by current and former scientists from the Institute of Molecular Biology at Bulgarian Academy of Sciences. Assen Roguev, Dragomir Krastev, and Anna Ivanova are currently working at the University of California, San Francisco, Max Planck Institute of Molecular Cell Biology and Genetics in Dresden and Carl Gustav Carus Medical School, Dresden University of Technology, respectively. Three of the co-authors (Rayna Kraeva Dragomir Krastev and Anna Ivanova) were diploma students while working on this study. “There is no adequate financial support for PhD students and postdoctoral fellows in Bulgarian scientific institutions. Therefore, I am working predominantly with well prepared and highly motivated diploma students,” says Stoynov.

The Institute of Molecular Biology at the Bulgarian Academy of Sciences was founded in 1960 and is the leading research and training institution in Bulgaria in the field of molecular biology and biochemistry.

Andrew Hyde | alfa
Further information:
http://www.plosone.org
http://dx.doi.org/10.1371/journal.pone.0000290

Further reports about: DNA DNA/DNA Nucleotide RNA/DNA Stoynov duplet mRNA mRNA/DNA thermodynamic

More articles from Life Sciences:

nachricht Protein interaction helps Yersinia cause disease
21.08.2018 | Schwedischer Forschungsrat - The Swedish Research Council

nachricht Nanobot pumps destroy nerve agents
21.08.2018 | American Chemical Society

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: It’s All in the Mix: Jülich Researchers are Developing Fast-Charging Solid-State Batteries

There are currently great hopes for solid-state batteries. They contain no liquid parts that could leak or catch fire. For this reason, they do not require cooling and are considered to be much safer, more reliable, and longer lasting than traditional lithium-ion batteries. Jülich scientists have now introduced a new concept that allows currents up to ten times greater during charging and discharging than previously described in the literature. The improvement was achieved by a “clever” choice of materials with a focus on consistently good compatibility. All components were made from phosphate compounds, which are well matched both chemically and mechanically.

The low current is considered one of the biggest hurdles in the development of solid-state batteries. It is the reason why the batteries take a relatively long...

Im Focus: Color effects from transparent 3D-printed nanostructures

New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference

Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

LaserForum 2018 deals with 3D production of components

17.08.2018 | Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

 
Latest News

A paper battery powered by bacteria

21.08.2018 | Power and Electrical Engineering

Protein interaction helps Yersinia cause disease

21.08.2018 | Life Sciences

Biosensor allows real-time oxygen monitoring for 'organs-on-a-chip'

21.08.2018 | Medical Engineering

VideoLinks
Science & Research
Overview of more VideoLinks >>>