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Rutgers chemist uses NMR to elucidate protein-DNA interaction

NEWARK — Determining exactly how proteins connect with specific DNA sequences in human cells has eluded researchers and scientists for years. While it has been possible to record the speed at which a protein could bond with DNA, little was known about how proteins located and connected with a specific pattern of DNA to allow genes to express themselves in the form of traits such as facial appearance, hair and eye color or behaviors.

In the July 16 issue of the journal Science, Rutgers-Newark chemistry professor Babis Kalodimos offers a solution to this puzzle in his paper, "Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes." Kalodimos' findings may be the clue researchers need to develop future methods to inhibit the expression of certain genes that may pre-dispose individuals to harmful diseases such as cancer and Alzheimer's disease.

Through the use of the nuclear magnetic resonance (NMR) spectroscopy, Kalodimos and his co-workers were able to determine how proteins slide along the lengthy strands forming the helix structure of DNA until they reach their intended destination a specific DNA sequence. More important, they illustrated in detail how proteins single out their partner DNA out of millions of non-functional ones.

To better understand the scope of the question facing researchers, consider that billions of DNA codes exist within an individual's genetic make-up and the protein must work its way through millions of non-specific DNA sequences in order to locate the correct connection.

DNA (Deoxyribonucleic acid) is a chemical structure that forms chromosomes. Structurally, DNA is a double helix made up of two strands of genetic material spiraled around each other. Each strand contains a sequence of bases (also called nucleotides). A base is one of four chemicals (adenine, guanine, cytosine and thymine). The two strands of DNA are connected at each
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Contact: Peter Haigney
phaigney@andromeda.rutgers.edu
973-353-1663
Rutgers, the State University of New Jersey
15-Jul-2004


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