A team of researchers led by a National Institutes of Health (NIH) investigator, Teresa Przytycka, Ph.D., has developed a new software tool called AptaTRACE that could be an important advance for drug developers and other scientists who want to identify molecules that bind with high precision to targets of interest.

“This research is an excellent example of how the benefits of ‘big data’ critically depend upon the existence of algorithms that are capable of transforming such data into information,” said Dr. Przytycka, a senior investigator at the National Center for Biotechnology Information (NCBI), a division of the NIH’s National Library of Medicine.

Aptamers are short RNA or DNA molecules that are capable of binding with high affinity and specificity to diverse biological targets.  Aptamers bind to their targets because of features of their sequence and structure that are complementary to the biochemical characteristics of the target’s surface. Possible targets of aptamers include small organic molecules, proteins or protein complexes, virus surfaces and entire cells. This broad range of targets makes aptamers candidates for a wide variety of applications, ranging from molecular biosensors to drug delivery systems to antibody replacement.

AptaTRACE is designed for use in conjunction with High-Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX), a laboratory technique for identifying aptamers.  HT-SELEX allows analyses of millions of sequences to identify the candidates that undergo selection for binding to the target.

The AptaTRACE tool analyzes this data to find the common features (or “motifs”) among the sequences that bind.

AptaTRACE is the first algorithm that uses the full scope of sequencing data from a large number of selection rounds to capture sequence and structure features of aptamers that bind to the target. Such information allows researchers to better understand why some molecules bind and others do not. Understanding these binding motifs is critical for taking advantage of the aptamers identified via the HT-SELEX process to enable modifications that transform aptamers into drug delivery systems targeting specific cells, for example. Research describing AptaTRACE is published in the July 27 issue of Cell Systems.

AptaTRACE is the result of a collaboration between Dr. Przytycka’s group and researchers from the Beckman Research Institute of City of Hope, Duarte, California, led by Dr. John Burnett, and from Freiburg University, Breisgau, Germany, led by Dr. Rolf Backofen. The tool can be downloaded from NCBI at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#aptatools, as well as Cell Systems.

NCBI creates public databases in molecular biology, conducts research in computational biology, develops software tools for analyzing molecular and genomic data, and disseminates biomedical information, all for the better understanding of processes affecting human health and disease.

The world’s largest biomedical library, NLM maintains and makes available a vast print collection and produces electronic information resources on a wide range of topics that are searched billions of times each year by millions of people around the globe.

NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the US Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases.