Search NASA⌕ Search
Home/Archive/NASA NTRS

NASA NTRS · 20050000438

An RNA motif that binds ATP

Sassanfar, M.·Szostak, J. W.
View original source ↗Export metadata ↓

Abstract

RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.

Explore related subjects

NASA Discipline ExobiologyNon-NASA CenterNASA Program ExobiologyNASA Discipline Number 52-20Adenosine Triphosphate/metabolismRNA/chemistry/isolation & purification/metabolismChromatographySupport, Non-U.S. Gov'tDNAConsensus SequenceBase SequenceMolecular Sequence DataNucleic Acid ConformationBinding SitesSupport, U.S. Gov't, P.H.S

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sassanfar, M., Szostak, J. W.. 1993-08-05. An RNA motif that binds ATP. https://ntrs.nasa.gov/citations/20050000438

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related reports

NASA NTRS2003

Planetary protection and the search for life beneath the surface of Mars

The search for traces of extinct and extant life on Mars will be extended to beneath the surface of the planet. Current data from Mars missions suggesting the presence of liquid water early in Mars' history and mathematical modeling of the fate of water on Mars imply that liquid water may exist deep beneath the surface of Mars. This leads to the hypothesis that life may exist deep beneath the Martian surface. One possible scenario to look for life on Mars involves a series of unmanned missions culminating with a manned mission drilling deep into the Martian subsurface (approximately 3Km), collecting samples, and conducting preliminary analyses to select samples for return to earth. This mission must address both forward and back contamination issues, and falls under planetary protection category V. Planetary protection issues to be addressed include provisions stating that the inevitable deposition of earth microbes by humans should be minimized and localized, and that earth microbes and organic material must not contaminate the Martian subsurface. This requires that the drilling equipment be sterilized prior to use. Further, the collection, containment and retrieval of the sample must be conducted such that the crew is protected and that any materials returning to earth are contained (i.e., physically and biologically isolated) and the chain of connection with Mars is broken. c2002 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

NASA Discipline Exobiology↗
NASA NTRS2003

Common 5S rRNA variants are likely to be accepted in many sequence contexts

Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The results demonstrate that changes that occur multiple times in a local region of RNA sequence space in fact usually will be accepted in any sequence context in that same local region.

NASA Discipline Exobiology↗