Fingerprinting Non-Terran Biosignatures

Abstract

Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly different on other planets and moons, particularly as we expand our efforts to explore ocean worlds like Europa and Enceladus. We propose a new concept for life detection that harnesses the power of DNA sequencing to yield intricate informatics fingerprints, even for life that is not nucleic acid-based. The concept is based on the fact that folded nucleic acid structures (aptamers) have been shown to be capable of binding a wide variety of compounds, whether inorganic, organic, or polymeric, and irrespective of being from a biotic or abiotic source. Each nucleic acid sequence can be thought of as a code, and a combination of codes as a "fingerprint." Over multiple analytes, the "fingerprint" of a non-terran sample can be analyzed by chemometric protocols to provide a classifier of molecular patterns and complexity. Ultimately the chemometric fingerprints of living systems, which may differ significantly from nonliving systems, could provide an empirical, agnostic means of detecting life. Because nucleic acids are exponentially amplified by the polymerase chain reaction, even very small input signals could be translated into a robust readable output. The derived sequences could be identified by a small, portable sequencing device or by capture and optical imaging on a DNA microarray. Without presupposing any particular molecular framework, this agnostic approach to life detection could be used from Mars to the far reaches of the Solar System, all within the framework of an instrument drawing little heat and power. Key Words: Agnostic biosignatures-Astrobiology-Chemometrics-DNA sequencing-Life detection-Proximity ligation assay. Astrobiology 18, 915-922.

FIG. 1.

Primary, secondary, and tertiary structure contribute to single-stranded DNA sequences that fold into functional aptamers that can bind to a variety of analytes.

FIG. 2.

Nucleic acid binding can provide information that could reveal unknown life. After mixing a large, randomly generated library of folded oligonucleotides with a sample, many diverse oligonucleotides will bind to a complex surface like a cell membrane, whereas far fewer will bind to an inorganic crystalline substrate. Bound sequences can then be amplified and sequenced, revealing the diversity of binding sites within a sample.

FIG. 3.

For each library member, only one primer-binding site is present at the 35-mer terminus. For amplification to occur, two 35-mers must be ligated. Ligation can be carried out in the presence of a short binding DNA splint and a ligase, such as T4 DNA ligase, that utilizes a template to increase the efficiency of ligation (the ligation can also be carried out without a splint, using ligases that do not require templates).

FIG. 4.

Initial data demonstrate the power of chemometrics. A small collection of aptamers and four human cell lines suggest unique patterns of response to the sequenced aptamer panel, with some aptamers only binding to a particular cell line and with many aptamers binding to multiple cell lines in characteristic amounts. This PCA score plot shows that four cell lines can be classified based solely on the variance in the fold change of the aptamer pool. PCA reveals, with no prior bias, that the pool of nucleic acids could pattern differences between very similar cell surface attributes, yet reproducibly reveal differences in repetitions of the cell samples. While the focus of these results is on cells (useful from the point of view of identifying cell-like objects), they are equally applicable to smaller analytes as well. Adapted from the work of Goodwin et al. (2015).