The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5’-hydroxy-3’-phosphate partially self-complementary DNA 14mers with 3’-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.
Non-enzymatic ligation Liquid crystals DNA self-assembly Aqueous two-phase systems Compartmentalization Origin of life
This is a preview of subscription content, log in to check access
This work was supported by the Grant PRIN Program of the Italian MIUR Ministry and by NSF MRSEC Grants 0820579 and 1420736, and NSF Biomolecular Materials Grant 1207606. We are indebted to Rosanna Asselta and Giorgio Dieci for the useful suggestions and stimulating discussions.
T.B., N.A.C., G.Z., T.P.F. conceived the experiment; T.P.F., analyzed the PEG/EDC/DNA phase diagrams; T.P.F. performed the ligation experiments; T.P.F., V.R. performed the gel runs; T.B., T.P.F., G.Z., V.R. analyzed the gel profiles; T.B., N.A.C., T.P.F. wrote the paper.
Competing Financial Interests
The authors declare no competing financial interests.
De Duve C (2005) Singularities - landmarks on the pathways of life. Cambridge University Press, CambridgeCrossRefGoogle Scholar
De Michele C, Bellini T, Sciortino F (2012) Self-assembly of bifunctional patchy particles with anisotropic shape into polymers chains: Theory, simulations, and experiments. Macromolecules 45:1090–1106CrossRefGoogle Scholar
Kuriabova T, Betterton MD, Glaser MA (2010) Linear aggregation and liquid-crystalline order: comparison of Monte Carlo simulation and analytic theory. J Mater Chem 20:10366–10383. doi:10.1039/c0jm02355hCrossRefGoogle Scholar
Mamajanov I, Macdonald PJ, Ying J et al (2014) Ester formation and hydrolysis during Wet − Dry cycles : generation of Far-from-equilibrium polymers in a model prebiotic reaction. Macromolecules 47:1334–1343CrossRefGoogle Scholar
Maniatis T, Jeffrey A, Van deSande H (1975) Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 14:3787–3794. doi:10.1021/bi00688a010PubMedCrossRefGoogle Scholar
Mezzina E, Mariani P, Itri R et al (2001) The self-assembly of a lipophilic guanosine nucleoside into polymeric columnar aggregates: the nucleoside strucutre contains sufficient information to drive the process towards a strikingly regular polymer. Chemistry 7:388–395PubMedCrossRefGoogle Scholar
Mungi CV, Rajamani S (2015) Characterization of RNA-like oligomers from lipid-assisted nonenzymatic synthesis: implications for origin of informational molecules on early earth. Life (Basel, Switzerland) 5:65–84. doi:10.3390/life5010065Google Scholar
Shabarova ZA, Dolinnaya NG, Drutsa VL et al (1981) DNA like duplexes with repetitions III. Efficient template-guided chemical polymerization of d (TGGCCAAGCTp). Nucleic Acids Res 9:5747–5761PubMedCentralPubMedCrossRefGoogle Scholar
Taran O, Thoennessen O, Achilles K, von Kiedrowski G (2010) Synthesis of information-carrying polymers of mixed sequences from double stranded short deoxynucleotides. J Syst Chem 1:9CrossRefGoogle Scholar
Tombolato F, Ferrarini A (2005) From the double-stranded helix to the chiral nematic phase of B-DNA: a molecular model. J Chem Phys 122:054908CrossRefGoogle Scholar
Zanchetta G, Nakata M, Buscaglia M et al (2008c) Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers. Proc Natl Acad Sci U S A 105:1111–1117PubMedCentralPubMedCrossRefGoogle Scholar
Zielinski WS, Orgel LE (1987) Oligoanminonucleoside phosphoramidates. Oligomerization of dimers of 3’-amino-3’-deoxynucleotides (GC and CG) in aqueous solution. Nucleic Acids Res 15:1699PubMedCentralPubMedCrossRefGoogle Scholar