Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson–Crick selectivity

Smith, Gregory P.; Fraccia, Tommaso P.; Todisco, Marco; Zanchetta, Giuliano; Zhu, Chenhui; Hayden, Emily; Bellini, Tommaso; Clark, Noel A.

doi:10.1073/pnas.1721369115

Cited by 50 publications

(78 citation statements)

References 65 publications

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“…Hydrogen‐bond‐mediated pairing of nucleobases covalently linked to planar/aromatic molecules drives the formation of molecular cages or assemblies able to produce electron or energy transfer . Recently, it has been discovered that triphosphate nucleotides at low temperature and high concentration produce chromonic columnar liquid crystals, in which the bases are stacked and hydrogen bonded as in natural DNA duplexes …”

Section: Introductionmentioning

confidence: 99%

“…[4a] Recently,i t has been discovered that triphosphate nucleotides at low temperaturea nd high concentration produce chromonic columnar liquid crystals, in which the bases are stacked and hydrogen bonded as in natural DNA duplexes. [7] Molecules containing both ap eptideb ackbone anda nucleobase also show interesting properties;f or example, nucleopeptides, which are composed of short homo-or heteropeptides conjugated to nucleobases, have been shown to self-assemble into supramolecular nanofibers and hydrogels. [8] Recents tudies demonstrate that peptide nucleic acid (PNA)-based molecules self-assemblet oy ield fluorescent aggregates.…”

Section: Introductionmentioning

confidence: 99%

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Fluorescence and Morphology of Self‐Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates

Avitabile

Diaferia

Roviello

et al. 2019

Chemistry A European J

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Studies carried out in recent decades have revealed that the ability to self‐assemble is a widespread property among biomolecules. Small nucleic acid moieties or very short peptides are able to generate intricate assemblies endowed with remarkable structural and spectroscopic properties. Herein, the structural/spectroscopic characterization of aggregates formed by nucleobases and peptide nucleic acid (PNA)–peptide conjugates are reported. At high concentration, all studied nucleobases form aggregates characterized by previously unreported fluorescence properties. The conjugation of these bases, as PNA derivatives, to the dipeptide Phe–Phe leads to the formation of novel hybrid assemblies, which are characterized by an amyloid‐like association of the monomers. Although these compounds share the same basic cross‐β motif, the nature and number of PNA units have an important impact on both the level of structural order and the intrinsic fluorescence of the self‐assembled nanostructure.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fluorescence and Morphology of Self‐Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates

Avitabile

Diaferia

Roviello

et al. 2019

Chemistry A European J

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“…This might be due to the overall effect of PEG on the viscosity of the solution that levels the effect of nucleotide stacking on diffusion coefficients, such that no observable differences were detected in the diffusion coefficients, even at different concentrations. Importantly, spontaneous formation of columnar liquid crystals has been recently reported for, both, DNA and RNA monomers, at high concentrations and low temperature (Smith et al, 2018).…”

Section: Discussionmentioning

confidence: 96%

NMR-based analysis of nucleotide π-stacking in a crowded environment: Implications for prebiotic reactions

Paithankar

Chugh

Rajamani

2019

Preprint

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The inherent heterogeneity of the prebiotic milieu is often overlooked when studying nonenzymatic reactions. However, it is important to note that the prebiotic soup of a putative 'RNA World' would have been replete with a plethora of molecules resulting from complex chemical syntheses, as well as exogeneous delivery. The presence of such background molecules could lead to pertinent phenomenon such as molecular crowding, which can potentially affect how a reaction would advent in a crowded milieu. In the current study, we have analyzed the effect of crowding on the stacking ability of the RNA monomers, using Nuclear Magnetic Resonance (NMR) spectroscopy. Our findings corroborate that the purine monomers possess better stacking efficiency than pyrimidine based monomers. Significantly, this competence is further enhanced in the presence of a crowding agent. Interestingly, this enhanced stacking could result in higher sequestration of the purine monomers, putting their ready availability for relevant nonenzymatic polymerization and replication reactions into question. Taken together, this study demonstrates the need for systematic biophysical characterization of molecular crowding in the context of prebiotically pertinent processes. Unravelling such phenomena is essential to gather a real understanding of how the transition from abiotic to biotic, would have happened during the origin of life.

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“…3 Q ij Q ik;j Q kl;l (15) where L n are the elastic constants, and ;k ¼ @=@x k are the spatial derivatives. Comparing f FO and f g results in the following relations between the elastic constants:…”

Section: Fine Structures Of Topological Defects: a Study Of Disclinatmentioning

confidence: 99%

“…The formation of LCLC order helped the discovery of DNA structure [11]. Short DNA and RNA oligomers were shown to form chromonic LC phases [7,12,13] that might have played a role in the prebiotic synthesis of long RNA [14,15]. LCLCs have also found applications in real-time biosensors [16,17], polarisers [18,19], controlling nanoparticle self-assembly [20][21][22] and graphene orientations [23].…”

Section: Introductionmentioning

confidence: 99%

Recent progresses in lyotropic chromonic liquid crystal research: elasticity, viscosity, defect structures, and living liquid crystals

Zhou

2018

Liquid Crystals Today

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Lyotropic chromonic liquid crystals (LCLCs) are formed by linear stacks of disc-shaped molecular in water. Combined by weak, non-covalent forces, these aggregates are reversible, flexible and polydisperse. The self-assembly nature of the basic building units gives nematic LCLCs interesting physical properties, such as very small twist K 2 constant as compared with splay K 1 and bend K 3 constants, very large splay η splay and twist η twist viscosities, strong temperature dependence of K 1 , η splay , and η twist , diverse responses to different ionic additives, and large and azimuthally asymmetric disclination cores. We discuss our experimental studies on the viscoelastic properties and the fine structure of disclinations of LCLCs and attribute their unusual properties to the fact that LCLC aggregates are not fixed in size, but vary in response to changes of temperature, concentration and ionic content in the system. We further use these properties to explain intriguing phenomena in the 'living liquid crystals' composed of chromonic liquid crystal and motile bacteria Bacillus Subtilis.

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Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson–Crick selectivity

Cited by 50 publications

References 65 publications

Fluorescence and Morphology of Self‐Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates

Fluorescence and Morphology of Self‐Assembled Nucleobases and Their Diphenylalanine Hybrid Aggregates

NMR-based analysis of nucleotide π-stacking in a crowded environment: Implications for prebiotic reactions

Recent progresses in lyotropic chromonic liquid crystal research: elasticity, viscosity, defect structures, and living liquid crystals

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