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Adenosine monophosphate forms ordered arrays in multilamellar lipid matrices: insights into assembly of nucleic acid for primitive life.

Toppozini L, Dies H, Deamer DW, Rheinstädter MC - PLoS ONE (2013)

Bottom Line: Bragg peaks corresponding to the lateral organization of the confined AMP molecules were observed.Instead of forming a random array, the AMP molecules are highly entangled, with the phosphate and ribose groups in close proximity.This structure may facilitate polymerization of the nucleotides into RNA-like polymers.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada. toppozl@mcmaster.ca

ABSTRACT
A fundamental question of biology is how nucleic acids first assembled and then were incorporated into the earliest forms of cellular life 4 billion years ago. The polymerization of nucleotides is a condensation reaction in which phosphodiester bonds are formed. This reaction cannot occur in aqueous solutions, but guided polymerization in an anhydrous lipid environment could promote a non-enzymatic condensation reaction in which oligomers of single stranded nucleic acids are synthesized. We used X-ray scattering to investigate 5'-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix composed of dimyristoylphosphatidylcholine. Bragg peaks corresponding to the lateral organization of the confined AMP molecules were observed. Instead of forming a random array, the AMP molecules are highly entangled, with the phosphate and ribose groups in close proximity. This structure may facilitate polymerization of the nucleotides into RNA-like polymers.

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Related in: MedlinePlus

Projections of the 2-dimensional data in Figures 2 along the A in-plane and B out-of-plane axis. AMP:DMPC 3∶1 (red); AMP:DMPC 2∶1 (blue) AMP:DMPC 1∶1 (magenta); AMP:DMPC 1∶2 (cyan); DMPC only (green). The lateral arrangement of the AMP molecules was determined from the in-plane peaks in A. The distance between two bilayers in the stack is determined by the analysis of the out-of-plane reflections in B.
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pone-0062810-g003: Projections of the 2-dimensional data in Figures 2 along the A in-plane and B out-of-plane axis. AMP:DMPC 3∶1 (red); AMP:DMPC 2∶1 (blue) AMP:DMPC 1∶1 (magenta); AMP:DMPC 1∶2 (cyan); DMPC only (green). The lateral arrangement of the AMP molecules was determined from the in-plane peaks in A. The distance between two bilayers in the stack is determined by the analysis of the out-of-plane reflections in B.

Mentions: For a quantitative analysis of the diffracted intensity, the 2-dimensional data were cut along the out-of-plane and in-plane axes. As in-plane features are usually orders of magnitude weaker than the pronounced out-of-plane reflections, slices 0.03 Å−1< qz <0.3 Å−1 were integrated to enhance the data quality. The results for all samples are shown in Figure 3A and B. The lamellar spacings dz of the membrane/AMP complexes, i.e., the distance between two bilayers in the membrane stack, was determined from the specular reflectivity in Figure 3 b) and are shown in Figures 4A–E. Because the complexes were prepared by drying and fusion of unilamellar vesicles in an AMP solution [5], [6], two lipid bilayers enclose the AMP molecules from above and below. The AMP phase of the complex, therefore, coexists with a pure DMPC phase. The lowest slope of each plot was assigned to the pure DMPC bilayer spacing (dzlipid). Figure 4A shows the lamellar spacing of a single component lipid bilayer. Two distinct dz-spacings are observed for AMP:DMPC 1∶2 in Figure 4B. Figures 4C, D and E feature up to four different slopes for the higher concentrated samples, AMP:DMPC 1∶1, AMP:DMPC 2∶1 and AMP:DMPC 3∶1. For each concentration, the increase in lamellar spacing in the presence of AMP molecules was compared to the dzlipid of the coexisting DMPC phase, dz–dzlipid = mΔd, where m is an integer number. The result is plotted in Figure 5E. The data points for all concentrations fall on the same line through the origin and are well fit by a Δd of Δd = 2.67 Å. We assign this increment to the thickness of an interstitial single layer of AMP molecules. Δd = 2.67 Å indicates that the quasi 2-dimensional AMP molecules take a flat position between the stacked bilayers.


Adenosine monophosphate forms ordered arrays in multilamellar lipid matrices: insights into assembly of nucleic acid for primitive life.

Toppozini L, Dies H, Deamer DW, Rheinstädter MC - PLoS ONE (2013)

Projections of the 2-dimensional data in Figures 2 along the A in-plane and B out-of-plane axis. AMP:DMPC 3∶1 (red); AMP:DMPC 2∶1 (blue) AMP:DMPC 1∶1 (magenta); AMP:DMPC 1∶2 (cyan); DMPC only (green). The lateral arrangement of the AMP molecules was determined from the in-plane peaks in A. The distance between two bilayers in the stack is determined by the analysis of the out-of-plane reflections in B.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3646914&req=5

pone-0062810-g003: Projections of the 2-dimensional data in Figures 2 along the A in-plane and B out-of-plane axis. AMP:DMPC 3∶1 (red); AMP:DMPC 2∶1 (blue) AMP:DMPC 1∶1 (magenta); AMP:DMPC 1∶2 (cyan); DMPC only (green). The lateral arrangement of the AMP molecules was determined from the in-plane peaks in A. The distance between two bilayers in the stack is determined by the analysis of the out-of-plane reflections in B.
Mentions: For a quantitative analysis of the diffracted intensity, the 2-dimensional data were cut along the out-of-plane and in-plane axes. As in-plane features are usually orders of magnitude weaker than the pronounced out-of-plane reflections, slices 0.03 Å−1< qz <0.3 Å−1 were integrated to enhance the data quality. The results for all samples are shown in Figure 3A and B. The lamellar spacings dz of the membrane/AMP complexes, i.e., the distance between two bilayers in the membrane stack, was determined from the specular reflectivity in Figure 3 b) and are shown in Figures 4A–E. Because the complexes were prepared by drying and fusion of unilamellar vesicles in an AMP solution [5], [6], two lipid bilayers enclose the AMP molecules from above and below. The AMP phase of the complex, therefore, coexists with a pure DMPC phase. The lowest slope of each plot was assigned to the pure DMPC bilayer spacing (dzlipid). Figure 4A shows the lamellar spacing of a single component lipid bilayer. Two distinct dz-spacings are observed for AMP:DMPC 1∶2 in Figure 4B. Figures 4C, D and E feature up to four different slopes for the higher concentrated samples, AMP:DMPC 1∶1, AMP:DMPC 2∶1 and AMP:DMPC 3∶1. For each concentration, the increase in lamellar spacing in the presence of AMP molecules was compared to the dzlipid of the coexisting DMPC phase, dz–dzlipid = mΔd, where m is an integer number. The result is plotted in Figure 5E. The data points for all concentrations fall on the same line through the origin and are well fit by a Δd of Δd = 2.67 Å. We assign this increment to the thickness of an interstitial single layer of AMP molecules. Δd = 2.67 Å indicates that the quasi 2-dimensional AMP molecules take a flat position between the stacked bilayers.

Bottom Line: Bragg peaks corresponding to the lateral organization of the confined AMP molecules were observed.Instead of forming a random array, the AMP molecules are highly entangled, with the phosphate and ribose groups in close proximity.This structure may facilitate polymerization of the nucleotides into RNA-like polymers.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada. toppozl@mcmaster.ca

ABSTRACT
A fundamental question of biology is how nucleic acids first assembled and then were incorporated into the earliest forms of cellular life 4 billion years ago. The polymerization of nucleotides is a condensation reaction in which phosphodiester bonds are formed. This reaction cannot occur in aqueous solutions, but guided polymerization in an anhydrous lipid environment could promote a non-enzymatic condensation reaction in which oligomers of single stranded nucleic acids are synthesized. We used X-ray scattering to investigate 5'-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix composed of dimyristoylphosphatidylcholine. Bragg peaks corresponding to the lateral organization of the confined AMP molecules were observed. Instead of forming a random array, the AMP molecules are highly entangled, with the phosphate and ribose groups in close proximity. This structure may facilitate polymerization of the nucleotides into RNA-like polymers.

Show MeSH
Related in: MedlinePlus