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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

Structure in A:D 3∶1 bilayers.In the 3∶1 fit in Figure 3A, the planar structure (as in all other AMP/DMPC samples) was found to coexist with another structure. The new crystal structure is compatible with AMP molecules oriented perpendicular to the existing structure. A The coexistence of two crystal structures as viewed in the plane of the bilayers. A unit cell is drawn for clarity. B Crystal structures as viewed from out of the plane of the lipid bilayers. A molecular structure file of the structures is provided in Structure File S3.
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pone-0062810-g006: Structure in A:D 3∶1 bilayers.In the 3∶1 fit in Figure 3A, the planar structure (as in all other AMP/DMPC samples) was found to coexist with another structure. The new crystal structure is compatible with AMP molecules oriented perpendicular to the existing structure. A The coexistence of two crystal structures as viewed in the plane of the bilayers. A unit cell is drawn for clarity. B Crystal structures as viewed from out of the plane of the lipid bilayers. A molecular structure file of the structures is provided in Structure File S3.

Mentions: The positions of the in-plane correlation peaks did not change with increasing AMP concentrations, as indicated by the vertical lines in Figure 3A. The addition of more AMP molecules in more concentrated samples increases the thickness of the AMP layers but did not change the lateral structure. Additional peaks were observed at the highest concentration of AMP:DMPC 3∶1 at positions of q// = 1.1 Å−1, q// = 1.17 Å−1 and q// = 2.2 Å−1. The new peaks co-exist with the structural peaks from the entangled structure in Figure 5D and can be described by a tetragonal unit cell with lattice parameters of a = 5.35 Å and b = 5.7 Å. The resulting structure is compatible with AMP molecules taking an upright position between the bilayers, as shown in Figure 6. This occurs when the thickness of the AMP crystallites becomes larger than the length of an AMP molecule of ∼17.5 Å. The concentration of AMP:DMPC 2∶1, therefore, is the maximum concentration at which the purely 2-dimensional AMP structure in Figure 5D can be observed. The lowest concentration for which this entangled AMP structure was observed in the experiment was the AMP:DMPC 1∶2 ratio. This concentration was found to result in a single layer of AMP molecules between the membranes, as listed in Table 1. We can, however, not exclude that small ordered patches would form at even lower concentrations of AMP.


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)

Structure in A:D 3∶1 bilayers.In the 3∶1 fit in Figure 3A, the planar structure (as in all other AMP/DMPC samples) was found to coexist with another structure. The new crystal structure is compatible with AMP molecules oriented perpendicular to the existing structure. A The coexistence of two crystal structures as viewed in the plane of the bilayers. A unit cell is drawn for clarity. B Crystal structures as viewed from out of the plane of the lipid bilayers. A molecular structure file of the structures is provided in Structure File S3.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646914&req=5

pone-0062810-g006: Structure in A:D 3∶1 bilayers.In the 3∶1 fit in Figure 3A, the planar structure (as in all other AMP/DMPC samples) was found to coexist with another structure. The new crystal structure is compatible with AMP molecules oriented perpendicular to the existing structure. A The coexistence of two crystal structures as viewed in the plane of the bilayers. A unit cell is drawn for clarity. B Crystal structures as viewed from out of the plane of the lipid bilayers. A molecular structure file of the structures is provided in Structure File S3.
Mentions: The positions of the in-plane correlation peaks did not change with increasing AMP concentrations, as indicated by the vertical lines in Figure 3A. The addition of more AMP molecules in more concentrated samples increases the thickness of the AMP layers but did not change the lateral structure. Additional peaks were observed at the highest concentration of AMP:DMPC 3∶1 at positions of q// = 1.1 Å−1, q// = 1.17 Å−1 and q// = 2.2 Å−1. The new peaks co-exist with the structural peaks from the entangled structure in Figure 5D and can be described by a tetragonal unit cell with lattice parameters of a = 5.35 Å and b = 5.7 Å. The resulting structure is compatible with AMP molecules taking an upright position between the bilayers, as shown in Figure 6. This occurs when the thickness of the AMP crystallites becomes larger than the length of an AMP molecule of ∼17.5 Å. The concentration of AMP:DMPC 2∶1, therefore, is the maximum concentration at which the purely 2-dimensional AMP structure in Figure 5D can be observed. The lowest concentration for which this entangled AMP structure was observed in the experiment was the AMP:DMPC 1∶2 ratio. This concentration was found to result in a single layer of AMP molecules between the membranes, as listed in Table 1. We can, however, not exclude that small ordered patches would form at even lower concentrations of AMP.

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