Gözen Ertem

Comet Halley as an aggregate of interstellar dust and further evidence for the photochemical formation of organics in the interstellar medium

Photolysis of mixtures of CO:NH3:H2O at 12 K results in the formation of an organic residue which is not volatile in high vacuum at room temperature. Analysis of this fraction by GC-MS resulted in the detection of C2–C3 hydroxy acids and hydroxy amides, glycerol, urea, glycine, hexamethylene tetramine, formamidine and ethanolamine. Use of isotopically labeled gases made it possible to establish that the observed products were not contaminants. The reaction pathways for the formation of these products were determined from the position of the isotopic labels in the mass spectral fragments. The significance of these findings to the composition of comets and the origins of life is discussed.

THE ADSORPTION OF NUCLEOTIDES AND POLYNUCLEOTIDES ON MONTMORILLONITE CLAY

The binding of adenine derivatives to Na+-montmorillonite increases in the order 5′-AMP, 3′-AMP, 5′-ADP<adenosine<purine, adenine. With the exception of cytosine, cytosine derivatives bind less strongly than the corresponding adenine derivatives in the order 5′-CMP<cytidine<cytosine. There is little difference in the binding of uracil derivatives and these compounds bind less strongly than the corresponding adenine analogs. It is concluded that the adenine ring in adenine derivatives is protonated by the acidic montmorillonite surface and binding is a consequence of the electrostatic interaction between the protonated base and the negative charges on the surface of the montmorillonite. Different binding trends were observed with Cu2+-montmorillonite with AMP binding more strongly than adenosine and UMP binding more strongly than uridine. It is concluded that ligation to the Cu2+ is a major force in the binding of nucleotides to Cu2+-montmorillonite. RNA homopolymers exhibit strong adsorption to Na+- and Cu2+-montmorillonite and are not readily washed from the clay. Factors contributing to the binding are discussed. Watson-Crick hydrogen bonding of 5′-AMP to poly(U) and 5′-GMP to poly(C) was observed when the homopolymers are bound to the surface of the clay. No association of 5′-UMP to poly(U) bound to clay was detected. The possible role of montmorillonite clays in the prebiotic formation of RNA is discussed.

Sequence- and regio-selectivity in the montmorillonite-catalyzed synthesis of RNA.

The six binary montmorillonite clay-catalyzed reactions of the5′-phosphorimidazolides of adenosine, cytidine, guanosine anduridine were performed and the eight dimers from each reactionwere separated and analyzed by HPLC. A 16–51-fold higher yieldof the 5′-purine-pyrimidine dimers over that of the5′-pyrimidine-purines was observed. The total yield of the5′-purine-pyrimidine dimers was in the 50–70% range while thatof the 5′-pyrimidine-purine dimers was 1.3–7.0%. Less sequenceselectivity was observed in the homodimers formed.Regioselectivity for the formation of 3′, 5′-phosphodiesterbonds over that found in the absence of clay was observed. The5′-purine-pyrimidine, 5′-pyrimidine-pyrimidine and5′-purine-purine dimers had 3′, 5′-links in about half of theirphosphodiester bonds. The percent phosphodiester links in the5′-pyrimidine-pyrimidine dimers was 18%, a value close to thatobserved in the absence of the montmorillonite catalyst. Themontmorillonite-catalyzed reaction of all four activatednucleotides was performed and the 24 products were separated andanalyzed. The trends observed in the binary reactions wereconfirmed and the results also showed that the relativereactivity of the activated monomers was A>G>C>U in theratio 8.2: 4.8: 1.3: 1 respectively. No 5′-pyrimidine-purineswith a 5′-U and pG3′pU, pC3′pAand pC3′pG weredetected. These studies suggest that a limited population ofRNAs would have formed in catalyzed prebiotic reactions.

The binding and reactions of nucleotides and polynucleotides on iron oxide hydroxide polymorphs

The iron oxide hydroxide minerals goethite and akaganéite were likely constituents of the sediments present in, for instance, geothermal regions of the primitive earth. They may have adsorbed organics and catalyzed the condensation processes which led to the origins of life. The binding to and reactions of nucleotides and oligonucleotides with these minerals was investigated. The adsorption of adenosine, 5′-AMP, 3′-AMP, 5′-UMP, and 5′-CMP to these minerals was studied. Adenosine did not bind to goethite and akaganéite. The adsorption isotherms for the binding of the nucleotides revealed that they all had close to the same affinity for the mineral. Binding to goethite was about four times stronger than to akagan éite. There was little difference in the adsorption of each nucleotide suggesting the binding was between the negative charge on the phosphate group and the positive charges on the mineral surface. The absence of binding of adenosine is consistent with this explanation. Binding decreases as the pH increases due to the titration of the positive (acidic) centers on the minerals. Two times as many moles of polynucleotides were bound to these minerals as compared to the mononucleotides. Watson-Crick hydrogen bonding of adenosine and 5′-AMP to poly(U) complexes with goethite and akaganéite was observed. There was no interaction of uridine with the poly(U)-goethite complex as expected if Watson-Crick hydrogen bonding is taking place. Neither goethite nor akaganéite catalyzed the oligomerization of the phosphorimidazolide of adenosine (ImpA). The template directed synthesis of oligomers of 5′-GMP on the poly(C) bound to goethite was observed. Higher molecular weight oligomers were observed when the poly (C) was bound to goethite than was found in the absence of the mineral.

Oligomerization reactions of ribonucleotides: The reaction of the 5′-phosphorimidazolide of nucleosides on montmorillonite and other minerals

The reaction of ImpA in the presence of Na+-montmorillonite 22A or Na+-Volclay in aqueous, pH 8 solution gives a 50–60% yield of dimers and trimers (pA)2 and (pA)3. The ratio of 3′,5′-phosphodiester bond formation is twice as great as 2′,5′-bond formation. The reaction requires the presence of Mg2+ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li+- or Ca2+-montmorillonites were used in place of Na+-montmorillonite. Little or no phosphodiester bond formation was observed with Mg2+- or Al3+-montmorillonite. Montmorillonites other than 22A and Volclay exhibited little or no catalysis. In addition, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na+-montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.

Mineral catalysis of the formation of dimers of 5′-AMP in aqueous solution: The possible role of montmorillonite clays in the prebiotic synthesis of RNA

The reaction of the 5′-AMP with water soluble carbodiimide (EDAC) in the presence of Na+-montmorillonite 22A results in the formation of 2′,5′-(pA)2 (18.9%), 3′,5′-(pA)2 (11%), and AppA (4.8%). When poly(U) is used in place of the clay the product yields are 2′,5′-(pA)2 (15.5%), 3′,5′-(pA)2 (3.7%) and AppA (14.9%). The 3′,5′-cyclic dinucleotide, 3′,5′-c(pA)2, is also formed when poly(U) is used. AppA is the principal reaction product when neither clay nor poly(U) is present in the reaction mixture. Products which contain the phophodiester bond are formed at different ionic strengths, pH and temperatures using Na+-montmorillonite. Phosphodiester bond formation was not observed when Cu2+-montmorillonite was used or when DISN was used in the place of EDAC. The extent catalysis of phophodiester bond formation varied with the particular clay mineral used. Those Na+-clays which bind 5′-AMP more strongly are better catalysts. Cu2+-montmorillonite, which binds 5′-AMP strongly, exhibits no catalytic activity.

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation

Abstract2′-d-5′-GMP and 2′-d-5′-AMP bind 2 times more strongly to montmorillonite 22A than do 2′-d-5′-CMP and 5′-TMP. The dinucleotide d(pG)2 forms in 9.2% yield and the cyclic dinucleotide c(dpG)2 in 5.4% yield in the reaction of 2′-d-5′-GMP with EDAC in the presence of montmorillonite 22A. The yield of d(pC)2 (2.0%) is significantly lower but comparable to that obtained from 5′-TMP. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl2. A low yield of d(pA)2 was observed in the condensation reaction of 5′-ImdpA on montmorillonite 22A. The cyclic nucleotide (3′,5′-cdAMP) was obtained in 14% yield from 3′-ImdpA. The yield of d(pA)2 obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na+-montmorillonite used as catalyst. Evidence is presented which shows that the acidity of the Na+-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.

Oligomerization reactions of ribonucleotides: The reaction of the 5′ -phosphorimidazolide of adenosine with diadenosine pyrophosphate on montmorillonite and other minerals

The reaction of the 5′ -phosphorimidazolide of adenosine (5′-ImpA) with diadenosine pyrophosphate (A5′ppA) in the presence of Na+-montmorillonite in aqueous, pH 8 solution results in the regiospecific formation of A5′ppA3′pA and A5ppA3′pA3′ pA. The formation of oligomers of general structure (pA)n decreases in the presence of A5′ppA. A5′ppA3′pA is the principal reaction product when a 1:1 ratio of ImpA and A5′ppA is used. The yield of A5′ppA3′pA3′pA is optimal when 9:1 or 4:1 ratios of ImpA: A5′ppA are used. The overall regiospecificity of formation of 3′,5′-links is about 80%. The reaction between ImpA and A5′ppA on montmorillonite differs from the self-condensation of ImpA in that it proceeds in the absence of Mg2+ and there are only small differences in oligomer yields when Na+, Li+ Ca2+, and NH4+ are the exchangeable cations on the montmorillonite. The reaction is inhibited by 0.4 M imidazole but the inhibition is suppressed with 0.4 M Mg2+. Little or no phosphodiester bond formation was observed with Mg2+- or Al3+-montmorillonite. Montmorillonites other than 22A and Volclay exhibited no catalysis for the formation of adducts between ImpA and A5′ppA and no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, or sepiolite.

Bridging the Prebiotic and RNA Worlds: Prebiotic RNA Synthesis on Clay

Abstract Progress towards the laboratory demonstration of the steps in the prebiotic origin of the RNA world is reviewed. Montmorillonite clay catalyzes the formation of RNAs containing 6–14 monomer units from the activated mononucleotides of A, C, G, I and U. The RNAs formed have 3′, 5′- and 2′, 5′-links, pyrophosphate links and have both linear and cyclic chains. The purine oligonucleotides have more 3′, 5′- links while the pyrimidine nucleotides have more 2′, 5′-linkages. Template-directed synthesis on the heterogeneous oligo(C)s formed on mont- morillonite yields the corresponding oligo(G)s. The dimer fraction formed in the reaction of a binary mixture of a purine and pyrimidine nucleotide shows sequence selectivity with about a 20 fold excess of the 5′-purine-pyrimidine dimer over that of the 5′-pyrimidine-purine dimer. RNAs as long as 50 mers are formed by the elongation of a decamer bound to montmorillonite by the daily addition of activated monomer to it over a 14-day time period.

Adsorption of mono- and polynucleotides on iron oxide hydroxide polymorphs

Iron oxide hydroxide minerals (FeOOH) minerals are common and important constituents of aquatic sediments. They are especially abundant in environments characterized by shifts between reducing and oxidizing conditions, i.e. oxidation/reduction of Fe(II) and Fe(III). Such conditions can be found in the surface layer of sediments, in and around hydrothermal systems, at steep density gradients due to differences in temperature and salinity (thermoclines and haloclines respectively), etc. Iron oxide (Fe20~) deposits are well known from the geological recora. The mineral hematite is a main constituent of the oldest known sedimentary deposits of the Earth the Isua Formation of West Greenland. The hematite was most likely transformed from FeOOH polymorphs during late diagenesis. FeOOH polymorphs are, together with manganese oxide minerals, thought to be the most important components of removal mechanisms of many trace elements from seawater. The point of zero charge (pzc), expressed in pH units, of the FeOOH polymorphs is between 7 and 8. This means that the surface charge of the minerals is positive at the pH of most marine waters. Therefore the efficiency of FeOOH minerals as scavengers of trace elements is most pronounced for anions such as ortho-phosphate.