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New Eye WonderBooks!Alliance Art International 667-7007Nitrogen bases as efficient UV-quenchersIn general terms, UV irradiation of first RNA-like polymers could be damaging for their nitrogenous bases, their pentose-phosphate backbone and for the bonds between the bases and the backbone. It is known that the ether bonds in monomeric sugar phosphates are much more susceptible to UV damage than monomeric nitrogenous bases: e.g. the quantum yields of UV damage by 254 nm irradiation for sugar phosphates and monomeric nitrogenous bases are approx. 10-2 and 10-4, respectively (see ref. [21] for a comprehensive review). However, numerous studies of modern nucleic acids revealed an interesting paradox: nitrogenous bases, both purines and pyrimidines, of DNA and RNA are much more sensitive to the UV illumination than the pentose-phosphate backbone. It appears therefore that nitrogenous bases protect the pentose-phosphate backbone from the UV damage. Indeed, nitrogenous bases get rid of the absorbed UV energy extremely fast. Their fluorescence life times at room temperature are on the order of 10-12 sec [21]. This means that within 1 picosecond the energy of trapped UV quanta is dissipated, predominantly into heat. As a result, the probability of a transition into a potentially photochemically active, long-living triplet state is quite low, on the order of 10-3 at room temperature [21]. For comparison, the fluorescence life time of tryptophan, which has a comparably complex structure, is more than 1000-fold longer, on the order of 5 ns. Correspondingly, the quantum yield of the singlet ? triplet transition is higher, about 0.2 at room temperature [32]. The extremely efficient deactivation of the UV quanta by nitrogenous bases allows them to protect the compounds to which they are attached from UV-induced breakage. It has been demonstrated that the photo-cleavage of ortophosphate from the sugar moiety of AMP in response to irradiation by a mercury lamp with an emission at 254 nm proceeded (with a quantum yield of 5× 10-5 mol/Einstein) about 10 times slower than from glycerol 2-phosphate [22], although AMP molecules, because of their higher molar extinction at 254 nm, were hit by 103-104 times more quanta per unit of time as compared to glycerol 2-phosphate molecules. These data were explained by a prompt one-way spillover of the excitation energy adsorbed by sugar-phosphate moiety of AMP to the nitrogenous base [22]. The latter apparently served as an excellent sink for the UV energy because of the lower energy of the first singlet level as compared to sugar phosphates. In RNA from tobacco mosaic virus, the quantum yield for the breakage of the sugar-phosphate bonds by 254 nm UV light has been shown to be 3.5 × 10-6 mol/Einstein [23], which corresponds to a UV-protection factor of 70 as compared to bare sugar phosphates. In human skin DNA, the quantum yield for a single strand break by 254 nm UV was in the order of 10-8 [21,24], indicating an even higher backbone protection factor of about 2000. It is noteworthy that the quantum yield of photo-damage to nitrogenous bases proper in RNA and DNA is on the order of 10-4 mol/Einstein [21], i.e. it is 103-104 times higher than that of the backbone breakage. Apparently, the backbones of RNA and DNA can be rescued due to the partial victimization of nitrogenous bases. Further factors, which might contribute to the backbone protection, are the effective shielding of the backbone from the UV-light by nitrogenous bases, the excitonic coupling between the latter, and the elevated capacity of polymeric compounds to dissipate the excessive thermal energy without undergoing a mechanical damage.Model of nucleotide polymerization under the conditions of UV illuminationTo explore the significance of such a UV protection mechanism for the evolution of primordial polymers, we modeled the polymerization of sugar-phosphate monomers (R) in the presence of nitrogenous bases (N) under the conditions of UV illumination. The exact nature of the sugar moiety was of secondary importance for the model because of approximately similar susceptibility of various sugar-phosphates to UV cleavage [21]. The set of reactions considered is schematically depicted in Figure 1. As long as a UV quantum can split a polynucleotide chain at any point, we had to use the Monte-Carlo approach. Because the system was open and the chains were only transient objects, the model topology was described by three pointers assigned to individual monomers as shown in Figure 1. Namely, the polymerization state of monomer i was characterised by two pointers ileft and iright defined as follows: if the left bond of monomer i was unsaturated, we put ileft = 0; if the monomer i was left-bound to monomer j, then ileft = j; the same rules were used for the right pointer iright. The chemical state of monomer i was characterized by an additional variable inucl that took values 1 or 0 when the given monomer was, respectively, bound or not bound to a nitrogenous base.The reaction dynamics was considered in discrete time steps. The interval between steps ?t was chosen appropriately small so that differential equations of chemical kinetics could be replaced by their discrete analogues. At each step, sugar-phosphate monomers were added to the reaction volume ?V in the quantity to keep their total concentration constant. The value of ?V was chosen so that the system contained on average about 2000 monomers.At each time step the following reactions were considered:Each monomer i with unsaturated left (right) bond (ileft(right) = 0) could join a polymer chain reacting with monomer j having unsaturated right (left) bond (jright(left) = 0) under a condition that monomer j does not belong to the same chain as monomer i. The probability of such reaction was calculated as Ppoly(i, j) = kpoly·?t·?V-1. Each monomer i with saturated left (right) bond (ileft(right) ? 0) could re-dissociate with the probability Pmono = kmono·?t.Because the UV stability of nitrogenous bases is by factor of 102 higher than that of not protected, bare sugar-phosphates (see above), the former were assumed to be present in excess. Then each R monomer could bind nitrogenous base with the probability Pbind = kbind·?t and each RN nucleotide could dissociate with the probability Pdiss = kdiss·?t independently of the polymerization state. The ratio of the rate constants kbind and kdiss reflects the thermodynamic equilibrium of the nucleotide binding reaction: kbind/kdiss = = exp(-?Gnucl/kT).The probability of UV-decomposition for bare sugar-phosphate monomers was DUV = kUV·?t independently of whether they were part of a polymer chain or not. A nitrogenous base protected the sugar-phosphate to which it was bound from UV degradation by a factor U so that the probability of its decomposition was DUV = U-1·kUV·?t.Monte-Carlo simulationsOn simulation, we assumed, for simplicity, that each monomer is hit by a UV quantum once per second. On picking the values of polymerization rate constant kpoly, we assumed, in line with experimental observations [14-16], that this reaction was slow. The experimental observation of the formation of oligonucleotides of up to 50 units on clays [16-18] implies an equilibrium constant of an inorganic template-guided polymerization = kpoly·[R] / kmono 1. In contrast, nitrogenous base binding was assumed to be thermodynamically unfavorable, with a respective equilibrium constant = kbind / kdiss 1. The values of the UV-decay rate constant kUV and of the UV-protection factor U were varied around their experimentally established values of 10-1 - 10-3 and 10 - 103, respectively (see refs above).As long as parameters were varied in the indicated ranges, the simulation behavior of the system was qualitatively stable, with a typical example depicted in Figure 2. In the absence of UV protection (U = 1), the polymerization yield was marginal (Fig. 2a, circles) and the extent of nitrogenous base incorporation in the polymers was close to zero (Fig. 2b, circles). With the UV protection switched on (U 1), the length of formed polymers increased dramatically (Fig. 2a, triangles). Even more importantly, under these conditions the fraction of nitrogenous-base-carrying sugar-phosphates increased significantly (up to ~0.5 in the case presented in Fig. 2b by triangles). Thus, in our simulation, the UV selection caused a strong relative enhancement in oligonucleotide-like polymers even under conditions where the binding of nitrogenous bases to sugar-phosphate moieties was thermodynamically unfavorable.We also simulated the effect of partial funneling of UV energy into the condensation reactions. In Figure 2, we depict by squares a case where we accounted for a possibility of a productive binding of a nitrogenous base N by a photo-generated radical R.. The quantum yield of such a reaction was taken as small as 9 × 10-8. The resulting boost for the formation of oligonucleotides was remarkable concerning the length of the formed polymer chains (Fig. 2a, squares), the nitrogenous base incorporation rate, and the extent of the nitrogenous bases incorporation into oligomers (Fig. 2b, squares), so that polymers were built predominantly from nucleotides. (We neglected here the possibility that nucleotides could arise also from an interaction of light-generated nitrogenous base radicals N. with sugar-phosphates R. Because the extinction of nitrogenous bases in UV is by orders of magnitude higher than that of sugar phosphates, this possibility is more than real). The experimentally measured quantum yield (probability) of the compatible photo-condensation reaction was actually 103 times higher than we assumed in our simulation: the quantum yield of the 254 nm UV-driven AMP formation from adenine, ribose and ethyl metaphosphate reached 10-4 mol/Einstein after one hour of illumination [7]. The inclusion of the photo-condensation quantum yield values compatible to those measured in ref. [7] into the parameter set used for simulation in Fig. 2 led to an overload because of unmanageable increase in the polymer chain length. It is hard to believe that evolution has not used the opportunity to drive the primordial condensation by energy of light, with nitrogenous bases working as light-absorbing antenna.Top Sellers1. Sea Horses Postcard by Moskowitz2. Grilled Chicken Barbeque Apron by Wooket3. Baa-Baa Wooly Postcard by MoskowitzLimited EditionsPlease make your selection below by clicking the images:GMT ± Perpetual Limited Edition Forgerons Minute RepeaterThe Blue Max Genghis KhanSan Marco Cloisonné Marine Perpetual LimitedTellurium J. Kepler Limited Maxi SkeletonSan Marco Gigante Ulysse I Limited EditionBlue Wave Limited Edition Circus Minute RepeaterDo you really believe Arafat wants to throw us into the sea?2. Bill Hatches an Egg - Bedard, MichaelUsually dispatched within 2-3 working daysHardback - Published July 2003publisher Longman 8.50add item to basketParisBernard Villemot20 in. x 28 in.Buy ParisFramed | MountedComments [ 12 total ]-By -DeaftrapX | Thu 2nd, Sep 2004 3:29:49pmyou need screensAnne ParillaudSoccer Pictures, Posters, Art Prints, Ecards, Videos, DVDs, Players, Teams, Memorabilia, Books +more The greatest Teen Mags!: A list by shang-lin, Everything you need to know!Light-weight All-Cotton Jewelers Gloves - 2.95ppdI've seen this movie at least a dozen times and even though it's worn thing from over-viewing, it still remains to be one of my favorite movies in my collection. Some questions the movie suggests (like How would a storm cause a ship to travel through storm and How did it 'follow' the ship no matter which way it turned? ) go unanswered, but I think these are moot points when one keeps his/her attention on the main plot. I thought there was some overacting in this movie, but as the saying goes, If it ain't broke, don't fix it . I thought the surprise ending was excellent. Really top notch. It follows some of the time-travel theories that have been presented and seems to be a very logical conclusion to the movie. I really do recommend this movie to time travel fans. --This text refers to the VHS Tape edition| Home | FAQ/About us | Bookstores | Memo | Book Reviews |Art EnfantsWith advanced search you can find specific art prints the convenient way.Wait to deal with VoIP as part of a comprehensive rewrite of the Telecom Act beginning next yearBedard, Michael : Posters, art prints -- buy here and SAVE Nutcracker Suite Collector's Set 70.00

 

 

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