Nucleic Acid Bases Adenine Research Articles

Year-Long Stability of Nucleic Acid Bases in Concentrated Sulfuric Acid: Implications for the Persistence of Organic Chemistry in Venus' Clouds.

We show that the nucleic acid bases adenine, cytosine, guanine, thymine, and uracil, as well as 2,6-diaminopurine, and the "core" nucleic acid bases purine and pyrimidine, are stable for more than one year in concentrated sulfuric acid at room temperature and at acid concentrations relevant for Venus clouds (81% w/w to 98% w/w acid, the rest water). This work builds on our initial stability studies and is the first ever to test the reactivity and structural integrity of organic molecules subjected to extended incubation in concentrated sulfuric acid. The one-year-long stability of nucleic acid bases supports the notion that the Venus cloud environment-composed of concentrated sulfuric acid-may be able to support complex organic chemicals for extended periods of time.

Stability of nucleic acid bases in concentrated sulfuric acid: Implications for the habitability of Venus’ clouds

What constitutes a habitable planet is a frontier to be explored and requires pushing the boundaries of our terracentric viewpoint for what we deem to be a habitable environment. Despite Venus' 700 K surface temperature being too hot for any plausible solvent and most organic covalent chemistry, Venus' cloud-filled atmosphere layers at 48 to 60 km above the surface hold the main requirements for life: suitable temperatures for covalent bonds; an energy source (sunlight); and a liquid solvent. Yet, the Venus clouds are widely thought to be incapable of supporting life because the droplets are composed of concentrated liquid sulfuric acid-an aggressive solvent that is assumed to rapidly destroy most biochemicals of life on Earth. Recent work, however, demonstrates that a rich organic chemistry can evolve from simple precursor molecules seeded into concentrated sulfuric acid, a result that is corroborated by domain knowledge in industry that such chemistry leads to complex molecules, including aromatics. We aim to expand the set of molecules known to be stable in concentrated sulfuric acid. Here, we show that nucleic acid bases adenine, cytosine, guanine, thymine, and uracil, as well as 2,6-diaminopurine and the "core" nucleic acid bases purine and pyrimidine, are stable in sulfuric acid in the Venus cloud temperature and sulfuric acid concentration range, using UV spectroscopy and combinations of 1D and 2D 1H 13C 15N NMR spectroscopy. The stability of nucleic acid bases in concentrated sulfuric acid advances the idea that chemistry to support life may exist in the Venus cloud particle environment.

Real-time observation of a correlation-driven sub 3\u2009fs charge migration in ionised adenine

Sudden ionisation of a relatively large molecule can initiate a correlation-driven process dubbed charge migration, where the electron density distribution is expected to rapidly move along the molecular backbone. Capturing this few-femtosecond or attosecond charge redistribution would represent the real-time observation of electron correlation in a molecule with the enticing prospect of following the energy flow from a single excited electron to the other coupled electrons in the system. Here, we report a time-resolved study of the correlation-driven charge migration process occurring in the nucleic-acid base adenine after ionisation with a 15–35 eV attosecond pulse. We find that the production of intact doubly charged adenine – via a shortly-delayed laser-induced second ionisation event – represents the signature of a charge inflation mechanism resulting from many-body excitation. This conclusion is supported by first-principles time-dependent simulations. These findings may contribute to the control of molecular reactivity at the electronic, few-femtosecond time scale.

DETECTION OF SPECIFIC CAUSES OF TUBERCULOSIS IN THE DAIRY CATTLE OF BANGLADESH AGRICULTURAL UNIVERSITY BY SEQUENCING AND SEQUENCE ANALYSIS

Tuberculosis (TB) is a chronic disease of man and animal. In this study intradermal tuberculin test, necropsy, histopathology, polymerase chain reaction (PCR) and sequencing techniques were used to diagnose specific cause of TB in dairy cattle of Bangladesh Agricultural University, Mymensingh. Intradermal tuberculin tests were carried out on randomly selected 100 dairy cattle. Tuberculin test positive cattle (N=05) were examined at necropsy and granulomas in lungs was seen in three cattle. Caseous necrosis and swelling of lymphnodes was seen in prescapular (N=01) and mesenteric (N=02) lymphnodes. In a case nodular lesion was seen in lungs and mesenteric lymphnodes. Portion of infected lungs and lymphnodes were snap frozen, extracted genomic DNA and PCR protocols was adapted targeting MPB83 gene. Result of PCR showed amplification of 600bp fragments in five cases. The MPB83 gene although specific for M. Bovis, the gene is less abundantly expressed by M. tuberculosis. To differentiate infectivity due to M. Bovis and M. Tuberculosis, two more PCR were adapted targeting pncA and oxyR genes. Out of five cattle tested in PCR all samples generated pncA specific 185bp and oxyR gene specific 270bp amplicons. The sequencing of MPB83, pncA and oxyR genes were carried out. Results of sequencing did not show mutation in MPB83 gene. Sequencing of pncA gene showed replacement of nucleic acid base (guanine to cytosin) in position 169 in cattle no. 5. Similarly, sequence analysis of oxyR gene (n=05) showed replacement of nucleic acid base (adenine to guanine) in position 285 in cattle no. 5. The cattle no. 5 was confirmedly infected with M. Tuberculosis and rest of the cattle were infected with M. Bovis. The tuberculin tests, necropsy, histopathology and PCR amplification of MPB83 gene may not contribute species specific detection of Mycobacterial infectivity in cattle. Sequencing and sequence analysis of pncA and oxyR genes found to differentiate infectivity in cattle due to M. Bovis and M. Tuberculosis. Both of the bacterial species are extremely zoonotic and dairy cattle of Bangladesh Agricultural University were infected with both M. Bovis and M. Tuberculosis. It needs to tests all the dairy cattle twice in a year with tuberculin tests and dispose test reactors in order to minimize zoonotic risk.

First-principles study of interaction of serine with nucleobases of DNA and RNA.

The nature of interaction between serine-a vital molecule for cancer cell proliferation and nucleic acid bases-adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) is investigated within the framework of Møller-Plesset perturbation theory (MP2) and density functional theory (DFT). To quantify the interaction strength between serine and nucleobases, the corresponding binding energies were computed, showing energetic ordering such that G > C > T > A > U. This shows that the interaction energy of serine with guanine is the highest, while with uracil it is the lowest. The amount of charge transferred is the lowest in case of the serine-guanine complex and highest in case of the serine-uracil complex. The results show the serine-guanine complex to be more stable and to have a salt bridge structure involving the -COOH group. Theoretical analysis based on MP2 and DFT shows that the interaction between the serine and nucleobases is mainly determined by hydrogen bonding.

Solution conformation of 2-aminopurine dinucleotide determined by ultraviolet two-dimensional fluorescence spectroscopy

We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analogue of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS)—a fluorescence-detected variation of 2D electronic spectroscopy—to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point–dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 ± 0.5 Å , twist angle θ12 = 5° ± 5° ), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV–2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein–nucleic acid complexes.

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

A detailed understanding of how nucleobases interact with protein peptides will allow us to gain valuable insights into how these interesting biological molecules could be used to construct complex nanostructures and materials. In this work, the optimal structures and binding energies of 20 hydrogenbonded complexes, which contained the nucleic acid base adenine, N-methylacetamide, a glycine dipeptide, and an alanine dipeptide, were obtained. The site preferences of adenine hydrogen bonding to peptide amides were explored. The calculation results show that adenine can use two binding sites (site A1 and site A2) to form N―H...N or N―H...O=C hydrogen-bonded complexes with N-methylacetamide; the N―H...N hydrogen-bonded complexes formed at site A1 of adenine are more stable. The calculation results also show that the glycine dipeptide can use either site Gly7 or site Gly5, and the alanine dipeptide can use either site Ala7 or site Ala5 to form hydrogen-bonded complexes with adenine; the hydrogenbonded complexes formed at site Gly7 of the glycine dipeptide and at site Ala7 of the alanine dipeptide are more stable. The hydrogen-bonded complexes formed by adenine and a dipeptide have larger negative binding energies than the complexes formed by adenine and N-methylacetamide, indicating that the interaction between adenine and the peptide is preferred to that between adenine and N-methylacetamide. The nature of the hydrogen bonding in these complexes was further explored based on the atoms in molecules calculations and the natural bond orbital analysis. 2551 Acta Phys. -Chim. Sin. 2013 Vol.29

Asymmetric autocatalysis initiated by achiral nucleic acid base adenine: implications on the origin of homochirality of biomolecules

Enantiomorphous crystals of adeninium dinitrate acted as the source of chirality in asymmetric autocatalysis producing highly enantioenriched (S)- and (R)-5-pyrimidyl alkanols, with the absolute configurations corresponding to that of crystals.

Synthesis and self‐assembly of polymers containing dicarboximide groups by living ring‐opening metathesis polymerization

Polymers with narrow molecular weight distributions and controlled architectures were generated by living ring-opening metathesis polymerization of exo-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboximide. The dicarboximide units have been previously shown to exhibit biological activity, can selectively bind to the nucleic acid base adenine by hydrogen-bonding, and are readily functionalizable. Block copolymers containing these moieties were generated, and underwent self-assembly into nanoscale spherical aggregates, with surface localized molecular recognition motifs.

Specific visible spectral changes induced by guanine binding to cytosine-derivatized porphyrin

The interaction of the free nucleic acid bases adenine, cytosine, and thymidine with meso-tri(4-sulfonatophenyl) meso 4-phenyl porphyrin cytosine amide (TPSC) trisodium salt at pH 5.9, 7.4, and 9.3 results is a decrease in the absorbance of the Soret (B-band) at 413 nm of TPSC. A decrease in Soret band absorbance is observed with guanine below pH 8; at higher pH values a new absorbance band at 424 nm is observed. The appearance of the band is consistent with hydrogen bonding between the cytosine-functionalized porphyrin and guanine and the resulting perturbation of the electron orbitals of the porphyrin.

STM Structure Determination of Adenine Bilayers by Moir� Interpretation

Scanning tunnelling microscopy (STM) has been performed in air at room temperature on bilayers of the nucleic acid base adenine, adsorbed to a graphite surface following evaporation of saturated aqueous solutions. Our results indicate that the upper layer of the bilayer structure shows a structural change compared to the layer adsorbed directly to the graphite. The upper layer has a slightly larger unit cell, and is slightly sheared and rotated with respect to the layer directly adsorbed to the substrate. We can interpret these observations in terms of a model of rows of the adsorbate molecules stabilised by intermolecular hydrogen bonds.

Femtosecond photo-ionization of nucleic acid bases: electronic lifetimes and electron yields

Femtosecond spectroscopy of aqueous solutions of the four nucleic acid bases adenine, cytosine, thymine and uracil is presented with probing from 282 nm to 750 nm. After two-step excitation at 282 nm part of the molecules returns to the ground state allowing for the determination of the lifetime of the S 1 state yielding values of τ 1≃1 ps for the four bases. The remainder photo-ionize with an ionization yield of 0.7 for adenine, twice as large as for the other bases. The first intermediate is assigned to a (base +:e −)-pair with a lifetime of 10 ps for adenine, four times longer than for the other solutions.

Self-assembled monolayer of adenine base on graphite studied by noncontact atomic force microscopy

A monolayer of nucleic acid base adenine adsorbed on a graphite surface has been studied by noncontact-atomic-force-microscopy (AFM). The noncontact-AFM images showed molecular lattice that adenine molecules pack into a rectangular lattice. The detailed features in the adenine molecule were resolved with higher resolution imaging. Furthermore, the adenine molecules with different registry to the graphite lattice appeared differently even on the noncontact-AFM image.

Molecular mechanics study of hydrogen bonded self-assembled adenine monolayers on graphite

Molecular mechanics calculations using the Dreiding II force field were applied to self-assembled monolayer configurations of the nucleic acid base adenine adsorbed on graphite surfaces. Energy minimization calculations were used to refine the structures proposed by scanning tunneling microscopy (STM) studies and low energy electron diffraction (LEED), and allowed discrimination between competing models on the basis of final configurations and local minima convergence. This allowed the relative position of the adenine molecules within the unit cell of p2gg symmetry to be inferred.

Liquid Phase Synthesis of Peptide Nucleic Acid (or Polyamide Nucleic Acid) Dimers

The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.

Study of localized levels in proflavine complexes with nucleic acid bases

The semiconduction activation energies of the nucleic acid bases adenine, guanine, thymine and uracil complexes with proflavine dye at various dye concentrations are measured in both the ohmic and the space-charge-limited (SCL) regions. The complexes are found to be nonextrinsic at high dye concentration but approach the extrinsic situation as the dye concentration decreases. From the SCL data analysis various transport parameters are evaluated.

A study of the major gas-phase tautomer of adenine by microwave spectroscopy

The microwave spectrum of the nucleic acid base adenine in a cw seeded supersonic beam has been analyzed indicating that the amino, N (9) H tautomer is the most stable in an isolated environment. A comparison of the experimental rotational constants is made with those obtained using ab initio 3–21G basis SCF calculations for three of the lower- energy tautomers.

Ab-initio quantum mechanical calculations of NMR chemical shifts in nucleic acid constituents. I. The Watson-Crick base pairs.

The magnetic shielding constants of the different nuclei of the four nucleic acid bases adenine, uracile, guanine and cytosine are calculated by a non empirical method using a minimal basis set and compared to the available corresponding experimental data. The same calculations carried out for AU and GC pairs give not only the values of the chemical shift variations due to the formation of the pairs but also the relative importance of the three different contributions (geometric, polarization and charge transfer plus exchange) to the total value of delta delta. Their analysis shows the importance of the polarization term. The magnitude of the charge transfer plus exchange term which is obtained for the nuclei belonging to the hydrogen bonding sites indicates that the hydrogen bond length is the major factor in the determination of the magnetic shielding constants of these atoms. On the other hand it appears that the pairing of the bases has a negligible effect on the "geometric" magnetic shielding due to the bases.

Crystallographic and1H nuclear magnetic resonance studies of 5′-deoxy-5′-adenosineacetic acid; a model nucleotide of adenosine-5′-monophosphate

In order to elucidate the substrate specificity of adenosine-5′-monophosphate utilizing enzymes, the spatial conformation of 5′-deoxy-5′-adenosineacetic acid has been studied by X-ray crystallography and 1H n.m.r. spectroscopy, and the results compared with those for adenosine-5′-monophosphate. In the crystal, the conformation about the glycosyl bond is anti with the torsion angle χ[O(1′)–C(1′)–N(9)–C(8)] equal to 50.7(9)°. The puckering of the ribose ring is C(3′)-exo(3E). The significant conformational discrepancy between 5′-deoxy-5′-adenosineacetic acid and adenosine-5′-monophosphate was in the orientations of their exocyclic C(4′)–C(5′) bonds: gauche-trans for the former and gauche-gauche for the latter. These conformational characteristics were also observed in 2H2O solution by 1H n.m.r. spectroscopy.The intermolecular hydrogen bonding mode between the carboxyl group and the adenine ring found in the crystal would constitute a good model for the specific interaction between the acidic amino-acid and the nucleic acid base adenine.

Study of nucleic acid bases by the DADI method

The DADI spectra of the nucleic acid bases adenine (I), guanine (II), Uracil (III), thymine (IV), cytosine (V), and 5-methylcytosine (VI) have been studied. It has been established that the samples of nucleic acid bases investigated are characterized by a specific pattern of the DADI spectra which reflects the nature of the molecular ion due to the structure of the given base and, in the case of M+ for (IV) and (VI) also the tautomeric state. The possibility has been shown of using the information obtained for the quantitative determination of (VI) in a mixture of bases.