Diaminopurine Research Articles

Denaturation and electrophoresis of RNA with formaldehyde.

Electrophoretic size fractionation can be used to denature and separate large mRNA molecules (0.5-10 kb) on formaldehyde-containing agarose gels. Formaldehyde contains a carbonyl group that reacts to form Schiff bases with the imino or amino groups of guanine, adenine, and cytosine. These covalent adducts prevent normal base pairing and maintain the RNA in a denatured state. Because these adducts are unstable, formaldehyde must be present in the gel to maintain the RNA in the denatured state. This protocol describes the preparation of an agarose gel with formaldehyde and its setup in a horizontal electrophoresis apparatus. RNA samples are prepared and denatured in a solution of formamide and formaldehyde and, with 0.5- to 10-kb size markers, subjected to electrophoresis through the gel. Following electrophoresis, the gel is stained to visualize RNA markers or rRNA using one of several different types of stains.

Terahertz Spectroscopic Analysis of Adenine and Fumaric Acid Cocrystals

The absorption spectra of adenine, fumaric acid, and their cocrystal were measured using terahertz time-domain spectroscopy(THz-TDS) at room temperature. Experimental results show that they all have distinct fingerprint spectra in the terahertz region. The absorption peaks observed in the terahertz spectra of the cocrystal were at 0.92, 1.24, and 1.52 THz. These are very different from the corresponding reagents. Based on the characteristic hydrogen donor and/or acceptor behavior of adenine, density functional theory(DFT) was used to simulate three possible theoretical cocrystal structures with a focus on hydrogen bond formation between adenine and fumaric acid. The theoretical result shows that one of three possible simulated cocrystal structures had absorption peaks at 0.89, 1.16, and 1.41 THz, which is in agreement with the terahertz experimental result. Therefore, the structure of the cocrystal was confirmed wherein the first hydrogen bond is formed between the amino group of adenine and the hydroxyl group of fumaric acid. The second hydrogen bond is formed between the nitrogen atom of the nitrogen ring in adenine and the carbonyl group of fumaric acid.The characteristic absorption bands of the cocrystal between adenine and fumaric acid are also assigned based on the simulation results from the DFT calculation.

Effect of H-bonding and complexation with metal ions on the π-electron structure of adenine tautomers

Influence of H-bonding and interactions with metals via complexation (probed by HF, F(-), Li(+) and Na(+)) on structural and π-electronic changes in four of the most stable amino adenine tautomers has been studied in the gas phase using the B3LYP/6-311++G(2d,2p) computational level. It has been found that the presence of the amino group in adenine increases its energetic sensitivity to structural changes caused by tautomeric effects as compared to its analogue deprived of this group (purine). Furthermore, its shape depends not only on tautomerism but also on intermolecular interactions. The observed variability of its pyramidalizations caused by H-bonding indicates the dramatic changes of electron donating/accepting properties of -NH2 as a substituent, which results in a variation of aromaticity of particular rings in adenine tautomers. Bifurcated coordination of metal cations by two nitrogen atoms of adenine is also an important factor influencing aromaticity. The overall range of H-bond strengths is between -4.64 and -26.39 kcal mol(-1), whereas energies for Li(+) and Na(+) complexes are in the ranges -41.45 to -67.50 and -25.04 to -51.39 kcal mol(-1), respectively. However, the highest aromaticity changes, expressed by the HOMA index, have been found to be about 24% of the HOMA scale for all types of complexes depending on the location of the intermolecular interaction.

The Effects of Base Stacking on DNA Flexibility

DNA is the main genetic component of life and understanding its basic properties is crucial for advancement in applied sciences. DNA, a long macromolecule, must complex with proteins and other molecules for packaging and condensing to fit in the nucleus of a cell. Persistence length is a physical property that defines the stiffness of a polymer, ranging from rod-like to string-like. The persistence length of double-stranded DNA is ∼150bp or ∼50nm making it a relatively inflexible molecule. It is hypothesized that the two main contributors limiting DNA flexibility are mutual charge repulsions along the DNA backbones and attractive base stacking interactions. However, the relative contributions to DNA stiffness of electrostatic repulsion and base stacking forces are unknown. We use experimental T4 DNA ligase-mediated cyclization kinetics experiments to measure the physical properties of DNA, specifically DNA longitudinal and torsional flexibilities and helical repeat.We measured the impact on DNA stiffness of enhancing or diminishing stacking energy involving modified adenine and guanine bases. Diaminopurine (DAP) is hypothesized to increase DNA bending stiffness by changing the base geometry and dipole moment so as to enhance stacking energy and inosine (dITP) is hypothesized to decrease DNA bending stiffness. Cyclization assays were performed with radiolabeled DNA probes varying in length from 211bp to 201bp. The free ends of the probes are complementary and, in the presence of T4 DNA ligase, yield various linear and circular species in vitro. The J-factor (related to persistence length through the worm-like chain polymer model) can be estimated in such assays. We found that the bending persistence length changed slightly relative to natural DNA but it is the twist persistence length that has a more dramatic change.

Computational study on the deamination reaction of adenine with OH−/nH2O (n= 0, 1, 2, 3) and 3H2O

Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH−has a high activation barrier (190 kJ mol−1using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1for the gas phase and PCM, respectively.

Amino–Imino Adenine Tautomerism Induced by the Cooperative Effect between Metal Ion and H2O/NH3

Tautomerization processes of amino-imino adenine isomer (A → A1) in five different environments are studied by the density functional theory (B3LYP) method. The five environments are metal ion (M, M = K(+), Na(+), Cu(+), Zn(+), Ca(2+), Mg(2+), Cu(2+), Zn(2+)) coordinated bidentate system, either monowater (W) or monoammonia (N) attached system, both metal ion and monowater cooperative system (M-W), and both metal ion and monoammonia cooperative system (M-N). Results show that the complexes formed by noncanonical rare imino form A1 are more stable than those formed by the canonical amino one in most of these environments. The tautomerization of A → A1 becomes quite easy in either M-W or M-N system. It is noteworthy that under divalent M-N environment the A → A1 process meets with particularly lower and even free energy barrier, indicating the instability of the amino adenine isomer and probable existence of more stable imino adenine isomer. Expanding studies for the microhydration at the metal ion of the M-N system predict the required number (n) of water molecules to remain the amino adenine isomer A (AMNnW) stable. The number of n is 2, 3, 3, and 4 for M = Ca(2+), Zn(2+), Cu(2+), and Mg(2+), respectively. The present study provides further understanding for the amino-imino tautomerization behavior of the most stable adenine under the influence of several related closely factors, and is useful for rational design of these different environments for the purposes of prevention and control of pyrimidines mispairing, which is responsible for the mutagenic properties of the nucleic acid bases.

Impact of base pair identity 5′ to the spliceosomal branch site adenosine on branch site conformation

The branch site helix from Saccharomyces cerevisiae with pseudouridine (ψ) incorporated in a phylogenetically conserved position of U2 snRNA features an extrahelical branch site adenosine (A) that forms a base triple interaction with the minor groove edge of a widely conserved purine(U2 strand)-pyrimidine(intron strand) (R(U2)-Y(intron)) base pair two positions upstream. In these studies, NMR spectra of a duplex in which 2-aminopurine (2ap), a fluorescent analog of adenine lacking the proposed hydrogen bond donor, was substituted for the branch site A, indicated that the substitution does not alter the extrahelical position of the branch site residue; thus, it appears that a hydrogen bond between the adenine amino group and the R-Y pair is not obligatory for stabilization of the extrahelical conformation. In contrast, reversal of the orientation of A(U2)-U(intron) to U(U2)-A(intron) resulted in an intrahelical position for the branch site A or 2ap. Fluorescence intensity of 2ap substituted for the branch site A with the original R(U2)-Y(intron) orientation (AU or GC) was high, consistent with an extrahelical position, whereas fluorescence in helices with the reversed R-Y orientation, or with a mismatched pair (A-U → G•A or U•C), was markedly quenched, implying that the residue was stacked in the helix. The A 5' to the branch site residue was not extrahelical in any of the duplexes. These findings suggest that the R(U2)-Y(intron) base pair orientation in the ψ-dependent branch site helix plays an important role in positioning the branch site A for recognition and/or function.

Immobilization of flavin adenine dinucleotide (FAD) onto carbon cloth and its application as working electrode in an electroenzymatic bioreactor

A high porosity carbon cloth with immobilized FAD was employed as working electrode in electrochemical NADH-regeneration procedure. Carbon cloth was oxidized with hot acids to create surface carboxyl group and then coupled by adenine amino group of FAD with carbodiimide in the presence of N-hydroxysulfosuccinimide. The bioelectrocatalytic NADH-regeneration was coupled to the conversion of achiral substrate pyruvate into chiral product l-lactate by l-lactate dehydrogenase (l-LDH) within the same reactor. The conversion was completed at 96h in bioreactor with FAD-modified carbon cloth, resulting in about 6mM of l-lactate from 10mM of pyruvate. While with bare carbon cloth, the yield at 120h was around 5mM. Immobilized FAD on the surface of carbon cloth electrode facilitated it to carry electrons from electrode to electron transfer enzymes; thereby NADH-regeneration was accelerated to drive the enzymatic reaction efficiently.

SYNTHESIS AND PHOTO- IRRADIATION OF SOME PYRIMIDINE AND PURINE DERIVATIVES

The current study included the synthesis of a series of azo compounds. These compounds were prepared by coupling nitrogen bases with phenyl diazonium salts. While the azo Schiff compounds were prepared by direct condensation of the prepared azoaldehydes with the nitrogen bases (2-amino pyrimidine & guanine ). The Schiff base derivatives were prepared by direct condensation of nitrogen bases (2-amino pyrimidine & adenine) with substituted benzaldehyde and chloral.The structures of the prepared compounds were confirmed by spectral analysis including ultra-violet visible and infra red spectra. Also photo irradiation of these compounds at (=356nm) has been done to study the stability of these compounds. The results revealed complete disappearance of the (OH) and (NH) bands in a number of compounds and partial disappearance in others which reflects the photo-oxidation or hydrogen bonding for the groups of (OH) or (NH).The disappearance of the (NH2) and (C=O) bands conforms the successful of prepared compounds.

Triple Hydrogen Bonds in DNA Modify the Transition from Right- to Left- Handed Forms

Double-stranded DNA usually adopts a right-handed B-form in aqueous solution, but alternative DNA conformations can also exist and play important roles in a wide range of cellular processes. For example, DNA melting (strand separation) is required to initiate DNA replication as well as transcription. Moreover, the over-production of left-handed Z-form DNA in cells is thought to be the trigger for auto-immunity in lupus. Therefore, understanding the underlying mechanics of right- to left-handed DNA transitions is very important to begin to understand how cellular processes depend on alternative DNA conformations. Two of the most influential factors related to this transition are the tension on DNA and the degree of hydrogen bonding. Magnetic Tweezers enable us to unwind single DNA molecules to investigate the dynamics of right- to left-handed DNA transitions at different tensions. Moreover, by substituting diaminopurine (DAP) deoxyribonucleotides for dATP in PCR reactions, completely triply hydrogen-bonded DNA fragments have been produced. These and normal DNA fragments were used to observe the dynamics of right- to left-handed DNA transitions under tension. We found that this transition is highly hydrogen bond dependent. Although DAP and normal DNA exhibit similar patterns of conformational change, DAP DNA converted to left-handed DNA at lower tension. Also, we found pronounced hysteresis for normal DNA upon re-winding from a left- to right-handed form, which indicated the that heterogeneity of the number of hydrogen bonds between base pairs in normal DNA contributes to non-equilibrium conformational changes. The results suggest that hydrogen bonding can significantly affect cellular processes requiring certain under-wound DNA conformations, and DAP DNA provides a sequence-independent model for studying the effects of hydrogen bonding on conformational changes of DNA.

Role of High-Fidelity Escherichia coli DNA Polymerase I in Replication Bypass of a Deoxyadenosine DNA-Peptide Cross-Link

Reaction of bifunctional electrophiles with DNA in the presence of peptides can result in DNA-peptide cross-links. In particular, the linkage can be formed in the major groove of DNA via the exocyclic amino group of adenine (N⁶-dA). We previously demonstrated that an A family human polymerase, Pol ν, can efficiently and accurately synthesize DNA past N⁶-dA-linked peptides. Based on these results, we hypothesized that another member of that family, Escherichia coli polymerase I (Pol I), may also be able to bypass these large major groove DNA lesions. To test this, oligodeoxynucleotides containing a site-specific N⁶-dA dodecylpeptide cross-link were created and utilized for in vitro DNA replication assays using E. coli DNA polymerases. The results showed that Pol I and Pol II could efficiently and accurately bypass this adduct, while Pol III replicase, Pol IV, and Pol V were strongly inhibited. In addition, cellular studies were conducted using E. coli strains that were either wild type or deficient in all three DNA damage-inducible polymerases, i.e., Pol II, Pol IV, and Pol V. When single-stranded DNA vectors containing a site-specific N⁶-dA dodecylpeptide cross-link were replicated in these strains, the efficiencies of replication were comparable, and in both strains, intracellular bypass of the lesion occurred in an error-free manner. Collectively, these findings demonstrate that despite its constrained active site, Pol I can catalyze DNA synthesis past N⁶-dA-linked peptide cross-links and is likely to play an essential role in cellular bypass of large major groove DNA lesions.

Sensitive and selective detection of adenine using fluorescent ZnS nanoparticles

We have used fluorescent ZnS nanoparticles as a probe for the determination of adenine. A typical2 × 10 − 7 Mconcentration of adenine quenches 39.3% of the ZnS fluorescence. The decrease in ZnS fluorescenceas a function of adenine concentration was found to be linear in the concentration range5 × 10 − 9–2 × 10 − 7 M. The limit of detection (LOD) of adenine by this method is 3 nM. Among the DNAbases, only adenine quenched the fluorescence of ZnS nanoparticles in the submicromolarconcentration range, thus adding selectivity to the method. The amino groupof adenine was important in determining the quenching efficiency. Steady-statefluorescence experiments suggest that one molecule of adenine is sufficient toquench the emission arising from a cluster of ZnS consisting of about 20 molecules.Time-resolved fluorescence measurements indicate that the adenine moleculesblock the sites on the surface of ZnS responsible for emission with the longestlifetime component. This method may be applied for the determination of adeninein biological samples since the measurements have been carried out at pH 7.

Syntheses of Aliphatic Polycarbonates from 2′-Deoxyribonucleosides

Poly(2'-deoxyadenosine) and poly(thymidine) constructed of carbonate linkages were synthesized by polycondensation between silyl ether and carbonylimidazolide at the 3'- and 5'-positions of the 2'-deoxyribonucleoside monomers. The N-benzoyl-2'-deoxyadenosine monomer afforded the corresponding polycarbonate together with the cyclic oligomers. However, the deprotection of the N-benzoyl group resulted in the scission of the polymer main chain. Thus, the N-unprotected 2'-deoxyadenosine monomers were examined for polycondensation. However, there was involved the undesired reaction between the adenine amino group and the carbonylimidazolide to form the carbamate linkage. In order to exclude this unfavorable reaction, dynamic protection was employed. Strong hydrogen bonding was used in place of the usual covalent bonding for reducing the nucleophilicity of the adenine amino group. Herein, 3',5'-O-diacylthymidines that form the complementary hydrogen bonding with the adenine amino group were added to the polymerization system of the N-unprotected 2'-deoxyadenosine monomer. Consequently, although the oligomers (M(n) = 1000-1500) were produced, the contents of the carbamate group were greatly reduced. The dynamic protection reagents were easily and quantitatively recovered as the MeOH soluble parts from the polymerization mixtures. In the polycondensation of the thymidine monomer, there tended to be involved another unfavorable reaction of carbonate exchange, which consequently formed the irregular carbonate linkages at not only the 3'-5' but also the 3'-3' and 5'-5' positions. Employing the well-designed monomer suppressed the carbonate exchange reaction to produce poly(thymidine) with the almost regular 3'-5'carbonate linkages.

Dynamics of DNA Supercoil Relaxation by Type II Topoisomerases

Dynamics of DNA supercoil relaxation by type II topoisomerasesQing Shao∗, Laura Finzi∗, and David Dunlap#Dept. of Physics∗ and Cell Biology#, Emory University, Atlanta, GA 30322Type II topoisomerases are some of the main targets of anti-cancer drugs, since they catalyze DNA decatenation and unwinding which is crucial for cell division. A recent crystal structure shows that, during the catalytic cycle, a yeast type II topoisomerase can bend a 34 base pair DNA segment by up to 150 degrees. Bacterial gyrase, another type II topoisomerase, can wrap an approximately 100 bp DNA segment into a tight 180 degree turn. By substituting diaminopurine (DAP) deoxyribonucleotides for dATP in PCR reactions, completely triply hydrogen-bonded DNA fragments have been produced and found to be stiffer than normal DNA. These and normal DNA fragments were used as substrates for observations of topoisomerase II-mediated relaxation of plectonemes introduced in single molecules using magnetic tweezers. Observations at several ATP concentrations revealed bursts of stepwise events separated by pauses. Michaelis-Menten fitting of the data for both recombinant human topoisomerase II alpha and E. coli gyrase showed that Vmax and Km both decrease in DAP-substituted with respect to normal DNA. However, while the characteristic pause interval increased for human topoisomerase II alpha operating on DAP-substituted with respect to normal DNA, it was unchanged for E. coli gyrase. These dynamic measurements not only support the hypothesis that the strand passage reaction involves DNA bending but also suggest that DNA bending and subsequent steps in the catalytic cycle, perhaps involving ATP hydrolysis, are more efficiently coupled in gyrase than in human topoisomerase II alpha.

The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A

The highly conserved Kinase, Endopeptidase and Other Proteins of small Size (KEOPS)/Endopeptidase-like and Kinase associated to transcribed Chromatin (EKC) protein complex has been implicated in transcription, telomere maintenance and chromosome segregation, but its exact function remains unknown. The complex consists of five proteins, Kinase-Associated Endopeptidase (Kae1), a highly conserved protein present in bacteria, archaea and eukaryotes, a kinase (Bud32) and three additional small polypeptides. We showed that the complex is required for a universal tRNA modification, threonyl carbamoyl adenosine (t6A), found in all tRNAs that pair with ANN codons in mRNA. We also showed that the bacterial ortholog of Kae1, YgjD, is required for t6A modification of Escherichia coli tRNAs. The ATPase activity of Kae1 and the kinase activity of Bud32 are required for the modification. The yeast protein Sua5 has been reported previously to be required for t6A synthesis. Using yeast extracts, we established an in vitro system for the synthesis of t6A that requires Sua5, Kae1, threonine, bicarbonate and ATP. It remains to be determined whether all reported defects of KEOPS/EKC mutants can be attributed to the lack of t6A, or whether the complex has multiple functions.

Synthesis of histidine-stabilized cadmium sulfide quantum dots: Study of their fluorescence behaviour in the presence of adenine and guanine

Cadmium sulfide particles have been synthesized in the aqueous medium using the amino acid histidine as a stabilizing agent. These particles demonstrate the phenomenon of size quantization effect. The fluorescence of histidine-stabilized CdS was found to be enhanced and quenched by the addition of DNA bases adenine and guanine, respectively. The fluorescence enhancement of CdS in the presence of adenine has been explained on the basis of interaction between the quantum dot stabilizer and the amino group of adenine. Quenching of CdS fluorescence by guanine occurs due to interaction of the substrate with the quantum dot surface.

Modeling the formation and reactions of benzene metabolites

One or more of the muconaldehyde isomers is a putative product of benzene metabolism. As muconaldehydes are highly reactive dienals and potentially mutagenic they might be relevant to the carcinogenicity of benzene. Muconaldehydes may be derived through the action of a cytochrome P450 mono-oxygenase on benzene oxide–oxepin, which are established metabolites of benzene. Oxidation of benzene oxide–oxepin either by the one-electron oxidant cerium(IV) ammonium nitrate (CAN) or by iron(III) tris(1,10-phenanthroline) hexafluorophosphate in acetone at −78 °C or acetonitrile at −40 °C gave ( E, Z)-muconaldehyde, which was a single diastereoisomer according to analysis by 1H NMR spectroscopy. Reaction of toluene-1,2-oxide/2-methyloxepin with CAN gave (2 E,4 Z)-6-oxo-hepta-2,4-dienal. Similarly, the action of CAN on 1,6-dimethylbenzene oxide-2,7-dimethyloxepin gave (3 Z,5 E)-octa-3,5-diene-2,7-dione. In vivo, benzene oxide–oxepin could suffer one-electron oxidation by cytochrome P450 mono-oxygenase giving ( E, Z)-muconaldehyde. The observations presented may be relevant to the toxicology of benzene oxide–oxepin and other arene oxide–oxepins as we have previously shown that ( E, Z)-muconaldehyde, analogously to ( Z, Z)-muconaldehyde, affords pyrrole adducts with the exocyclic amino groups of the DNA bases adenine and guanine. Independent of their possible toxicological significance, the experiments described provide preparatively useful routes to ( E, Z)-muconaldehyde and its congeners. Methods are also described for the trapping and analysis of reactive benzene metabolites, e.g. using the Diels–Alder reaction with the dienophile 4-phenyl-1,2,4-triazoline-3,5-dione to trap arene oxides and with the diene 1,3-diphenylisobenzofuran to trap enals.

Dynamic Investigation of DNA Bending and Wrapping By Type II Topoisomerases

Type II topoisomerases catalyze DNA decatenation and unwinding which is crucial for cell division, and therefore type II topoisomerases are some of the main targets of anti-cancer drugs. A recent crystal structure shows that, during the catalytic cycle, a yeast type II topoimerase can bend a 34 base pair DNA segment by up to 150 degrees. Bacterial gyrase, another type II topoisomerase, can wrap an approximately 100 bp DNA segment into a tight 180 degree turn. Bending a stiff polymer like DNA requires considerable energy and could represent the rate limiting step in the catalytic (topological) cycle. By substitututing diaminopurine (DAP) deoxyribonucleotides for dATP in PCR reactions, stiffer DNA fragments have been produced and used as substrates for topoisomerase II-mediated relaxation of plectonemes introduced in single molecules using magnetic tweezers. The overall rate of relaxation of plectonemes by recombinant human topoisomerase II alpha decreased on the stiffer DNA. In addition the ability of recombinant E. coli gyrase to wrap DNA also decreased for DAP-substituted DNA in which every base pair has three hydrogen bonds. These dynamic measurements of DNA bending and wrapping by type II topisomerases are consistent with the hypothesis that DNA flexibility affects the rate determining step for type II topoisomerase activity.

Tautomerism, normal coordinate analysis, vibrational assignments, calculated IR, Raman and NMR spectra of adenine

The Raman (3700–100 cm −1), infrared (4000–200 cm −1), mass spectrum and 1H NMR temperature-dependent study of adenine have been recorded. Quantum chemical calculations were carried out for N(9)H- amino, N(7)H- amino, N(9)H- imino and N(7)H- imino adenine tautomers using RHF, B3LYP and MP2 with full electron correlation up to 6-311++G(d,p) basis set. The computational results reveal the non-planar N(9)H- amino conformer of adenine to be the most stable structure of adenine. The planar (C s) form of N(9)H- amino adenine is found to represent a transition state, lying 8 cm −1 above the non-planar conformer and with one imaginary frequency. Comparison between theoretical and experimental 1H NMR spectra favors the assignment of the signals to N9(H) and N7(H)- amino tautomers over the corresponding imino tautomers. On the other hand, the recorded IR, Raman and 13C NMR spectra were fully consistent with N9(H)- amino adenine tautomer, therefore it is the only tautomer in both the gas and solid phases and in solution. Moreover, the results of NH 2 potential surface scans utilizing B3LYP and MP2 = full methods at 6-31G(d) basis also support the non-planarity of N(9)H- amino adenine. The mass spectral measurements indicate the presence of 3% adenine dimmer which indicates weak inter-molecular hydrogen bonding interactions in adenine. Additionally, intramolecular hydrogen bonding is also predicted between N 1 and H 15 atoms. The theoretical infrared and Raman spectra have been successfully simulated by means of both DFT and MP2 calculations, allowing the interpretation of the complex bands observed. Aided by normal coordinate analysis, potential energy distributions and the calculated force constants, a revised and accurate vibrational assignment for all fundamentals has been provided for the non-planar N(9)H-adenine tautomer. The results are reported herein and compared with similar molecules whenever appropriate.

DNA cross-link generated by a novel modified DNA containing a formyl group

We here report the synthesis of novel modified nucleic acid containing a formyl group and the evaluation of interstrand cross-linking between the modified DNA and the complementary strand. The synthesis of the formyl-containing oligodeoxynucleotide (ODN) was achieved by a post synthetic modification of corresponding ODN containing a 1,2-diol. The ODN containing the diol moiety was successfully synthesized by a standard phosphoramidite method, and was quantitatively converted to the desired formyl-containing ODN by sodium periodate oxidation. Hybridizaiton of the formyl ODN and the complementary ODN produced the interstrand cross-link between the formyl group and N(6)-exocyclic amino group of adenine.