Nucleobase Interactions Research Articles

On the stability of peptide nucleic acid duplexes in the presence of organic solvents

Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the medium decreases. Study of nucleobase paired duplexes in the absence of water and ultimately in pure aprotic, non-polar organic solvents is not possible with natural phosphodiester nucleic acids due to the ionic phosphate groups and the associated cations, but could be possible with non-ionic nucleic acid analogues or mimics such as peptide nucleic acids. We now report that peptide nucleic acid (PNA) (in contrast to DNA) duplexes show almost unaffected stability in up to 70% dimethylformamide (DMF) or dioxane, and extrapolation of the data to conditions of 100% organic solvents indicates only minor (or no) destabilization of the PNA duplexes. Our data indicate that stacking forces contribute little if at all to the duplex stability under these conditions. The differences in behaviour between the PNA and the DNA duplexes are attributed to the differences in hydration and counter ion release rather than to the differences in nucleobase interaction. These results support the possibility of having stable nucleobase paired double helices in organic solvents.

Utilization of L‐α‐Nucleobase Amino Acids (NBAs) as Protein Engineering Tools: Construction of NBA‐Modified HIV‐1 Protease Analogues and Enhancement of Dimerization Induced by Nucleobase Interaction

Utilization of <scp>L</scp>‐α‐Nucleobase Amino Acids (NBAs) as Protein Engineering Tools: Construction of NBA‐Modified HIV‐1 Protease Analogues and Enhancement of Dimerization Induced by Nucleobase Interaction

Supramolecular architectures assembled by the interaction of purine nucleobases with metal-oxalato frameworks. Non-covalent stabilization of the 7H-adenine tautomer in the solid-state

The synthesis, crystal structure and variable-temperature magnetic measurements of the compounds [Mn(mu-ox)(H2O)(7H-pur-kappaN9)]n (1), {[Mn(mu-ox)(H2O)2].(7H-ade).(H2O)}n (2) and {[Cu(mu-ox)(H2O)(7H-ade-kappaN9)][Cu(mu-ox)(mu-H2O)(7H-ade-kappaN9)]. approximately 10/3H2O}n (3), (where ox: oxalato dianion, pur: purine, and ade: adenine) are reported. Compounds 1and 2 contain one-dimensional chains in which manganese(II) atoms are bridged by bis-bidentate oxalato ligands. The distorted octahedral geometry around each metal centre is completed in compound 1 by one water molecule and the imidazole N9 donor site of the purine ligand, which is a rare example of direct binding between the Mn(II) ion and the N donor site of an isolated nucleobase. Unlike 1, the adenine moiety in compound 2 is not bonded to manganese atoms and the metal coordination polyhedron is filled by two water molecules in a cis-arrangement. Its crystal building is constructed from pi-stacked layers of Watson-Crick hydrogen-bonded adenine...(H2O2)...adenine aggregates and zig-zag Mn(II)-oxalato chains held together by means of a strong network of hydrogen bonding interactions. The nucleobase exists in the lattice as the 7H-adenine tautomer which represents an unprecedented solid-state characterization of this minor tautomer as free molecule (without metal coordination) stabilized through non-covalent interactions. Compound consists of two slightly different [Cu(ox)(H2O)(7H-ade-kappaN9)] units in which the nucleobase coordinates through the imidazole N9 atom. The planar complex entities are parallel stacked and joined by means of long Cu-O bonds involving oxygen atoms from the oxalato and the aqua ligands, giving one-dimensional chains with a [4 + 1] square-planar pyramidal and a [4 + 2] octahedral coordination around the metal centre, respectively. Self-assembled process of compound 3 is further driven by an in-plane network of hydrogen bonding interactions to generate a porous 3D structure containing parallel channels filled by guest water molecules. Variable-temperature magnetic susceptibility measurements of all the complexes show the occurrence of antiferromagnetic interactions between the paramagnetic centres. DFT calculations have been performed to check the influence of packing in the stability of the 7H-amino tautomer of 2 and in the complex geometry of 3.

Nucleobase Orientation and Ordering in Films of Single-Stranded DNA on Gold

We demonstrate how the orientation and ordering of DNA bases in ultrahigh vacuum (UHV) and ambient environments can be determined using complementary spectroscopic methods. Near-edge X-ray absorption fine structure (NEXAFS) with fluorescence detection, X-ray photoelectron (XPS), and Fourier transform infrared (FTIR) spectroscopies are used to quantify the coverage, chemical composition, orientation, and ordering of thymine bases in model self-assembled monolayers of thymine homo-oligonucleotides [oligo(dT)] on gold. We find that, in monolayers of thiol-modified oligo(dT), thymine bases tend to orient parallel to the Au substrate, and this preferential orientation is significantly more pronounced in monolayers of thiolated 5-mers compared to 25-mers. We interpret this preferential orientation as a signature of significant correlations (local ordering) between individual nuleobases, which offers a way to quantify and compare nucleobase interactions in films under both ambient and UHV conditions.

Metal–nucleobase interactions: Interplay of coordination and hydrogen bonding in cadmium (II) complexes of N6-substituted adenines

The X-ray crystal structures of 1 [Cd 2(BAD +) 2(μ-Cl) 4Cl 2] n (BAD + = N3 protonated N 6-benzyladenine)] and 2 [Cd 2(FAD +) 2(μ-Cl) 4Cl 2] n (FAD + = N3 protonated N 6-furfuryladenine) reveal an one-dimensional polymer. In both the structures, the interplay of coordination and hydrogen bonding results in the formation of almost the same type of supramolecular architectures via N–H⋯Cl, C–H⋯Cl and C–H⋯N hydrogen bonds.

Nucleic Acid Complexing Glycosyl Nucleoside-Based Amphiphile

A neutral amphiphile derived from uridine featuring two oleyl chains and one glucose for DNA binding was prepared using a convenient four-step synthetic route. The nucleic acid binding capabilities of this amphiphile were investigated by UV-vis, quasi-elastic light scattering (QELS), transmission electronic microscopy (TEM), gel electrophoresis, 31P NMR, IR, and circular dichroism (CD). Amphiphile-nucleic acid complex formation is a consequence of the amphiphilic character of the molecule, phosphate-sugar, and nucleobase-nucleobase interactions. This work presents for the first time a glyco-nucleo-amphiphile capable of binding efficiently the nucleic acid double helix structure.

The Multiplicity, Strength, and Nature of the Interaction of Nucleobases with Alkaline and Alkaline Earth Metal Cations: A Density Functional Theory Investigation

Density functional theory (DFT) calculations were performed at the B3LYP/6-311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li+, Na+, K+, Be2+, Mg2+, and Ca2+ (Mn+, hereinafter), with nucleobases, namely, adenine, cytosine, guanine, thymine, and uracil. Morokuma decomposition and orbital analysis were used to analyze the binding components. A total of 150 initial structures were designed and optimized, of which 93 optimized structures were found, which could be divided into two different types: cation−π complex and cation−heteroatom complex. In the former, a Mn+ is located above the nucleobase ring, while in the latter a Mn+ directly interacts in flank with the heteroatom(s) of a nucleobase. The strongest binding of −319.2 kcal/mol was found in the Be2+−guanine complex. Furthermore, the planar ring structures of the nucleobases in some cation−π complexes were deformed, destroying more ...

Electron Channels in Biomolecular Nanowires

We report a first-principle study of the electronic and conduction properties of a quadruple-helix guanine wire (G4 wire), a DNA derivative, with inner potassium ions. The analysis of the electronic structure highlights the presence of energy manifolds that are equivalent to the bands of (semi)conducting materials and reveals the formation of extended electron channels available for charge transport along the wire. The specific metal−nucleobase interactions affect the electronic properties at the Fermi level, leading the wire to behave as an intrinsically p-doped system.

Complementary Nucleobase Interaction Enhances Peptide—Peptide Recognition and Self‐Replicating Catalysis.

The availability of the complementary interaction of nucleobases for influencing the formation of peptide architectures was explored. Nucleobases were incorporated as additional recognition elements in coiled-coil peptides by employing nucleobase amino acids (NBAs), which are artificial L-alpha-amino gamma-nucleobase-butyric acids. The effect of the base-pair interaction on intermolecular recognition between peptides was evaluated through a self-replication reaction. The self-replication reactions of the peptides with complementary base pairs such as thymine-adenine or guanine-cytosine at the g-g' heptad positions were accelerated in comparison with those of the peptides with mismatched base pairs or without nucleobases. However, thymine-adenine pairs at the e-e' positions did not enhance the self-replication. In the presence of a denaturant, the enhancement effects of complementary base pairs on the reaction disappeared. Thermal denaturation studies showed that the thymine-adenine pairs contributed to stabilization of the coiled-coil structure and that the pairs at the g-g' positions were more effective than those at the e-e' positions. The peptide-peptide interaction was reinforced by complementary nucleobase interactions appropriately arranged in the peptide structure; these led to acceleration of the self-replication reactions.

Evaluating the contributions of desolvation and base-stacking during translesion DNA synthesis.

DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a guide. Numerous factors such as hydrogen bonding interactions, base-stacking contributions, and desolvation play important roles in controlling the efficiency and fidelity of this process. We previously demonstrated that 5-nitro-indolyl-2'-deoxyriboside triphosphate, a non-natural nucleobase with enhanced base-stacking properties, was more efficiently inserted opposite a non-templating DNA lesion compared to natural templating nucleobases (E. Z. Reineks and A. J. Berdis, Biochemistry, 2004, 43, 393-404). The catalytic enhancement was proposed to reflect increased base-stacking interactions of the non-natural nucleobase with the polymerase and DNA. However, the effects of desolvation could not be unambiguously refuted. To further address the contributions of base stacking and desolvation during translesion DNA replication, we synthesized indolyl-2'-deoxyriboside triphosphate, a nucleobase devoid of nitro groups, and measured its efficiency of enzymatic insertion into modified and unmodified DNA. Removal of the nitro group reduces the catalytic efficiency for insertion opposite an abasic site by 3600-fold. This results from a large decrease in the rate of polymerization (similar 450-fold) coupled with a modest decrease in binding affinity (similar 8-fold). Since both non-natural nucleobases show the same degree of hydrophobicity, we attribute this reduction to the loss of base-stacking contributions rather than desolvation capabilities. Indolyl-2'-deoxyriboside triphosphate can also be inserted opposite natural nucleobases. Surprisingly, the catalytic efficiency for insertion is nearly identical to that measured for insertion opposite an abasic site. These data are discussed within the context of pi-electron interactions of the incoming nucleobase with the polymerase:DNA complex. Despite this lack of insertion selectivity, the polymerase is unable to extend beyond the non-natural nucleobase. This result indicates that indolyl-2'-deoxyriboside triphosphate acts as an indiscriminate chain terminator of DNA synthesis that may have unique therapeutic applications.

An aqua-adenine H-bonding interaction controlling the formation of the rare Zn(II)–N9(adenine) bond in crystal structure of diaqua(adenine)(iminodiacetato)zinc(II)

A novel mixed-ligand zinc(II) complex with iminodiacetato(2-) (IDA) and adenine (AdeH) ligands has been obtained. Its crystal consists of octahedral molecules [Zn(IDA)(AdeH)(H 2O) 2] where the selective Zn–N9(AdeH) bond, involving the most basic N(AdeH) donor atom, occupies the trans position versus the Zn–N(IDA) bond. The Zn(II)–N9(AdeH) binding mode seems to be rare enough in comparison to those previously reported for Zn(II) and AdeH or a variety of related ligands. The chelate-nucleobase recognition process is further accomplished by an O–H(aqua)⋯N3(adenine) inter-ligand H-bonding interaction, without any intra-molecular IDA–nucleobase interaction. This finding is attributed to the polarizing effect of Zn(II) on the aqua ligand and the possibilities of AdeH acting as N-donor for the metal(II) atom and H-acceptor for an intra-molecular inter-ligand H-bonding interaction. There are no aromatic π,π-stacking contributions in the 3D H-bonded network, where all polar N–H (IDA or AdeH) and O–H (aqua) bonds are involved as donors in H-bonding interactions, which include AdeH:AdeH and IDA:AdeH pairing by double inter-molecular bridges.

Metal-stabilized rare tautomers of nucleobases. 8. Promotion of rare cytosine tautomer upon complex formation with (dien)M2+ (M=Pt, Pd)

Reactions of (dien)M2+ (M=Pt, Pd) with cytosine (CH) lead to mixtures of linkage isomers with N3 and N1 bonded metal entities as well as N3,N1 bridged species, as demonstrated by 1H NMR spectroscopy. The N3 linkage isomer is preferred over the N1 linkage isomer throughout the pH range studied (2.5–9), but the ratio does not parallel the equilibrium constant between the aminooxo tautomer (I) (proton at N1) and the aminooxo tautomer (II) (proton at N3), which has been estimated to be close to 1000 in solution. Rather, the minor tautomer (II) is complexed to a much higher extent. This finding is potentially significant for any metal–nucleobase interaction in that it suggests that metal complexes of rare tautomers may be formed more readily than generally assumed. X-ray data of four (CH-N3) complexes as well as of the first example of a (C-N1,N3) bridged compound are reported.

Synthesis of ribonucleic guanidine: replacement of the negative phosphodiester linkages of RNA with positive guanidinium linkages

Replacement of the negatively charged phosphodiester linkages of RNA with positively charged guanidinium linkages provides the polycationic ribonucleic guanidine (RNG). RNG is designed to bind strongly to target DNA/RNA through the specific interactions of nucleobases and the attractive electrostatic interactions of backbones, thus RNG is a putative antisense/antigene agent. Preparation of uridine and adenine building blocks for the RNG synthesis, as well as the stepwise synthesis of oligomeric RNG are reported. Pentameric homo uridyl, adenyl, and a pentameric mixed base sequence have been synthesized. The methods were also applied to a convenient solid-phase synthesis of RNG.

Investigating the effect of transition metal ion oxidation state on oligodeoxyribonucleotide binding by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry

Investigations of the interactions of metals with nucleotides and oligonucleotides are important for a variety of areas, including understanding nucleic acid metabolism and ability of the metals to stabilize or destablize the double-stranded helix of DNA. This report illustrates the application of matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry for the study of the fundamental interactions of metal ions with small, single-stranded oligonucleotides, with a specific focus on evaluation of sequential metal ion attachment and binding site(s) determination. Whereas incorporation of Cu (I) into dinucleotides reveals the maximum number of protons that can be replaced by singly charged metal ions, incorporation of iron (II, III) into the same biomolecules is sensitive to steric binding factors as well. These results suggest a mechanism in which complexes of the metal ion and the laser matrix compound (2,5-dihydroxybenzoic acid, or DHB) coordinate with the oligonucleotides and attach metal ions by eliminating neutral DHB molecules. Ions of divalent (Zn 2+, Fe 2+), trivalent (Fe 3+, Ce 3+), and tetravalent (Ce 4+, Th 4+) metals all bind strongly to oligonucleotides and are retained even in the fragment ions. Based on high-resolution mass measurements and fragmentation information, structures are proposed for these gas phase species in which the metal ion coordination to the oligonucleotide involves both phosphate and nucleobase interactions. These studies provide molecular level information about metal ion interactions with oligonucleotides, and may be the basis for determining how certain metal ions can be exploited as selective probes for biomolecular structure interrogation.

Metastable decay of negatively charged oligodeoxynucleotides analyzed with ultraviolet matrix-assisted laser desorption/ionization post-source decay and deuterium exchange

In an effort to understand the initiating step in metastable-ion decay of UV matrix-assisted laser desorption/ionization (MALDI)-produced ions, we conducted experiments in which we exchanged all active protons for deuterons of tetrameric and hexameric oligodeoxynucleotides. We wish to address the controversial proposal that in the negative-ion mode, as in the positive-ion mode, fragmentation is driven by nucleobase protonation. The results show unambiguously that proton transfer, leading to zwitterion formation, charges a nucleobase prior to its elimination. The zwitterion formation directs fragmentation of both positive and negative oligodeoxynucleotide ions. Poly-T-rich oligodeoxynucleotide tetramers show surprising differences in the negative compared to the positive-ion mode, as thymine is preferentially expelled, instead of a nucleobase with higher proton affinity. For the exceptional case of negatively charged poly-T-rich oligodeoxynucleotide tetramers generated by MALDI, we propose that zwitterion formation with positive charging of a nucleobase leads to base stabilization in the negative-ion mode through an interaction of the positive nucleobase with the excess negative charge. Moreover, backbone cleavages (accompanied by H rearrangement) of a phosophodiester bond give first-generation products that can be traced back to this tripolar complex bearing one positive and two negative charges, all of which may be interacting.

Substitution of inosine and guanosine 5′-monophosphate for chloride, and water on Pd II(polyaminopolycarboxylate) complexes: mechanistic controls in forming Pd II(pac)L or Pd II(pac)L 2 products

The substitution of one inosine (Ino) with [Pd II(pac)(D 2O)] complexes (pac=polyaminopolycarboxylate with pac=mida 2−) and [Pd 2 II (pac)(D 2O) 2] (pac=hdta 4− and egta 4− produce products in which the entering Ino ligand resides trans to the iminodiacetate N donor and the two glycinato arms of the iminodiacetate donor have a ‘one on, and one off’ arrangement. Reactions were carried out in the pD range of 5.0–6.0 in order to assure that glycinato carboxylates would be coordinated in the starting [Pd(pac)(D 2O)] complex and in a range such that the final coordination of inosine is favored at the N-7 donor site. The structure of the product was deduced from 1H and 13C NMR studies. These [Pd(pac)L] products are consistent with a common trigonal bipyramidal intermediate with the entering Ino group displacing an in-plane glycinato group. Substitution of one Ino on [Pd II(mida)Cl] − results in both glycinato donors being made pendant. A different, more square–pyramidal intermediate leads to this product whereas a TBP geometry will not. The tendency toward formation of stable bis [Pd II(pac)L 2] products increases in the order of the pac ligand of 1/2 egta 4−>1/2 hdta 4−>mida 2−, indicating that strain at the central iminodiacetates’ nitrogen donor favors displacement of the second glycinato chelate, but that having binuclear Pd II centers too close disfavors forming bis-derivatized Pd II headgroups. Rather, the longer eight methylene equivalent spacer in [Pd 2(egta)(H 2O) 2] compared to six methylenes in [Pd 2(hdta)(H 2O) 2] allows for bis addition at both Pd II centers to proceed to completion. If the entering ligand is the anionically charged 5′-GMP nucleotide instead of the neutrally charged Ino, addition stops at the ‘one on, one off’ 1:1 complex per Pd II center with [Pd 2(egta)(H 2O) 2], just as Ino addition to the anionically charged [Pd(mida)Cl] − stops at the first addition step. Two types of Pd II derivatized isomer are detected for the [Pd 2(Ino) 4(hdta)] complex, e.g. with Ino groups either trans or cis to each other. 31P NMR studies show that association of the phosphate ester unit of 5′-GMP or of H 2PO 4 − make only transitory interactions with the Pd II center such that a rearrangement that is observed on a slow time scale of >24 h for the decay of an unstable isomer of [Pd 2(5′-GMP) 2(egta)] 2 − must be due to an N-1 to N-7 rearrangement, rather than a phosphate ester coordination to N-4 migration. Likewise, unstable species are found by 1H NMR for Ino substitutions on [Pd(mida)Cl] − and [Pd 2(hdta)(D 2O) 2]. The processes that alter the initial distribution of species are attributed to N-1 to N-7 isomerisms. The major substitution product for Ino or 5′-GMP, in all cases of Pd(pac) substitutions, is the N-7 coordinated purine nucleoside or nucleotide, as shown by 1H NMR parameters of the several species. In this manner, the behavior of Pd II(pac) coordination of purine nucleobases parallels the behavior of Pd II–dipeptide and tripeptide complexes in forming ternary complexes with DNA nucleobases. Both Pd II(pac) and Pd II(peptide) complexes have neutral or anionic reaction centers. In contrast, the cationic Pd II(dien) purine complexes favor N-1 coordination much more strongly, and are therefore poorer models of ternary protein–metal ion–DNA nucleobase interactions of importance in transcription processes and cytotoxic DNA–protein crosslinks.

Replacement of the phosphorodiester linkages of RNA with guanidinium linkages: the solid-phase synthesis of ribonucleic guanidine.

[reaction: see text] Replacement of the negatively charged phosphodiester linkages of RNA with positively charged guanidinium linkages provides the polycationic ribonucleic guanidine (RNG). RNG is anticipated to bind strongly to target DNA/RNA through the specific interactions of nucleobases and the attractive electrostatic interactions of backbones. Preparation of building blocks and the solid-phase synthesis of RNG are reported. Both trimeric and pentameric uridyl RNG have been synthesized.

The ATP substrate site of a cyclic-nucleotide-independent protein kinase from porcine liver nuclei.

The ATP substrate site of a second messenger-independent protein kinase of the type NII from porcine liver nuclei was mapped using a series of 30 ATP derivatives with modifications at the base, ribose or triphosphate moiety. Ki values for these derivatives were determined by competition with [gamma-32P]ATP; they range from 4 microM to 1.5 mM. For a comparison with data previously reported for the catalytic subunit of cAMP-dependent protein kinase I from rabbit skeletal muscle, the Ki values were transformed into delta delta values. These values are related to the Ki value of unsubstituted ATP and indicate the decrease of affinity caused by the different substitutions. With both enzymes the major binding affinity is derived from the interaction of the adenine base. The contributions of the two ribosyl OH groups are marginal and the triphosphate moiety interacts most strongly with its beta-phosphoryl group. Between the two enzymes the most striking differences, however, were observed for the specificity of the nucleobase interaction. While an unmodified N-6 amino group is required in the case of the cAMP-dependent protein kinase, the nuclear enzyme seems to tolerate extensive modification at this position, such as the introduction of a keto group or a bulky benzyl residue. Obviously, the ATP site of the nuclear kinase has an open cleft next to the N-6 of the adenine and binding of the adenine occurs by hydrophobic interaction without the formation of hydrogen bonds to any of the adenine nitrogens.

Stacking interaction of nucleobases: NMR investigations. III. Molecular aspects of the solvent dependence.

The stacking interaction between nucleic acid bases has been investigated by the determination of the self-association of 6-methylpurine in various mixtures of water and nonaqueous solvents in order to elucidate the solvent effect. The parameters of stacking association as well as of local solvent-solute interactions have been measured by means of NMR technique. The influences of local hydration and of solvent-solvent interactions on the stacking ability are discussed.

Stacking interactions of nucleobases: NMR-investigations. I. Self association of N6, N9-dimethyladenine and N6-dimethyl-N9-ethyladenine.

The selfassociation of N6,N9-dimethyladenine and N6-dimethyl-N9-ethyladenine has been studied by means of NMR technique. The thermodynamic quantities have been calculated using an isodesmic NMR model with three NMR parameters (the monomer shift deltaM and two complex shifts delta2 and delta3). The dependence of the thermodynamic quantities on the NMR parameters is discussed. Special attention is given to the determination of deltaM and its temperature dependence. Calculations with delta3 = 2 - delta2 and deltaM taken independently of temperature result in an average entropy deltaS = - 17.9 +/- 1.8 e.u. for N6,N9-dimethyladenine and deltaS = - 16.7 +/- 1.7 e.u. for N6-dimethyl-N9-ethyladenine and in an average enthalpy deltaH = - 7.2 +/- 0.6 kcal - mol-1 for both substances investigated.