Types Of Base Pairs Research Articles

How well can new-generation density functional methods describe stacking interactions in biological systems?

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.

Tetraplex Structure Formation in the Thrombin-Binding DNA Aptamer by Metal Cations Measured by Vibrational Spectroscopy

Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K+, Pb2+, Ba2+, Sr2+ and Mn2+ has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2′endo/anti and C2′endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb2+ ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb2+ ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb2+ ions (ΔT = 15 °C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.

Structural significances of pseudouridination and methylation of uridine residues in tRNA: X-Ray analyses of DNA dodecamers containing uridine and pseudouridine

Pseudouridine (psi) and 5-methyluridine (T) residues found in tRNA are prepared through modification of the uridine residues by specific enzymes just after transcription. On the other hands, thymidine residues in DNA are incorporated using dTTP which is derived from UTP before replication. In order to investigate the necessity of such modification and the structural properties of these residues, we have determined two X-ray structures of DNA dodecamers containing dU or d psi, and compared with that containing dT. There is found remarkable difference in arrangement of water molecules hydrogen-bonded to these residues, which form a Watson-Crick type base pair. The psi residue stabilizes the phosphate-backbone conformation of the phosphate group via water mediated hydrogen bond networks, while dT residues seem to prevent from attacking of water molecules.

Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs

In addition to the canonical base-pairs comprising the standard Watson-Crick (C:G and U:A) and wobble U:G conformations, an analysis of the base-pair types and conformations in the rRNAs in the high-resolution crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits has identified a wide variety of non-canonical base-pair types and conformations. However, the existing nomenclatures do not describe all of the observed non-canonical conformations or describe them with some ambiguity. Thus, a standardized system is required to classify all of these non-canonical conformations appropriately. Here, we propose a new, simple and systematic nomenclature that unambiguously classifies base-pair conformations occurring in base-pairs, base-triples and base-quadruples that are associated with secondary and tertiary interactions. This system is based on the topological arrangement of the two bases and glycosidic bonds in a given base-pair. Base-pairs in the internal positions of regular secondary structure helices usually form with canonical base-pair groups (C:G, U:A, and U:G) and canonical conformations (C:G WC, U:A WC, and U:G Wb). In contrast, non-helical base-pairs outside of regular structure helices usually have non-canonical base-pair groups and conformations. In addition, many non-helical base-pairs are involved in RNA motifs that form a defined set of non-canonical conformations. Thus, each rare non-canonical conformation may be functionally and structurally important. Finally, the topology-based isostericity of base-pair conformations can rationalize base-pair exchanges in the evolution of RNA molecules.

Mutational and Structural Analysis of Stem-loop IIIc of the Hepatitis C Virus and GB Virus B Internal Ribosome Entry Sites

Translation of the open reading frames (ORF) of the hepatitis C virus (HCV) and closely related GB virus B (GBV-B) genomes is driven by internal ribosome entry site (IRES) elements located within the 5' non-translated RNA. The functioning of these IRES elements is highly dependent on primary and higher order RNA structures. We present here the solution structures of a common, critical domain within each of these IRESs, stem-loop IIIc. These ten-nucleotide hairpins have nearly identical sequences and similar overall tertiary folds. The final refined structure of each shows a stem with three G:C base-pairs and a novel tetraloop fold. Although the bases are buckled, the first and fourth nucleotides of both tetraloops form a Watson-Crick type base-pair, while the apical nucleotides are located in the major groove where they adopt C(2)-endo sugar puckering with B-form geometry. No hydrogen bonding interactions were observed involving the two apical residues of the tetraloop. Stability of the loops appears to be derived primarily from the stacking of bases, and the hydrogen bonding between the fourth and seventh residues. Mutational analysis shows that the primary sequence of stem-loop IIIc is important for IRES function and that the stem and first and fourth nucleotides of the tetraloop contribute to the efficiency of internal ribosome entry. Base-pair formation between these two positions is essential. In contrast, the apical loop nucleotides differ between HCV and GBV-B, and substitutions in this region of the hairpin are tolerated without major loss of function.

Effect of base-pair inhomogeneities on charge transport along the DNA molecule, mediated by twist and radial polarons

Some recent results for a three-dimensional, semi-classical, tight-binding model for DNA show that there are two types of polarons, namely radial and twist polarons, which can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA makes it crucial to find out if charge transport also exists in DNA chains with different base pairs. In this paper, we address this problem in its simple case, a homogeneous chain except for a single different base pair, which we call a base-pair inhomogeneity, and its effect on charge transport. Radial polarons experience either reflection or trapping. However, twist polarons are good candidates for charge transport along real DNA. This transport is also very robust with respect to weak parametric and diagonal disorder.

Charge Transport in Poly(dG)–Poly(dC) and Poly(dA)–Poly(dT) DNA Polymers

We investigate the charge transport in synthetic DNA polymers built up from single type of base pairs. In the context of a polaronlike model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity, the breather mobility in the latter case is comparatively restrained, inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibit better conductance than poly(dA)-poly(dT) ones.

Tools for the automatic identification and classification of RNA base pairs.

Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.

The aldol condensation of acetaldehyde and heptanal on hydrotalcite-type catalysts

The aldol condensation of acetaldehyde and heptanal has been carried out in the liquid phase between 353 and 413 K using different types of solid base catalysts: MgO with strong Lewis basic sites, Mg(Al)O mixed oxides with acid–base pairs of the Lewis type obtained from hydrotalcite precursor, and rehydrated Mg(Al)O mixed oxides with Brønsted basic sites. The influence of several reaction parameters, temperature, acetaldehyde to heptanal molar ratio, nature of solvent (hexane, toluene, ethanol), has been investigated. A comparative study of the catalysts has been performed in the such defined optimal reaction conditions, i.e., 373 K, acetaldehyde/heptanal molar ratio, 2/1; and ethanol/reactants molar ratio, 5/1. Mg(Al)O mixed oxides calcined below 673 K are the most selective catalyst to 2-nonenal, the cross-condensation product formed when in the first step proton abstraction occurs from acetaldehyde. Acid–base pairs of moderate basic strength are suitable when this cross-condensation is the desired reaction. Stronger Lewis basic sites of MgO or Brønsted-type basic sites of the rehydrated mixed oxide tend to favor the formation of carbanion from heptanal. This latter leads to the formation of 2-pentyl-2-butenal and 2-pentyl-2-nonenal by cross-condensation with acetaldehyde and self-condensation, respectively.

Nuclear magnetic resonance studies of ribonucleic acids

Ribonucleic acids (RNA) and RNA−protein complexes are essential components of biological information transfer, catalytic processes and are associated with regulatory functions. This broad range of biological functions is paralleled at the conformational level by a large number of non-canonical structural elements or sequences with non-standard backbone conformations, e.g., loops, bulges, pseudo-knots and complex tertiary folds. NMR spectroscopy has evolved to a powerful tool for the determination of ribonucleic acid structures of up to 20 kDa. Uniform or selective stable isotope labelling aids in solving assignment problems arising from the inherently limited chemical shift dispersion and overlap of resonances for larger nucleotide sequences. Recent developments of multi-dimensional heteronuclear NMR pulse sequences allow e.g., to directly observe the hydrogen bonding pattern of canonical Watson−Crick base pairs as well as of unusual types of base pairs, thereby opening up a fast access to secondary structure screening of RNA. Detailed conformational descriptions are obtained using conventional NOE andJcoupling-derived data, nowadays supplemented by information from residual dipolar couplings. The latter method also provides a new means for the probing of dynamical features of ribonucleic acids.

The Lonepair Triloop: A New Motif in RNA Structure

The lonepair triloop (LPTL) is an RNA structural motif that contains a single (“lone”) base-pair capped by a hairpin loop containing three nucleotides. The two nucleotides immediately outside of this motif (5′ and 3′ to the lonepair) are not base-paired to one another, restricting the length of this helix to a single base-pair. Four examples of this motif, along with three tentative examples, were initially identified in the 16 S and 23 S rRNAs with covariation analysis. An evaluation of the recently determined crystal structures of the Thermus thermophilus 30 S and Haloarcula marismortui 50 S ribosomal subunits revealed the authenticity for all of these proposed interactions and identified 16 more LPTLs in the 5 S, 16 S and 23 S rRNAs. This motif is found in the T loop in the tRNA crystal structures. The lonepairs are positioned, in nearly all examples, immediately 3′ to a regular secondary structure helix and are stabilized by coaxial stacking onto this flanking helix. In all but two cases, the nucleotides in the triloop are involved in a tertiary interaction with another section of the rRNA, establishing an overall three-dimensional function for this motif. Of these 24 examples, 14 occur in multi-stem loops, seven in hairpin loops and three in internal loops. While the most common lonepair, U:A, occurs in ten of the 24 LPTLs, the remaining 14 LPTLs contain seven different base-pair types. Only a few of these lonepairs adopt the standard Watson–Crick base-pair conformations, while the majority of the base-pairs have non-standard conformations. While the general three-dimensional conformation is similar for all examples of this motif, characteristic differences lead to several subtypes present in different structural environments. At least one triloop nucleotide in 22 of the 24 LPTLs in the rRNAs and tRNAs forms a tertiary interaction with another part of the RNA. When a LPTL containing the GNR or UYR triloop sequence forms a tertiary interaction with the first (and second) triloop nucleotide, it recruits a fourth nucleotide to mediate stacking and mimic the tetraloop conformation. Approximately half of the LPTL motifs are in close association with proteins. The majority of these LPTLs are positioned at sites in rRNAs that are conserved in the three phylogenetic domains; a few of these occur in regions of the rRNA associated with ribosomal function, including the presumed site of peptidyl transferase activity in the 23 S rRNA.

Theoretical study of substitution effect of the hydrogen bond stability of 9-methylguanine derivatives and 1-methylcytosine.

The substitution effect on hydrogen bond stability of the Watson-Crick type base pair between 1-methylcytosine (C) and substitution-introduced 9-methylguanine derivatives (Gx) was studied by an ab initio molecular orbital theory. Introduction of an electron-withdrawing group on the 8-position or on the exo-cyclic amino moiety enforced the base pair stability.

ANALYSIS OF RELATIVE POSITIONS OF RIBONUCLEOTIDE BASES IN A CRYSTAL STRUCTURE OF RIBOSOME

ABSTRACT Relative positions of bases to bases in a crystal structure of ribosome were analyzed extensively. It was found that there is no clear relation between bases apart more than 15 Å and, thus, the relative location of bases can be analyzed within 15 Å of the reference bases. As for base pairing, major positioning was found to be due to the Watson-Crick type base pairs. Some other positions corresponding to non-Watson-Crick type base pairs were also found in some extents. As for base–base stacking, it was observed that the bases stacked to adenine base are dispersive. It was found that less non-Watson-Crick base pairs was found close to the protein binding site, suggesting that the protein components have a tendency to bind to the regular stem structures. The database of relative location of bases must be useful for improvement of structural determination and structural modeling systems.

Use of 2-Aminopurine and Tryptophan Fluorescence as Probes in Kinetic Analyses of DNA Polymerase β

Although the use of 2-aminopurine (2-AP) as a probe in stopped-flow analyses of DNA polymerase beta (Pol beta) had provided important mechanistic insight, the conditions used were limited by the location of 2-AP and the use of a combination of tryptophan (Trp) and 2-AP fluorescence. This study examined different DNA substrates to identify several factors that can affect the observed signal in stopped-flow experiments. Both Trp and 2-AP emissions were separately excited and monitored. It was found that both probes show a fast phase and a slow phase of fluorescence changes, but the direction and the amplitude vary greatly between the two probes and between different DNA substrates. Detailed analyses suggested that the location of 2-AP in the template has a significant impact on the fluorescence properties of 2-AP and that a location opposite the incoming dNTP, which has been used in all such studies in the past, is not optimal. In particular, the results show that placing 2-AP one base after the templating base greatly enhances the signal intensity, which suggests a significant change in base stacking interactions at this position during nucleotide incorporation. These results allowed us to derive an improved set of conditions which were then used to reevaluate results from previous reports. It also allows greater freedom in the type of base pairs studied, since 2-AP is not the templating base in the nascent base pair. Kinetic constants were determined for dNTP and catalytic Mg(2+). The results obtained from stopped-flow experiments were compared to results from chemical quench. Stopped flow of incorrect dNTP incorporation and the reverse reaction are also reported, which provide useful information to the mechanism of Pol beta.

Molecular recognition of adenine, adenosine and ATP at the air–water interface by a uracil appended fullerene

A new C60-uracil adduct capable of hydrogen bonding, via complimentary base pairing, of adenine, adenosine, and adenosine 5′-triphosphate (ATP) was synthesized and characterized by UV-visible and 1H NMR spectroscopy, cyclic voltammetry and differential pulse voltammetry, as well as ESI-mass spectrometry. Molecular modeling by ab initio B3LYP/3–21G(*) calculations revealed the Watson–Crick type base pairing. Stable “expanded liquid” Langmuir films of the C60-uracil–adenine, C60-uracil–adenosine and C60-uracil–ATP complexes were prepared and characterized by isotherms of surface pressure versus area per molecule as well as the Brewster angle microscopy imaging. The area per molecule at infinite adduct dilution in the film was dependent on composition of the subphase solution and increased in the order: water < adenine < adenosine < ATP solution. Comparison of experimental and calculated areas per molecule and dipole moment components normal to the subphase–air interface indicated prevailing horizontal orientation of the complexes in the films. The Langmuir films were transferred, by using the Langmuir–Blodgett technique, onto quartz slides and characterized by the UV-visible spectroscopy.

Theoretical investigation on the substitution effect of the hydrogen bond energy of the Watson–Crick type base pair between substituted 1-methyluracil and 9-methyladenine

Basis set effect in evaluation of base pair formation energy of the Watson–Crick type base pair between substituted 1-methyluracil and 9-methyladenine was studied in the Hartree–Fock and second-order Møller–Plesset level of theory. The same trend was observed in the substitution effect in all basis sets attempted; thus, the error depending on the basis set incompleteness is minimal in the evaluation of the substitution effect of the base pair formation energy. Neither the hydrogen bond distance nor the atomic charge was a valid index for the hydrogen bond status in base pairing.

Highly emissive, nine-coordinate enantiopure lanthanide complexes incorporating tetraazatriphenylenes as probes for DNA.

The interaction of q = 0 delta- and lambda-Tb and Eu complexes with poly(dAdT), poly(dGdC) and calf-thymus DNA has been examined by absorption, emission and chiroptical spectroscopy and is sensitive to complex helicity, base-pair type and the nature of the lanthanide excited state.

An Ab Initio Study of the Hydrogen Bond Energy of Base Pairs Formed between Substituted 9-Methylguanine Derivatives and 1-Methylcytosine

The substitution effect on hydrogen-bond energy of the Watson-Crick type base pair formation between 1-methylcytosine and chemically modified 9-methylguanine derivatives was evaluated by an ab initio molecular orbital theory. Introduction of an electron-withdrawing group on the 8-position or on the exo-cyclic amino moiety enforced the hydrogen bond. Neither the charge distribution nor the separation between the hydrogen bonding sites is found to be directly correlated with the strength of the hydrogen bonds.

Ab initio molecular orbital evaluation of the hydrogen bond energy of base pairs formed between substituted 1-methylcytosine derivatives and 9-methylguanine.

The substitution effect on hydrogen bond energy of the Watson-Crick type base pair between 9-methylguanine (G) and chemically modified 1-methylcytosine (CX) derivatives was evaluated by ab initio molecular orbital theory. A remarkable trend was observed in the substitution effect of the hydrogen bond stability: Cytosine derivatives possessing an electron-donating group form stable base pairs with guanine. However, both the hydrogen bond distance and the charge distribution were not good indexes for the hydrogen bond status in CX-G base pairing.

Theoretical Study of the Hydrogen Bond Energy of Base Pairs Formed between Substituted 1-Methylcytosine Derivatives and 9-Methylguanine

The substitution effect on hydrogen bond energy of the Watson−Crick type base pair between 9-methylguanine and chemically modified 1-methylcytosine derivatives was evaluated by an ab initio molecular orbital theory. A remarkable tendency was observed, namely, that cytosine derivatives possessing an electron-donating group form a stable base pair with guanine. Nevertheless, neither the hydrogen bond distance nor the charge distribution was a valid index for the hydrogen bond status in CX−G base pairing. An intramolecular hydrogen bond between the substituent and the exo-cyclic amino moiety also had an important role in the substitution effect of the base pair stability.