Base Pairs In Duplex DNA Research Articles

Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex.

In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease. Here, we report the crystal structure of AddAB bound to DNA. The structure allows identification of a putative Chi-recognition site in an inactivated helicase domain of the AddB subunit. By generating mutant protein complexes that do not respond to Chi, we show that residues responsible for Chi recognition are located in positions equivalent to the signature motifs of a conventional helicase. Comparison with the related RecBCD complex, which recognizes a different Chi sequence, provides further insight into the structural basis for sequence-specific ssDNA recognition. The structure suggests a simple mechanism for DNA break processing, explains how AddAB and RecBCD can accomplish the same overall reaction with different sets of functional modules and reveals details of the role of an Fe-S cluster in protein stability and DNA binding.

Natural versus Artificial Creation of Base Pairs in DNA: Origin of Nucleobases from the Perspectives of Unnatural Base Pair Studies

Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the chemical evolution and selection of the natural nucleobases. Interestingly, the initial structures designed by each research group were quite similar to those of the latest successful unnatural base pairs. In this regard, it is tempting to form a hypothesis that the base pairs on the primordial Earth, in which the natural purine bases, A and G, and pyrimidine bases, C and T(U), originated from structurally similar compounds, such as hypoxanthine for a purine base predecessor. Subsequently, the initial base pair evolved to the present two sets of base pairs via a keto-enol tautomerization of the initial compounds.

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 106M−1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg2+–double T:T mismatched base pair interaction, the affinity for the second Hg2+ binding was significantly larger than that for the first Hg2+ binding. The positively cooperative binding may be favorable to align multiple Hg2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

Thermodynamic Properties of the Specific Binding Between Ag+ Ions and C:C Mismatched Base Pairs in Duplex DNA

Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag+ ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag+ ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag+ ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 106 M−1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. The specific binding between the Ag+ ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag+ ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag+ binding. The binding affinity for the second Ag+ binding was similar to that for the first Ag+ binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag+ ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.

Detection of single nucleotide polymorphisms by the specific interaction between transition metal ions and mismatched base pairs in duplex DNA

Single nucleotide polymorphisms (SNPs) are base differences in the human genome. These differences are favorable markers for genetic factors including those associated with risks of complex diseases and individual responses to drugs. When two duplex DNAs with different types of SNPs are mixed and reannealed, the two novel heteroduplexes containing mismatched base pairs are formed in addition to the two initial perfectly matched homoduplexes. Heteroduplex analysis recognizing the newly formed mismatched base pairs is useful for SNP detection. Various strategies to detect the mismatched base pairs were devised due to the potential applications of SNPs. However, they were not always convenient and accurate. Here, we propose a novel strategy to detect the mismatched base pairs by the specific interaction between the Hg2+ ion and a T:T mismatched base pair and that between the Ag+ ion and a C:C mismatched base pair. UV melting indicated that the melting temperature of only the heteroduplexes with the T:T and C:C mismatched base pair specifically increased on adding the Hg2+ and Ag+ ion, respectively. Fluorescence resonance energy transfer analyses indicated that the intensity of fluorophore emission of only the fluorophore and quencher-labeled heteroduplexes with the T:T and C:C mismatched base pair specifically decreased on adding the Hg2+ and Ag+ ion, respectively. We propose that the addition of the metal ion could be a convenient and accurate strategy to detect the mismatched base pair in the heteroduplex. This novel strategy might make the heteroduplex analysis easy and eventually lead to better SNP detection.

Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

2D 1H NOESY NMR spectroscopy is routinely used to give information on the closeness of hydrogen atoms through space. This work is based on a 2D 1H NOESY NMR spectrum of a 12 base-pair DNA duplex. This 6-h laboratory workshop aims to provide advanced-level chemistry students with a basic, yet solid, understanding of how the 3D structure of a double-stranded DNA sequence can be determined using 2D 1H NOESY NMR spectroscopy and, hence, how structural perturbations induced by DNA binding agents such as platinum anticancer drugs are studied. Students are supplied with various sections of the 2D 1H NOESY spectrum of the DNA sequence. Using these, as well as a molecular model as a visual aid and tool for measuring interproton distances, they are able to sequentially assign the structure of the DNA.

Efficient Charge Transport in DNA Diblock Oligomers

The realization of highly efficient photoinduced charge separation across the pi-stacked base pairs in duplex DNA remains elusive. The low efficiencies (<5%) typically observed for charge separation over a dozen or more base pairs are a consequence of slow charge transport and rapid charge recombination. We report here a significant (5-fold or greater) enhancement in the efficiency of charge separation in diblock purine oligomers consisting of two or three adenines followed by several guanines, when compared to oligomers consisting of a single purine or alternating base sequences. This approach to wire-like behavior is attributed to both slower charge recombination and faster charge transport once the charge reaches the G-block in these diblock systems.

Dimer of 2,7-diamino-1,8-naphthyridine for the detection of mismatches formed by pyrimidine nucleotide bases

Discrimination of base mismatches from normal Watson–Crick base pairs in duplex DNA constitutes a key approach to the detection of single nucleotide polymorphisms (SNPs). We have developed a sensor for a surface plasmon resonance (SPR) assay system to detect G–G, A–A, and C–C mismatch duplexes by employing a surface upon which mismatch-binding ligands (MBLs) are immobilized. We synthesized a new MBL consisting of 2,7-diamino-1,8-naphthyridine (damND) and immobilized it onto a CM5 sensor chip to carry out the SPR assay of DNA duplexes containing a single-base mismatch. The SPR sensor with damND revealed strong responses to all C–C mismatches, and sequence-dependent C–T and T–T mismatches. Compared to ND- and naphthyridine-azaquinolone hybrid (NA)-immobilized sensor surfaces, with affinity to mismatches composed of purine nucleotide bases, the damND-immobilized surface was useful for the detection of the mismatches composed of pyrimidine nucleotide bases.

Bisintercalator natural products with potential therapeutic applications: isolation, structure determination, synthetic and biological studies

Echinomycin is the prototypical bisintercalator, a molecule that binds to DNA by inserting two planar chromophores between the base-pairs of duplex DNA, placing its cyclic depsipeptide backbone in the minor groove. As such, it has been the focus of an extensive number of investigations into its biological activity, nucleic acid binding and, to some extent, its structure-activity relationships. However, echinomycin is also the parent member of an extended family of natural products that interact with DNA by a similar mechanism of bisintercalation. The structural variety in these compounds leads to changes in sequence selectivity and and biological activity, particularly as anti-tumour and anti-viral agents. One of the more recently identified marine natural products that is moving close to clinical development is thiocoraline, and it therefore seems timely to review the various bisintercalator natural products.

Transplatin Is Cytotoxic When Photoactivated: Enhanced Formation of DNA Cross-Links

It is well-known that although cisplatin, [cis-[PtCl2(NH3)2], is an anticancer drug, its isomer transplatin is not cytotoxic. Here we show that transplatin is almost as cytotoxic as cisplatin when treated cells (human keratinocytes HaCaT and ovarian cancer A2780 cells) are irradiated with UVA light (50 min, 1.77 mW cm-2). Chemical studies show that light activates both chloride ligands of transplatin, and experiments on pSP73 plasmid DNA and a 23 base-pair DNA duplex show that irradiation can greatly enhance formation of interstrand cross-links and of DNA-protein cross-links (which are not formed in the dark). Comet assays showed that UVA irradiation of transplatin-treated cells resulted in an increased inhibition of H2O2-induced DNA migration, supporting the conclusion that the cytotoxicity of photoactivated transplatin is mainly due to formation of DNA interstrand and DNA-protein cross-links.

Differential analysis of biomolecular rupture forces

After a brief overview over the development of single molecule force spectroscopyand the basic concepts of bond dissociation under external force, we discuss therecently developed differential force assay, where a molecular bond serves as amicroscopic force sensor. We introduce the basic concept of this novel biomolecularassay, discuss its requirements, capabilities and limitations, and present the latestadvances in the design of the assay itself, as well as its appropriate hardware. Thenecessary data analysis procedures are introduced, and recent results showing thediscrimination of single CC and GG mismatches within a 30 base pair DNA duplex arepresented.

Examining [2,2′-bipyridyl]-3,3′-diol as a possible DNA model base pair

[2,2′-Bipyridyl]-3,3′-diol (BP(OH) 2) is known to undergo excited state intramolecular double proton transfer in solution. Steady state absorption and fluorescence spectra of BP(OH) 2 were studied here in solvents of varying polarity and hydrogen bonding capability, and in binary mixtures of p-dioxane/water in order to test its applicability as a model base pair. Unique absorption due to water solvation was observed in the region of 400–450 nm. Only the di-keto-tautomer fluoresces in all the solvents studied here. A large blue-shift in the fluorescence band due to intermolecular hydrogen bonding was observed in polar, protic solvents which increases with increasing solvent polarity. Results from the absorption spectra in the binary mixtures were fitted to a binding isotherm model and three water molecules were found to solvate each of the two hydrogen bonding centers in BP(OH) 2. Molecular dynamics simulations were performed for a dodecamer duplex DNA containing BP(OH) 2 as a model base pair in the center of the duplex. The results of the simulations indicate that BP(OH) 2 can serve as a good mimic of a natural base pair with no major perturbation to the helical structure's stability. One of the two hydrogen bonds in BP(OH) 2 resides in the major groove of the duplex DNA, whereas the other one is situated in the minor groove. The preferential stacking between the flanking base pairs of duplex DNA and its unique spectroscopic features in water make BP(OH) 2 a potential probe for tautomerization in DNA and a possible sensor for water accessibility in the major and minor grooves of DNA.

Tetraplatinated Artificial Oligopeptides Afford High Affinity Intercalation into dsDNA

This paper reports the binding of an artificial tetrapeptide to which are tethered four Pt(II) complexes (i.e., [Pt(tpy)(py)]48+) with a 12 base pair duplex DNA oligonucleotide. Isothermal Titration Calorimetry reveals that two tetrametallic peptides stoichiometrically bind to each DNA duplex with a binding constant, KB, of 1.7 x 106 M-1, with a change in free energy of -8.5 kcal/mol. This KB represents an affinity 2 orders of magnitude greater than that of the monometallic analogue [Pt(tpy)(pic)]2+ for the same dsDNA sequence. The metalated peptides bind by intercalation into the DNA, partially unwinding the helix while stabilizing the structure, causing an increase in the dsDNA melting temperature of 25 degrees C.

Mutations in the Spacer Region of Drosophila Mitochondrial DNA Polymerase Affect DNA Binding, Processivity, and the Balance between Pol and Exo Function

The catalytic subunit (alpha) of mitochondrial DNA polymerase (pol gamma) shares conserved DNA polymerase and 3'-5' exonuclease active site motifs with Escherichia coli DNA polymerase I and bacteriophage T7 DNA polymerase. A major difference between the prokaryotic and mitochondrial proteins is the size and sequence of the region between the exonuclease and DNA polymerase domains, referred to as the spacer in pol gamma-alpha. Four gamma-specific conserved sequence elements are located within the spacer region of the catalytic subunit in eukaryotic species from yeast to humans. To elucidate the functional roles of the spacer region, we pursued deletion and site-directed mutagenesis of Drosophila pol gamma. Mutant proteins were expressed from baculovirus constructs in insect cells, purified to near homogeneity, and analyzed biochemically. We find that mutations in three of the four conserved sequence elements within the spacer alter enzyme activity, processivity, and/or DNA binding affinity. In addition, several mutations affect differentially DNA polymerase and exonuclease activity and/or functional interactions with mitochondrial single-stranded DNA-binding protein. Based on these results and crystallographic evidence showing that the template-primer binds in a cleft between the exonuclease and DNA polymerase domains in family A DNA polymerases, we propose that conserved sequences within the spacer of pol gamma may position the substrate with respect to the enzyme catalytic domains.

Inhibition of DNA mismatch repair by cadmium and oxidative damage

Inhibition of DNA mismatch repair by cadmium and oxidative damage

GA and AG Sequences of DNA React with Cisplatin at Comparable Rates.

The sequence selectivity of the antitumor drug cisplatin (cis-[PtCl(2)(NH(3))(2)] (1)) between the 5'-AG-3' and 5'-GA-3' sites of DNA has been a matter of discussion for more than twenty years. In this work, we compared the reactivity of GA and AG sequences of DNA towards the aquated forms of cisplatin (cis-[PtCl(NH(3))(2)(H(2)O)](+) (2), cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) (3), and cis-[Pt(OH)(NH(3))(2)(H(2)O)](+) (4)) using two sets of experiments. In the first, we investigated a DNA hairpin, whose duplex stem contained a TGAT sequence as the single reactive site, and determined the individual rate constants of platination with 2 and 3 for G and A in acidic solution. The rate constants at 20 degrees C in 0.1M NaClO(4) at pH 4.5+/-0.1 were 0.09(4) M(-1)s(-1) (G) and 0.11(3) M(-1)s(-1) (A) for 2, and 9.6(1) M(-1)s(-1) (G) and 1.7(1) M(-1)s(-1) (A) for 3. These values are similar to those obtained previously for an analogous hairpin that contained a TAGT sequence. The monoadducts formed with 2 by both GA purines are extremely long-lived, partly as a result of the slow hydrolysis of the chloro monoadduct at A, and partly because of the very low chelation rate (1.4 x 10(-5)s(-1) at 20 degrees C) of the aqua monoadduct on the guanine. In the second set of experiments, we incubated pure or enriched samples of 1, 2, 3, or 4 for 18-64 h at 25 degrees C with a 19 base pair (bp) DNA duplex, whose radiolabeled top strand contained one GA and one AG sequence as the only reactive sites. Quantification of the number of GA and AG cross-links afforded a ratio of about two in favor of AG, irrespective of the nature of the leaving ligands. These results disagree with a previous NMR spectroscopy study, and indicate that GA sequences of DNA are substantially more susceptible to attack by cisplatin than previously thought.

Energetics of sequence-specific protein-DNA association: binding of integrase Tn916 to its target DNA.

The DNA binding domain of the transposon Tn916 integrase (INT-DBD) binds to its DNA target site by positioning the face of a three-stranded antiparallel beta-sheet within the major groove. Binding of INT-DBD to a 13 base pair duplex DNA target site was studied by isothermal titration calorimetry, differential scanning calorimetry, thermal melting followed by circular dichroism spectroscopy, and fluorescence spectroscopy. The observed heat capacity change accompanying the association reaction (DeltaC(p)) is temperature-dependent, decreasing from -1.4 kJ K(-1) mol(-1) at 4 degrees C to -2.9 kJ K(-1) mol(-1) at 30 degrees C. The reason is that the partial molar heat capacities of the free protein, the free DNA duplex, and the protein-DNA complex are not changing in parallel when the temperature increases and that thermal motions of the protein and the DNA are restricted in the complex. After correction for this effect, DeltaC(p) is -1.8 kJ K(-1) mol(-1) and temperature-independent. However, this value is still higher than DeltaC(p) of -1.2 kJ K(-1) mol(-1) estimated by semiempirical methods from dehydration of surface area buried at the complex interface. We propose that the discrepancy between the measured and the structure-based prediction of binding energetics is caused by incomplete dehydration of polar groups in the complex. In support, we identify cavities at the interface that are large enough to accommodate approximately 10 water molecules. Our results highlight the difficulties of structure-based prediction of DeltaC(p) (and other thermodynamic parameters) and emphasize how important it is to consider changes of thermal motions and soft vibrational modi in protein-DNA association reactions. This requires not only a detailed investigation of the energetics of the complex but also of the folding thermodynamics of the protein and the DNA alone, which are described in the accompanying paper [Milev et al. (2003) Biochemistry 42, 3492-3502].

Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase.

To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a "transcription bubble" interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the elongation complex. Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex.

Crystallization and preliminary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA.

For protein-DNA complex crystallization, the choice of the DNA fragment is crucial. With the aim of crystallizing the 31 kDa Fpg DNA-repair enzyme bound to DNA, oligonucleotide duplexes varying in length, sequence, end type and nature of the specific DNA target site were used. Crystals of several protein-DNA combinations grew from solutions containing both polyethylene glycol and salt. This systematic crystallization screening followed by optimization of the crystallization conditions by microseeding led to crystals of Fpg bound to a 13 base-pair duplex DNA carrying the 1,3-propanediol abasic site analogue which are suitable for crystallographic analysis. Complete native data sets have been collected to 2.1 A resolution.

Tautomerization dynamics of a model base pair in DNA.

Osama K. Abou-Zied, Ralph Jimenez, andFloyd E. Romesberg*Department of Chemistry, The Scripps Research Institute10550 North Torrey Pines Road, La Jolla, California 92037ReceiVed October 11, 2000Structural and dynamic properties of DNA base pairs arevirtually always discussed in terms of the keto-amine tautomers,which are thought to be the dominant forms of the base pairs induplex DNA.