NMR studies of DNA duplexes containing alpha-anomeric nucleotides and polarity reversals

We present a summary of our research to date on a family of self-complementary DNA decamers containing single alpha-anomeric nucleotides flanked by 3'-3' and 5'-5' phosphodiester linkages from the perspective of the salient NMR techniques employed to shed light on the structural and dynamic properties of these sequences. Research into this class of synthetic alpha-/beta-oligonucleotides containing mixed strand disposition may have medical relevance given their recently documented efficacy as antisense therapeutics.     

Synthesis and properties of covalently-closed DNA duplexes containing pyrophosphate and and substituted pyrophosphate internucleotide groups

A new method for the efficient synthesis of covalently closed DNA duplexes (DNA dumbbells) and the introduction of pyrophosphate and substituted pyrophosphate internucleotide groups into their structure is proposed. The method is based on chemical ligation in DNA duplexes that are formed by a polynucleotide the ends of which are brought together due to the introduction of the minihairpin structure [sequence: see text]. DNA dumbbells containing a pyrophosphate (substituted pyrophosphate) group result from the interaction as being between the 3'-terminal phosphate (methylphosphate) group of the polynucleotide and the 5'-terminal phosphate group of deoxyguanosine of the minihairpin sequence, which flanks the polynucleotide from the 5' end. 1-Ethyl-3-(3'-dimethylaminopropyl) carbodiimide was used as a condensing agent. The yield of covalently closed 42-mer DNA duplexes containing a pyrophosphate group was 98%, that of duplexes with a substituted pyrophosphate group was 25%. The reactivity of the substituted pyrophosphate group incorporated into DNA dumbbells was studied. It is shown that the group efficiently interacts with nucleophiles in an aqueous medium at pH 8.0.     

Mechanistic studies on the neighboring base damage induced by KMnO4 oxidation of 8-oxoguanine in DNA

New types of DNA substrates containing an 8-oxoguanine residue (8-oxo-G) were prepared in order to examine the mechanisms for the neighboring base damage initiated by KMnO4 oxidation of the 8-oxo-G. The results obtained from the reactions suggested that the damage at remote sites in the single strands can be explained by an electronic interaction (redox reaction) between an oxidized 8-oxo-G species and the base (to be damaged), which are close each other in a loop structure. For the inefficient damage observed in duplex substrates, electron transfer through stacked bases might be involved.     

Rat 7,8-dihydro-8-oxoguanine DNA glycosylase: substrate specificity, kinetics and cleavagemechanism at an apurinic site

Reactive oxygen species produce different lesions in DNA. Among them, 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major oxidative products implicated in mutagenesis. This lesion is removed from damaged DNA by base excision repair, and genes coding for 8-oxoG-DNA glycosylases have been isolated from bacteria, yeast and human cells. We have isolated and characterized the cDNA encoding the rat 8-oxoG-DNA glycosylase (rOGG1). Expression of the cDNA in the fgp mutY Escherichia coli double mutant allowed the purification of the untagged rOGG1 protein. It excises 8-oxoG from DNA with a strong preference for duplex DNA containing 8-oxoG:C base pairs. rOGG1 also acts on formamidopyrimidine (FaPy) residues, and the K m values on 8-oxoG and FaPy residues are 18.8 and 9.7 nM, respectively. When acting on an oligonucleotide containing an 8-oxoG residue, rOGG1 shows a beta-lyase activity that nicks DNA 3' to the lesion. However, rOGG1 acts on a substrate containing an apurinic site by a beta-delta elimination reaction and proceeds through a Schiff base intermediate. Expression of rOGG1 in E.coli fpg mutY suppresses its spontaneous mutator phenotype.     

Parallel-stranded duplexes and quartet assemblies formed by oligonucleotides containing isoguanine

Oligonucleotides with isoguanine-cytosine base pairs form duplexes with parallel chain orientation. This strong base pair dictates the strand polarity when additional dA-dT or N7Ad-dT pairs are present. The same is observed for the isocytosine-guanine pair. Quartet structures are built by the self-assembly of oligonucleotides containing short runs of isoguanine or 7-deazaisoguanine. New base pairs between isoguanine or guanine and 5-aza-7-deazaguanine are presented.     

The sequence dependence of circular dichroism spectra of DNA duplexes

The three satellite DNAs of Drosophila virilis, that approximate to poly d(CAAACTA)-poly d(TAGTTTG), poly d(TAAACTA)-poly d(TAGTTTA), poly d(CAAATTA)-poly d(TAATTTG), the satellite DNA of Drosophila melanogaster that approximates to poly d(AATAT)-poly d(ATATT), the synthetic DNA duplexes, poly dG-poly dC, poly d(AT)-poly d(AT), poly d(AAT)-poly d(ATT), poly d(AAC)-poly d(GTT), poly d(TAC)-poly d(GTA) and the block copolymer d(C15A15)-d(T15G15) all have circular dichroism spectra consistent with the propositions that they have the same molecular geometry in solution and that it is the kind and frequency of nucleotide triplet sequences that determines their spectral characteristics. Poly dA-poly dT is apparently an exception.     

Thermodynamics of dT--dT base pair mismatching in linear DNA duplexes and three-arm DNA junctions

We have used a combination of magnetic-suspension densimetry and calorimetry to derive complete thermodynamic profiles, including volume changes, for the formation of linear DNA duplexes and three-arm branched DNA junctions, from their component strands, with and without dT-dT mismatches. The formation of each type of complex at 20 degrees C is accompanied by a favorable free energy, with a favorable enthalpy term partially compensated by an unfavorable entropy. Formation is associated also with net uptake of water molecules. Using the formation of the fully-paired linear duplex or three-arm junction as reference states, we can establish a thermodynamic cycle in which the contribution of the single-strand species cancels. From this cycle, we determine that substitution of dA for dT has a differential free energy of deltadeltaG degrees of +2.4 kcal mol(-1) for mismatched duplex and +2.0 kcal mol(-1) (on the average) for the mismatched junction. These unfavorable differential free energies result from an unfavorable enthalpy, partially compensated by a favorable entropy, and a negative deltadeltaV. The free energies in the two cases have signs opposed to those of deltadeltaV, a situation that implicates hydration changes in creating the mismatch. When the deltadeltaV terms are normalized by the total number of base pairs involved, the immobilization of structural water molecules (and/or substitution of electrostricted for hydrophobic water molecules) is about 7 times greater for junctions than duplexes. This is consistent with more extensive hydrophobic hydration of branched DNA structures than of duplexes.     

The critical active-site amine of the human 8-oxoguanine DNA glycosylase, hOgg1: direct identification, ablation and chemical reconstitution

BACKGROUND: Base-excision DNA repair (BER) is the principal pathway responsible for the removal of aberrant, genotoxic bases from the genome and restoration of the original sequence. Key components of the BER pathway are DNA glycosylases, enzymes that recognize aberrant bases in the genome and catalyze their expulsion. One major class of such enzymes, glycosylase/lyases, also catalyze scission of the DNA backbone following base expulsion. Recent studies indicate that the glycosylase and lyase functions of these enzymes are mechanistically unified through a common amine-bearing residue on the enzyme, which acts as both the electrophile that displaces the aberrant base and an electron sink that facilitates DNA strand scission through imine (Schiff base)/conjugate elimination chemistry. The identity of this critical amine-bearing residue has not been rigorously established for any member of a superfamily of BER glycosylase/lyases. RESULTS: Here, we report the identification of the active-site amine of the human 8-oxoguanine DNA glycosylase (hOgg1), a human BER superfamily protein that repairs the mutagenic 8-oxoguanine lesion in DNA. We employed Edman sequencing of an active-site peptide irreversibly linked to substrate DNA to identify directly the active-site amine of hOgg1 as the epsilon-NH2 group of Lys249. In addition, we observed that the repair-inactive but recognition-competent Cys249 mutant (Lys249-->Cys) of hOgg1 can be functionally rescued by alkylation with 2-bromoethylamine, which functionally replaces the lysine residue by generating a gamma-thia-lysine. CONCLUSIONS: This study provides the first direct identification of the active-site amine for any DNA glycosylase/lyase belonging to the BER superfamily, members of which are characterized by the presence of a helix-hairpin-helix-Gly/Pro-Asp active-site motif. The critical lysine residue identified here is conserved in all members of the BER superfamily that exhibit robust glycosylase/lyase activity. The ability to trigger the catalytic activity of the Lys249-->Cys mutant of hOgg1 by treatment with the chemical inducer 2-bromoethylamine may permit snapshots to be taken of the enzyme acting on its substrate and could represent a novel strategy for conditional activation of catalysis by hOgg1 in cells.     

Synthesis and properties of mixed ribodeoxyribooligonucleotide duplexes containing an internucleotide trisubstituted pyrophosphate bond

To assess the early stage of atherosclerosis of the thoracic descending aorta, we evaluated morphological atheromatous lesions (atherosis) and the stiffness parameter of the artery (beta; sclerosis) in 24 male rabbits using echography. Male Japanese white rabbits weighing 2.5-3.0 kg were fed a diet containing 1% cholesterol for 7 (n = 8) or 14 weeks (n = 8). Rabbits fed a normal diet were used as controls (n = 8). Atheromatous lesions were evaluated with intravascular ultrasound (IVUS: Aloka, 20 MHz, 6F). We also calculated beta using M-mode echography (7.5 or 10 MHz) and direct aortic pressure measurement. Thickening of the intima-media complex was clearly observed with IVUS in the 14-week group but was not detected in the others. Histologically, only a thin layer of foamy cells on the intima (thickness < 20 microns) was observed in the 7-week group. The value of beta was significantly increased in both the 7-week (4.7 +/- 2.2) and 14-week groups (4.5 +/- 0.8) compared with controls (1.7 +/- 0.9, both p < 0.01). These results suggest that the development of atherosis might be preceded by vascular sclerosis during the early stage of atherosclerosis when the serum cholesterol level is high: at a time when the thin layer of foamy cells could not be detected by conventional IVUS.     

Oligonucleotide duplexes containing 2''-amino-2''-deoxycytidines: thermal stability and chemical reactivity

Oral iodized oil is the major alternative to iodized salt for correcting endemic iodine deficiency. This study responds to a need for better guidelines in its use. Schoolchildren, aged 6-11 yr, from a severely iodine-deficient area of Algeria received iodized poppy seed oil (Lipiodol) in a single oral dose containing 120, 240, 480, or 960 mg iodine (groups A-D) or in an im injection of 480 mg iodine (group E). Thyroid volume by ultrasonography had not changed 395 days after treatment in groups A, B, and C, had decreased in groups D and E. Urinary iodine concentration rose rapidly from an initial median of 0.21 mumol/L, but fell below 0.79 mumol/L (the currently accepted level for indicating iodine deficiency) by 150 days for groups A and B, and by 395 days for groups C and D. Median serum TSH and T4 levels were normal before and after treatment, whereas high initial serum thyroglobulin values decreased in all groups after iodized oil treatment. For correcting iodine deficiency in children, we recommend single oral doses of Lipiodol containing 240 mg iodine for 6-month coverage or 480 mg for 12 months. These doses may not completely sustain iodine sufficiency, but will prevent the worst of the iodine deficiency disorders. Additionally, we conclude that the urinary iodine concentration is the most useful epidemiological indicator for assessing current iodine status, and thyroid volume and serum thyroglobulin levels are the best markers for assessing chronic effects.     

Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT

Cis-syn dimers, (6-4) products and their Dewar valence isomers are the major photoproducts of DNA and have different mutagenic properties and rates of repair. To begin to understand the physical basis for these differences, the thermal stability and base pairing properties of the corresponding photoproducts of the TT site in d(GAGTATTATGAG) were investigated. The (6-4) and Dewar products destabilize the duplex form by approximately 6 kcal/mol of free energy at 37 degreesC relative to the parent, whereas a cis-syn dimer only destabilizes the duplex form by 1.5 kcal/mol. Duplexes with G opposite the 3'-T of the (6-4) and Dewar products are more stable than those with A by approximately 0.4 kcal/mol, whereas the cis-syn dimer prefers A over G by 0.7 kcal/mol. Proton NMR suggests that wobble base pairing takes place between the 3'-T of the cis-syn dimer and an opposed G, whereas there is no evidence of significant H-bonding between these two bases in the (6-4) product. The thermodynamic and H-bonding data for the (6-4) product are consistent with a 4 nt interior loop structure which may facilitate flipping of the photoproduct in and out of the helix.     

Selective stabilization of AT-rich DNA duplexes by oligodeoxyribonucleotide conjugates with distamycin analogues

Oligodeoxyribonucleotide conjugates with distamycin analogues containing up to five pyrrolecarboxamide moieties were synthesized. The stability of duplexes formed by these conjugates was shown to depend directly upon the number of pyrrolecarboxamide moieties in the ligand molecule. For the duplexes formed by octaadenylate and octathymidilate conjugates with the distamycin pentapyrrole analogue, stability was demonstrated to be achieved by either one or two ligand molecules; however, duplexes containing two ligand molecules are more stable.     

Restriction endonucleases can be used to confirm a structure of unusual DNA duplexes

Cyclic and polycyclic oligonucleotides were synthesized using chemical ligation. Two types of catenanes with one and several intertwinings were produced. The yield of these molecules depended on the ligation conditions and nucleotide sequence of the ligated oligonucleotide and its template. Structure of ligation products was investigated and confirmed using restriction endonuclease MvaI. Interaction of the synthesized molecules with restriction endonucleases SsoII, EcoRII and HindIII was also studied.     

Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues

Chemically modified nucleic acids are currently being evaluated as potential antisense compounds for therapeutic applications. 2'-O-Ethylene glycol substituted oligoribonucleotides are second-generation antisense inhibitors of gene expression with promising features for in vivo use. Relative to DNA, they display improved RNA affinity and higher nuclease resistance. Moreover, chimeric oligonucleotides with 2'-O-methoxyethyl ribonucleoside wings and a central DNA phosphorothioate window have been shown to effectively reduce the growth of tumors in animal models at low doses. Using X-ray crystallography, we have determined the structures of three A-form DNA duplexes containing the following 2'-O-modified ribothymidine building blocks: 2'-O-methoxyethyl ribo-T, 2'-O-methyl[tri(oxyethyl)] ribo-T, and 2'-O-ethoxymethylene ribo-T. In contrast to 2'-O-ethylene glycol substituents, the presence of a 2'-O-ethoxymethylene group leads to slightly reduced RNA affinity of the corresponding oligonucleotides. The three structures allow a qualitative rationalization of the differing stabilities of duplexes between oligonucleotides comprising these types of 2'-O-modified ribonucleotides and complementary RNAs. The stabilizing 2'-O-ethylene glycol substituents are conformationally preorganized for the duplex state. Thus, the presence of one or several ethylene glycol moieties may reduce the conformational space of the substituents in an oligonucleotide single strand. In addition, most of these preferred conformations appear to be compatible with the minor groove topology in an A-type duplex. Factors that contribute to the conformational rigidity of the 2'-O-substituents are anomeric and gauche effects, electrostatic interactions between backbone and substituent, and bound water molecules.     

An approach to predicting the stabilities of peptide nucleic acid:DNA duplexes

Exposure to synthetic glucocorticoids (GCs) or other stimuli around birth may affect neuroendocrine and immune responsiveness in the offspring. Experiments were conducted to investigate whether maternal manipulation with saline or with GCs alters the corticosterone (CORT) response to a mild stressor in the offspring, and whether maternal manipulation results in long-term altered in vivo humoral and cellular immune responsiveness in the offspring. Pregnant rats were given dexamethasone (DEX, 1.2 mg/kg body weight, i.p.) or saline (SAL) at day 17 and 19 of gestation. A third group of pregnant rats was left undisturbed (UNTR-group). After maternal DEX treatment, no altered CORT response was seen to a novel environment at 20 days of age, as compared to both the SAL-treated group and the UNTR-group. However, saline administration to pregnant rats caused an increased CORT response in female offspring, but not male offspring, as compared to the UNTR-group (P < or = 0.01). Furthermore, no effects of maternal DEX exposure were seen on IgG2a production after immunization with a conjugated pneumococcal polysaccharide (PPS-14-CRM197) at 6 weeks of age. However, maternal SAL treatment enhanced anti-PPS-14 IgG2a antibody levels in female offspring, but not in male offspring, as compared to the UNTR-group (P < or = 0.05). Cellular immune responses were measured by an oxazolone-induced contact hypersensitivity response (CHS-response), at 8 weeks of age. Maternal SAL treatment increased the CHS response in adult male rats, but not in female rats, as compared to both the UNTR-group and the DEX-group (P < or = 0.005). These data suggest that manipulations during late pregnancy not only affect endocrine responsiveness, but also influence immune responsiveness in the rat offspring. Furthermore, these effects may be long-term and gender-specific.     

A formula for thermal stability (Tm) prediction of PNA/DNA duplexes

An empirical formula for thermal stability (T m) prediction of PNA/DNA duplexes has been derived. The model is based on the T m as calculated for the corresponding DNA/DNA duplex employing a nearest neighbour approach, by including terms for the pyrimidine content and length of the PNA to take into account the increased thermostability of PNA/DNA hybrids and the asymmetry of the PNA-DNA heteroduplex. The predictive power of the T m prediction formula was challenged with an independent data set not used for model building. The T m of >90% of the sequences was predicted within 5 K; 98% of the predicted T ms differ by not more than 10 K from the experimentally determined T m.     

Single-stranded shuttle phagemid for mutagenesis studies in mammalian cells: 8-oxoguanine in DNA induces targeted G.C-->T.A transversions in simian kidney cells

A single-stranded shuttle vector has been developed for the purpose of investigating translesional events in mammalian cells. The vector is designed to permit site-specific introduction of defined DNA lesions between a gene for neomycin resistance and its promoter. Efficiencies of translesional synthesis in simian kidney cells (COS) and Escherichia coli are established by determining the number of neomycin- and ampicillin-resistant colonies recovered, respectively, after introduction of a modified vector. Fidelity of translesional synthesis is evaluated by analyzing the nucleotide sequence of progeny phagemid DNA in the region corresponding to the lesion site. This experimental system, capable of detecting mutagenic and nonmutagenic events at and adjacent to the lesion site, was used to establish the mutagenic potential of a single 8-oxoguanine residue in DNA. This modified base, produced by attack of reactive oxygen species on cellular DNA, did not cause a decrease in the number of transformants when single-stranded DNA containing the lesion replicated in COS cells or E. coli. The predominant mutations observed (> 78%) were G-->T transversions targeted to the site of the lesion. The mutation frequencies for this event were 2.5-4.8% in COS cells and 1.8% in E. coli. It is concluded that a single-stranded shuttle vector, utilized in conjunction with a site-specific approach, can be used to investigate translesional events in mammalian cells and in bacteria.     

DNA labeling reagent containing carbodiimide

We have synthesized a number of fluorescent compounds having a carbodiimide function and tested if it can be used to label DNA. They all reacted well with DNA in a very short time. Some of them showed different fluorescent characteristics when they bound to DNA such as band shift or change in fluorescent intensity.