Phosphate-methylated DNA aimed at HIV-1 RNA loops and integrated DNA inhibits viral infectivity.

Phosphate-methylated DNA hybridizes strongly and specifically to natural DNA and RNA. Hybridization to single-stranded and double-stranded DNA leads to site-selective blocking of replication and transcription. Phosphate-methylated DNA was used to interrupt the life cycle of the human immunodeficiency virus type-1 (HIV-1), the causative agent of acquired immunodeficiency syndrome (AIDS). Both antisense and sense phosphate-methylated DNA 20-nucleotide oligomers, targeted at the transactivator responsive region and the primer binding site, caused complete inhibition of viral infectivity at a low concentration. Hybridization of phosphate-methylated DNA with folded and unfolded RNA was studied by ultraviolet and proton nuclear magnetic resonance spectroscopy. The combined results of hybridization studies and biological experiments suggest that the design of effective antisense phosphate-methylated DNA should focus on hairpin loop structures in the viral RNA. For sense systems, the 5' end of the integrated viral genome is considered to be the important target site.

Sustained local drug delivery from a radiopaque implanted reservoir.

A new polymeric biomaterial that contains covalently bound iodine, and is therefore radiopaque, was used to construct a sustained local drug-delivery device. A polymeric wall was designed to be porous (i.e., passage of low-molecular-weight molecules across the wall is possible), self-healing, and biocompatible. Once implanted, the sphere cavity can be filled and refilled with a concentrated solution of a (cytostatic) drug, which is subsequently released by slow diffusion into the tissue region surrounding the sphere. This principle of sustained local drug delivery is shown by a series of in vitro experiments on the release of 5-fluorouracil, and in vivo animal experiments, using x-ray fluoroscopic and scintigraphic techniques.

Photoimmobilisation of poly(N-vinylpyrrolidinone) as a means to improve haemocompatibility of polyurethane biomaterials.

A novel method to improve the haemocompatibility of polymeric biomaterials (in particular: polyurethane elastomers) is reported. The new approach essentially rests upon photochemical immobilisation of the highly biocompatible polymer poly(N-vinylpyrrolidinone) (poly(NVP)) onto the biomaterial's surface. One of the key steps in the surface modification procedure is the preparation of a copolymer of NVP and the photoreactive building block 4-[4'-azidobenzoyl]-oxo-n-butylmethacrylate (1). This copolymer is first dissolved in a volatile solvent, then sprayed onto the biomaterial's surface, and subsequently immobilised via irradiation with ultraviolet light. The paper describes: (i) preparation of 1, (ii) preparation of the copolymer (NVP + 1), (iii) physico-chemical characterisation of the modified surfaces, and (iv) results of two in vitro haemocompatibility assays (i.e. thrombin generation and adhesion of blood platelets from recalcified human platelet-rich plasma). Furthermore, the surface modification was performed with a microporous polyurethane vascular graft (Chronoflex), which is already in clinical use. The in vitro experiments revealed that significant improvement of the haemocompatibility of polyurethanes can be achieved through this method.

In vivo tissue compatibility of two radio-opaque polymeric biomaterials.

Polymeric biomaterials featuring intrinsic radio-opacity continue to attract considerable scientific attention. This work focusses on two polymers that contain covalently bound iodine, rendering the materials radio-opaque. The first material is hard, transparent and glass-like, and consists of methyl methacrylate, 2-(2'-iodobenzoyl)-ethyl methacrylate (1) and 2-hydroxyethyl methacrylate (HEMA), in the molar ratio 65:20:15, respectively. The second material is a cross-linked hydrophilic network, consisting of HEMA and 1, in the molar ratio 80:20, respectively. Both materials were characterized by means of different physico-chemical techniques, including magic-angle-spinning solid state NMR spectroscopy, infrared spectroscopy and differential scanning calorimetry. Moreover, both materials were implanted subcutaneously in rats for 24 days. Upon explanation and histological examination, it appeared that both materials were well tolerated. No tissue necrosis, abscess formation or inflammation were observed. The samples were found to be surrounded by a vascularized capsule consisting of connective tissue cells. The results reveal excellent tissue compatibility for both materials. This is an important observation, since tissue compatibility is absolutely necessary for the applications which are foreseen for this type of radio-opaque biomaterials.

Studies on radio-opaque polymeric biomaterials with potential applications to endovascular prostheses.

A new polymeric biomaterial, which uniquely combines radio-opacity (X-ray visibility) and low thrombogenicity, is described. First, preparation, purification, and identification of the essential monomeric building block, 2-[2'-iodobenzoyl]-ethyl methacrylate (3), are outlined. Second, [Figure: See text] the synthesis of the biomaterial, a terpolymer with composition MMA: HEMA: 3 = 65:15:20 (mole/mole/mole) is described. Third, the physico-chemical characteristics of the polymer (e.g. NMR spectroscopy, thermal behaviour) are given. Fourth, the in vitro thrombogenicity of the material was characterized by means of recent test assay. The combined results reveal that the terpolymer is very suitable for prosthetic applications in the cardiovascular system. A new prototype of an endovascular stent, made from the terpolymer, is presented. Stents find clinical use in interventional cardiology, in conjunction with percutaneous transluminal coronary angioplasty (PTCA). It is put forward that the stent prototype presented herein has, at least in principle, some advantages over existing (metallic) stents; these advantages are primarily owing to the unique combination of X-ray visibility and haemocompatibility which is presently achieved.

Photo-immobilization of dipyridamole (Persantin) at the surface of polyurethane biomaterials: reduction of in-vitro thrombogenicity.

Dipyridamole is a well-known vasodilator and a powerful inhibitor of activation and aggregation of blood platelets. Moreover, dipyridamole is essentially non-toxic. The drug is used extensively in clinical anti-coagulation regimes, for example pre- and post-coronary angioplasty procedures. Recently, we have found that photochemical, covalent coupling of dipyridamole to polyurethane surfaces leads to improved thromboresistance in vitro. This phenomenon is now studied in more detail. Both qualitative and more quantitative biochemical experiments were performed in order to characterize the in vitro blood compatibility of a set of polyurethane surfaces onto which dipyridamole was immobilized. First, scanning electron microscopy was used to examine the morphology of platelets which adhered during incubation with platelet-rich plasma. These experiments showed that immobilization of dipyridamole leads to a clearly decreased number of adherent platelets and to a largely diminished propensity of the surface to activate adherent platelets. Secondly, an in vitro thrombogenicity assay was run. These experiments showed that the thromboresistance increased with increasing surface density of immobilized dipyridamole. A short spacer chain separating dipyridamole from the polymer surface, was found to improve the thromboresistance further. Such a spacer chain apparently increases the efficacy of the immobilized drug. Collectively, the present results further substantiate the idea that dipyridamole retains its inhibitory activity with respect to activation and aggregation of blood platelets, when the compound is covalently attached to a polymer surface. The possible utility of these findings with respect to the development of an artificial blood vessel prosthesis is discussed briefly.

Biodegradable three-dimensional networks of poly(dimethylamino ethyl methacrylate). Synthesis, characterization and in vitro studies of structural degradation and cytotoxicity.

In ophthalmology, there is a need for novel degradable biomaterials for e.g. controlled drug release in the vitreous body. These degradable materials should feature both excellent biocompatibility, and well-defined kinetics of degradation. In most cases, poly(D,L-lactic acid), or poly(lactic-co-glycolic acid) are used. These materials, however, suffer from some serious drawbacks, since the degradation kinetics are difficult to control, especially since the so-called 'burst-degradation' occurs. Here, we describe a set of novel polymeric networks which largely consist of poly(dimethylamino ethyl methacrylate) (poly(DMAEMA)); these materials are crosslinked via a dimethacrylate molecule that contains two carbonate groups. This system is susceptible to hydrolytic scission. The degradation products do not exert a catalytic effect on the ongoing degradation reaction (i.e. there is no burst effect). We describe the synthesis of three of these materials, which differ merely with regard to the crosslinker content. These materials were characterized through DMTA, 1H NMR and FT-IR spectroscopy, and scanning electron microscopy. The reaction DMAEMA + 2-hydroxyethyl methacrylate (HEMA) was studied in detail, using 1H NMR spectroscopy, and these experiments revealed that the reaction of DMAEMA and HEMA produces a random (Bernouillian-type) copolymer. From this, we contend that the new materials have more or less uniform distribution of the crosslinks throughout their volume. Structural degradation of the three materials was studied in vitro, at pH 7.4, 9.1 and 12.0. It is found that the materials exhibit smooth hydrolysis, which can be controlled via the crosslink density and the pH, as was expected a priori. It should be noted that degradation of these materials produces non-hydrolysable, but water-soluble, oligo(DMAEMA) and poly(DMAEMA) molecules. We subsequently performed in vitro studies on the biocompatibility of these materials. The MTT cytotoxicity assay revealed that the materials were cytotoxic to chondrosarcoma cells. This is most probably due to local increase of the pH due to the basic character of the pending dimethylamino groups. Cytotoxicity remained virtually unchanged after extended washing with water. This indicates that the cytotoxicity is an intrinsic property of the material and was not caused by remnants of free monomer. Cytotoxicity was also seen in cell cultures (human fibroblasts isolated from donor corneas) which were grown in contact with the materials. It is concluded that the new materials have attractive degradation characteristics, but their cytotoxicity makes them unsuitable for applications in ophthalmology.

Studies on a new radiopaque polymeric biomaterial.

A new radiopaque polymeric biomaterial has been synthesized. The material, which actually represents an entire family of analogous radiopaque materials, is composed of 2-(p-iodobenzoyl)-ethyl methacrylate (compound 1, 21 mol%), methyl methacrylate (MMA, 60 mol%), and 2-hydroxyethyl methacrylate (HEMA, 19 mol%). The terpolymer was synthesized in a radical polymerization reaction at elevated temperature in N,N-dimethylformamide (DMF). The product was subjected to a set of physicochemical characterization techniques (gel permeation chromatography, 500 MHz 1H NMR in deuterated dimethylsulphoxide (d6-DMSO) solution, differential scanning calorimetry, dynamic water contact angle measurements), as well as to an in vitro thrombogenicity assay. Furthermore, scanning electron microscopy was used to study interactions of the material with blood platelets. The most important findings are: (a) the material is a genuine polymer with excellent X-ray visibility, even in the form of thin (0.4 mm) drawn fibres. This was established under realistic conditions. (b) The material exhibits low in vitro thrombogenicity, i.e. comparable to polyvinyl chloride, which is known as a passive material. These observations lead us to the suggestion that this type of radiopaque polymer holds promise with respect to application as a construction material for a new type of endovascular stent. This could be relevant in particular to stents to be used in conjunction with percutaneous transluminal coronary angioplasty (PTCA), also known as Dottering. Currently there is a clear trend away from metallic stents towards all-polymeric stents, since the latter have superior biocompatibility.(ABSTRACT TRUNCATED AT 250 WORDS)

Coils and tubes releasing heparin. Studies on a new vascular graft prototype.

Coiled metallic guidewires find widespread use, for instance in interventional cardiology. It is known that release of heparin from the surface of guidewires is advantageous to prevent formation of thrombotic emboli. New coiled tubular structures, having larger inner and outer diameter as compared to guidewires, are presented. In theory these tubes can be used as interposition vascular grafts. Ten coiled tubes with an internal diameter of 690 microm were made. Five different adherent polymeric coatings with increasing hydrophilicity were used. Five tubes contained heparin in the coating and the other five were unheparinised controls. The five tubes containing heparin were studied with respect to heparin release in vitro (amount released, kinetics), and immobilised heparin that is exposed at the surface. All tubes were studied with a direct cell contact assay using 3T3 mouse fibroblast cells, a dynamic thrombin generation test, and endothelial cell growth onto the coils. It was found that the heparinised tubes lead to very little thrombin formation. It is argued that this is due to heparin that is immobilised and exposed at the inner surface of such tubes. Furthermore the coils showed to be cytocompatible and endothelial cells adhere and proliferate well onto the coils. This concept is believed to hold promise for further development of small vascular grafts.

Platelet adhesion studies on dipyridamole coated polyurethane surfaces.

Surface modification of polyurethanes (PUs) by covalent attachment of dipyridamole (Persantin) is known to reduce adherence of blood platelets upon exposure to human platelet rich plasma (PRP). This effect was investigated in further detail. First platelet adhesion under static conditions was studied with four different biomaterial surfaces: untreated PU, PU immobilised with conjugate molecule 1, PU immobilised with conjugate molecule 2, and PU immobilised with conjugate molecule 3. In PU immobilised with 1 dipyridamole is directly linked to the surface, in PU immobilised with 2 there is a short hydrophilic spacer chain in between the surface and the dipyridamole, while conjugate molecule 3 is merely the spacer chain. Scanning electron microscopy (SEM) was used to characterise platelet adhesion from human PRP under static conditions, and fluorescence imaging microscopy was used to study platelet adhesion from whole blood under flow. SEM experiments encompassed both density measurements and analysis of the morphology of adherent platelets. In the static experiments the surface immobilised with 2 showed the lowest platelet adherence. No difference between the three modified surfaces emerged from the flow experiments. The surfaces were also incubated with washed blood platelets and labeled with Oregon-Green Annexin V. No capture of Oregon-Green Annexin V was seen, implying that the adhered platelets did not expose any phosphatidyl serine at their exterior surface.

Preparation, characterization and radiolabeling of a new amphiphilic derivative of DTPA.

A new derivative (1) of diethylenetriamine pentaacetic acid (DTPA) is described. Compound 1 contains a hydrophobic unit (a triphenyl methyl group) and a hydrophilic unit (a DTPA ester), and therefore behaves as an amphiphile in aqueous solution. Compound 1 appears to form a stable inclusion complex with 99mTc. A rabbit model was used in a scintigraphic study of the biodistribution of the complex 99mTc-1, using 99mTc-DTPA as a control. The resulting images revealed marked differences: 99mTc-1 showed rapid uptake in the liver followed by excretion in the gallbladder and intestines within 1 h, whereas 99mTc-DTPA appears, as expected, in the renal-pelvico system and in the bladder. These findings are significant as they provide more insight into the complex relationship between structural and physicochemical properties of radiopharmaceuticals and their biodistribution. Knowledge of such relationships is absolutely mandatory with respect to the development of new radiopharmaceuticals with increased efficacy and/or specificity.

Structural analysis of 2',3'-dideoxyinosine, 2',3'-dideoxyadenosine, 2',3'-dideoxyguanosine and 2',3'-dideoxycytidine by 500-MHz 1H-NMR spectroscopy and ab-initio molecular orbital calculations.

Solution structure of anti-AIDS drug, 2',3'-dideoxyinosine (ddI) has been assessed by NMR spectroscopy and pseudorotational analysis in conjunction with its analogues: 2',3'-dideoxyadenosine (ddA), 2',3'-dideoxyguanosine (ddG) and 2',3'-dideoxycytidine (ddC). The absence of 3'-hydroxyl groups in these compounds has prompted us to establish the relationship between proton-proton and corresponding endocyclic torsion angles in the 2',3'-dideoxyribofuranose moiety on the basis of five available crystal structures of 2',3'-dideoxynucleosides. A subsequent pseudorotational analysis on ddI (1), ddA (2), ddG (3) and ddC (4) shows that the twist C2'exo-C3'-endo forms of sugar are overwhelmingly preferred (75-80%) over the C2'-endo envelope forms. The phase angles (P) for North and South conformers with the corresponding puckering amplitude (psi m) for ddI (1), ddA (2) and ddG (3) are as follows: PN = 0.1 degrees, PS = 161 degrees and psi m = 34.1 degrees for ddI (1); PN = 1.4 degrees, PS = 160 degrees and psi m = 34.2 degrees for ddA (2) and PN = 2.4 degrees, PS = 163 degrees and psi m = 33.6 degrees for ddG (3). The predominant North conformer of ddC (4) is intermediate between twist C2'-exo-C3'-endo and C3'-endo envelope (P = 10.9 degrees) with a psi m of 34.7 degrees. Note that these preponderant North-sugar structures (approx. 75-80%) found in the solution studies of ddI (1), ddA (2), dG (3) and ddC (4) are not reflected in the X-ray crystal structures of 2',3'-dideoxyadenosine and 2',3'-dideoxycytidine. The constituent sugar residues in both of these crystal structures denosine and 2',3'-dideoxycytidine. The constituent sugar residues in both of these crystal structures are found to be in the South-type geometry (ddA crystalizes in C3'-exo envelope form, while ddC adopts the form intermediate between the C3'-exo envelope and C3'-endo-C4'-exo twist form). This means that X-ray structures of ddA (2) and ddC (4) only represent the minor conformer of the overall pseudorotamer population in solution. An assumption that the structure of the pentofuranose sugar (i.e. P and psi m) participating in conformational equilibrium described by the two-state model remains unchanged at different temperatures has been experimentally validated by assessing five unknown pseudorotational parameters with eight unique observables (3J1'2', 3J1'2", 3J2'3', 3J2'3", 3J2"3', 3J2"3", 3J3'4' and 3J3"4') for 2',3'-dideoxynucleosides.(ABSTRACT TRUNCATED AT 400 WORDS)

Why do all lariat RNA introns have adenosine as the branch-point nucleotide? Conformational study of naturally-occurring branched trinucleotides and its eleven analogues by 1H-, 31P-NMR and CD spectroscopy.

1H-NMR conformational studies of six branched triribonucleotides where the branch-point nucleotide was either U, C or G (4-9) have been carried out by assigning 1H resonances through 2D NMR and then observing the temperature-dependent (i) chemical shifts of the aromatic and the anomeric protons, and (ii) shifts of the equilibrium of N and S pseudorotamer populations of each sugar moiety. The data have been compared with those of 2'----5' dimers (1-3) and other branched trimers (10-16). It emerged that all the branched trimers (4-16) adopt a conformational state closer to the corresponding 2'----5' dimers than the corresponding 3'----5' dimers. A temperature-dependent 31P chemical shift study confirmed that the conformational constraint is mainly associated with the 2'----5' phosphate linkage. Although, it appeared with the CD data that when C or especially when U is at the branch-point the overall constraint is weak. This suggests that even if these trimers adopt a 2'----5' dimer geometry, there is a lack of stabilization by strong stackings within the molecule. This is in sharp contrast with the results found for A (10-16) and to a smaller extent for G (8, 9) at the branch-point.

Studies on a new strategy for surface modification of polymeric biomaterials.

A new methodology to improve the hemocompatibility of polyurethane (medical grade Pellethane D-55) surfaces is reported. The approach is essentially based on a photochemical immobilization reaction. Two new conjugate molecules, compounds 2 and 3, were prepared. They consist of (i) dipyridamole, a well-known inhibitor of platelet activation, and a vasodilating drug with clinical application, for instance before and during pecutaneous transluminar coronary angioplasty (Dottering); and (ii) an aryl azide, a moiety that exhibits marked photoreactivity. In 2, the dipyridamole unit is directly linked to the aryl azide (via an ester bond), while a short spacer chain separates both units in 3. Upon irradiation of 2 or 3, adsorbed onto the polyurethane foil, the aryl azide is converted into a highly reactive species which reacts with a nucleophilic group on the polymer surface. In this way, the dipyridamole is covalently linked to the polymer. The underlying principle is also used in photoaffinity labeling, a well-known technique in biochemical studies on enzyme structure and function. From UV extinction experiments it could be deduced that the surface-density of immobilized 2 is 4.9 nmol/cm2. The surface density for 3 was 14.6 nmol/cm2. The surfaces were subjected to an in vitro thrombin generation assay. This assay gives a valuable impression about the hemocompatibility of artificial surfaces. These experiments revealed that the clotting times were substantially prolonged as a result of the photoimmobilization of dipyridamole. This was especially the case for immobilized 3. This effect cannot be readily explained. Possibly, the enhanced activity of immobilized 3 is due to the spacer chain. An alternative explanation is that the surface density is larger for 3 than for 2. In addition, the photomodified surfaces were incubated with platelet-rich blood plasma (37 degrees C, 30 min) and subsequently examined by scanning electron microscopy. The morphology of the blood platelets adhered to the surface also showed that hemocompatibility increased in the order untreated polyurethane < polyurethane with immobilized 2 < polyurethane with immobilized 3. Future work will concentrate on evaluation of the role of the spacer (length, hydrophilicity, etc.), as well as on the possible use of this approach with respect to the construction of biomaterials with improved in vivo biocompatibility, in particular hemocompatibility.

Synthesis of a new photoreactive derivative of dipyridamole and its use in the manufacture of artificial surfaces with low thrombogenicity.

Photoimmobilization of dipyridamole (Persantin) was accomplished through the use of a new synthetic conjugate molecule, 1. Persantin is a powerful inhibitor of platelet activation and aggregation and is widely used as a vasodilator. Conjugate 1 consists of triply protected dipyridamole [three of the four hydroxyl groups carry a tert-butyldimethylsilyl (TBDMS) protective group) and the photoreactive 4-azidobenzoyl group. A short hydrophilic spacer chain, derived from triethylene glycol, separates the protected dipyridamole system and the photoreactive group. Compound 1 was immobilized on polyurethane sheets (Pellethane D-55) through irradiation with ultraviolet (UV) light, and the protective groups were removed afterward. The resulting modified polyurethane surfaces were characterized by different physicochemical techniques: UV extinction, contact angle measurements (captive bubble technique), and X-ray photoelectron spectroscopy (XPS). The UV extinction measurements showed the presence of 13 +/- 1 nmol of immobilized dipyridamole/cm2. The contact angle measurements revealed that the modified surface was markedly more hydrophilic than the control (i.e. unmodified polyurethane). XPS measurements clearly established the presence of immobilized dipyridamole in the outermost layers of the modified surface. This was especially clear from the XPS spectra recorded at a low take-off angle (approximately 6 degrees). Furthermore, the XPS spectra showed that the TBDMS protective groups had been quantitatively removed during the deprotection/washing treatment. The in vitro blood compatibility of the modified surface was studied with the thrombin generation assay as developed in our group, as well as with scanning electron microscopy. The thrombin generation test produced a lag time of 1275 s for the modified surface, as opposed to 569 s for the control. Scanning electron microscopy showed that far fewer platelets adhere to the modified surface (approximately 7 x 10(3)/mm2) as compared to the control (approximately 6 x 10(2)/mm2). Taken together, the experimental data reveal that the modified surface has excellent blood compatibility in vitro. It is discussed that the use of conjugate 1 leads to simultaneous exposure of dipyridamole at the modified surface and to a marked increase of the surface hydrophilicity, which is likely to hamper adsorption of plasma proteins. The combination of these effects is uniquely related to the molecular buildup of 1. Conjugate 1 will be used in future work that is aimed at preparing small-caliber polyurethane vascular grafts with a blood compatible lumenal surface.

A photochemical method for the surface modification of poly(etherurethanes) with phosphorylcholine-containing compounds to improve hemocompatibility.

Phosphorylcholine groups attached to polymer surfaces are known to improve hemocompatibility. A photochemical method is presented to couple phosphorylcholine-containing aryl azides to poly(etherurethane) surfaces (PEUs). Two aryl azides that consist of a photoactivatable 4-azidobenzoyl group, a short spacer chain, and a phosphorylcholine endgroup were synthesized. The two compounds differ only in the type of spacer used: triethylene glycol for compound 1 and hexanediol for compound 2. These compounds were physically adsorbed to PEU surfaces. Upon UV irradiation, reactive intermediates are formed that react with nucleophilic groups on the polymer surface. The modified surfaces showed decreased underwater contact angles, indicating that hydrophilic phosphorylcholine groups are present at the surface. ESCA measurements showed the presence of phosphorus and positively charged nitrogen atoms in the outermost polymer layers (analyzed depth about 50 A), which is a strong indication of the presence of phosphorylcholine groups. Hemocompatibility in vitro was tested with thrombin generation assays and platelet adhesion tests. In thrombin generation assays the clotting time of platelet-rich plasma in contact with the polymer surface is determined. Clotting times were clearly prolonged for the modified surfaces. Surfaces modified with compound 2 showed slightly higher clotting times than those modified with compound 1. Repeated surface modification with compound 2 further increased the clotting time. For the tested surfaces an increase in the clotting time corresponds to an increase in the concentration of phosphorylcholine groups at the surface (as measured by ESCA and contact angle). Platelet adhesion studies with scanning electron microscopy demonstrated that fewer platelets (showing less activation) adhered to the modified surfaces than to the unmodified polyurethane.

Peptide-induced parallel DNA duplexes for oligopyrimidines. Stereospecificity in complexation for oligo(L-lysine) and oligo(L-ornithine).

It is shown that the cationic oligopeptides octadeca(L-lysine) (Lys18) and octadeca(L-ornithine) (Orn18) can induce a parallel duplex for the natural DNA oligomer dT10 with thymine-thymine base pairs. Complexation of the ammonium groups in the peptide side chains with the DNA phosphates leads to diminished electrostatic phosphate-phosphate repulsions, which allows this T-T base pair formation. From combined NOESY 1H NMR and molecular mechanics studies, it follows that the parallel duplex is right-handed, with the peptide located in the groove of the duplex. For the natural DNA oligomers dC10, d(C6T6), and d(T6C2T2), only Lys18 is able to induce the formation of parallel duplexes with C-C and T-T base pairs. It is shown that, for Orn18, a complexation must occur with one of the nonbonded oxygen atoms in the phosphate groups (OR) in such a way that unfavorable steric interactions are present with the C-C base pairs, which have a larger propellor twist angle than T-T base pairs. An analogy is presented between peptide complexation with the phosphates and the neutralization of the phosphate groups by methylation, which is known to lead to parallel duplexes with T-T base pairs (for both the Sp and Rp configurations) and C-C base pairs (only for the Sp configuration).

Synthesis of well-defined phosphate-methylated DNA fragments: the application of potassium carbonate in methanol as deprotecting reagent.

A new deprotection procedure in the synthesis of (partially) phosphate-methylated oligodeoxynucleotides has been developed, involving treatment of fully protected DNA fragments with methanolic potassium carbonate. It is shown that base deprotection can be accomplished in potassium carbonate/methanol without affecting the methyl phosphotriesters. This methodology enables us to synthesize, both in solution and on a solid support, DNA fragments which are phosphate-methylated at defined positions. The solid phase synthesis, however, turns out to be accompanied by considerable demethylation of the phosphotriesters. It is demonstrated that this demethylation does not occur during the deprotection or work-up procedure. Furthermore, it was found that the latter side-reaction is suppressed when the standard capping procedure with acetic anhydride is included.