Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study

dApT, a modified deoxyribose dinucleoside phosphate with an uncharged methylphosphonate group, crystallizes as dihydrate in space group P2(1)2(1)2, a = 9.629(3), b = 20.884(6) and c = 14.173(4)A, Z = 4. The structure has been determined using 2176 X-ray diffractometer reflections and refined to a final R of 0.105. Torsion angles about P-O(5') and P-O(3') bonds are -91.8 degrees and 117.8 degrees. The former is in the normal (-)gauche range while the latter is eclipsed. Bases are oriented anti, the sugar of adenosine is puckered 2T3 (C(2')endo) whereas that of thymidine displays puckering disorder with major and minor occupancy sites. Major site is a half-chair 2T (C(2')endo-C(1')exo) and minor site an envelope 3T2 (C(3(1)endo). Adenine and thymine bases of symmetry related molecules form reversed Hoogsteen type base pairs, water molecules are disordered in the crystal lattice.

Synthesis and template properties of an ethyl phosphotriester modified decadeoxyribonucleotide

The phosphate groups of nucleic acids are often the targets of mutagenic and carcinogenic alkylating agents. In order to study the effects of alkyl phosphotriester modification on the physical and biochemical properties of DNA, two diastereomeric ethyl phosphotriester modified decadeoxyribonucleotides, d-CpCpApApGp(Et)ApTpTpGpG isomer I and isomer II, were prepared. A phosphotriester synthetic procedure was used to specifically place ethyl triester groups with either an R or S configuration in the central dimer region of the decamer. Terminal deoxynucleotidyl transferase was used to add oligodeoxyadenylate tails to the 3' end of the decamers. The resulting oligomers were tested as templates for Escherichia coli DNA polymerase I with d-(pT)8pCpC as a primer. The rates and extents of polymerization directed by the modified templates were 25% (isomer I) and 50% (isomer II) less than those of an unmodified control template. Thus the presence of an ethyl triester group inhibits polymerization, the effectiveness of which is determined by the orientation of the ethyl group relative to the rest of the template backbone. These results suggest ethyl phosphotriester lesions could inhibit replication rates of cellular DNA.

Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones as primers for DNA polymerase

Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones, d-Tp(TpTp)4T isomers I and II and d-Tp(TpTp)3T(pT)1-5 isomers I and II, were prepared by methods analogous to the phosphotriester synthetic technique. The designations isomer I nd isomer II refer to the configuration of the methylphosphonate linkage, which is the same through each isomer. Analogues with the type I methylphosphonate configuration form very stable duplexes with poly(dA) while those with the type II configuration form either 2T:1A triplexes or 1T:1A duplexes with poly(dA) of considerably lower stabilities. The oligothymidylate analogues were tested for their ability to initiate polymerizations catalyzed by Escherichia coli DNA polymerase I or calf thymus DNA polymerase alpha on a poly(dA) template. Neither d-Tp(TpTp)4T nor d-Tp(T]Tp)3TpT served as initiators of polymerization while d-Tp(TpTp)3T(pT)2-5 showed increasing priming ability as the length of the 3'-oligothymidylate tail increased. Analogues with type I methylphosphonate configuration were more effective initiators than the type II analogues at 37 degrees C. The apparent activation energies of polymerizations initiated by d-Tp(TpTp)3T-(pT)4 and 5 isomer I were greater than those for reactions initiated by isomer II or d-(Tp)11T. The results suggest that DNA polymerase interacts with the charged phosphodiester groups of the primer molecule and may help stabilize primer/template interaction. At least two contiguous phosphodiester groups are required at the 3' end of the analogue primers in order for polymerization to occur. Interactions between the polymerase and primer also appear to occur with phosphodiester groups located at sites remote from the 3'-OH polymerization site and may be influenced by the configuration of the methylphosphonate group.

Computer programming for nucleic acid studies. III. Calculated ultraviolet absorption spectra of protected oligodeoxyribonucleotides

A computer program called UV. FOR was written in FORTRAN. This program primarily utilizes the digitized UV absorption spectra of 8 protected deoxyribonucleosides in 95% ethanol solution to compose the UV spectrum of a oligodeoxynucleotide of any sequence. Both calculated and observed UV spectra of 2 protected oligodeoxynucleotides are carefully compared. The results show that the calculated UV spectrum is virtually identical to the observed spectrum. Thus, the calculated spectra provide rapid confirmation of oligonucleotide compositions during the course of oligonucleotide synthesis by the phosphotriester method.

Biochemical and biological effects of nonionic nucleic acid methylphosphonates

Oligodeoxyribonucleoside methylphosphonates with base sequences complementary to the anticodon loop of tRNALys and to the -ACCA-OH amino acid accepting stem of tRNA were prepared by chemical synthesis. Oligodeoxyadenosine methylphosphonates form stable, triple-stranded complexes with both poly(U) and poly(dT). These analogues selectively inhibit cell-free aminoacylation of tRNALys (E. coli) but have no effect on aminoacylation of tRNALys (rabbit). The extent of inhibition is temperature dependent and parallels the ability of the oligomer to bind to poly(U), which suggests that inhibition occurs as a result of oligomer binding to the -UUUU- anticodon loop of tRNALys (E. coli). The failure of the oligodeoxyadenosine methylphosphonates to inhibit tRNALys (rabbit) amino-acylation suggests that there may be a difference between the structure of tRNALys or its interaction with aminoacyl synthetase in the Escherichia coli and rabbit systems. The oligodeoxyadenosine analogues also effectively inhibit polyphenylalanine synthesis in cell-free translation systems derived from both E. coli and rabbit reticulocytes. The extent of inhibition parallels the Tm values of the oligo(A) phosphonate-poly(U) complexes and suggests that the inhibition is a consequence of complex formation with the poly(U) message. Tritium-labeled oligodeoxyribonucleoside methylphosphonates with a chain length of up to nine nucleotidyl units are taken up intact by mammalian cells in culture. All the oligomer analogues tested inhibited, to various extents, colony formation by bacterial, hamster, and human tumor cells in culture.

Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones. Synthesis and physical studies

Two decathymidylate analogues, d-(TpTp)4TpT-isomer 1 and isomer 2, having stereoregular, alternating methylphosphonate/phosphodiester backbones were prepared. The phosphodiester linkages of d-(TpTp)4TpT are cleaved slowly by snake venom phosphodiesterase in a stepwise manner, while slow random cleavage occurs with micrococcal nuclease which hydrolyzes isomer 2 faster than isomer 1. The CD spectra of isomer 1 and d-(Tp)9T are identical suggesting they have similar conformations, while that of isomer 2 shows an overall reduction of [theta]. Isomer 1 forms a 1T . 1A complex with poly(dA) and both 1T . 1A and 2T . 1A complexes with poly(rA), while isomer 2 forms a 2T . 1A complex of low thermal stability with poly(dA) and no complex with poly(rA). The Tm values of the partially nonionic d-(TpTp)4TpT . polynucleotide complexes are less dependent on salt concentration than are those of d-(Tp)9T. The stoichiometry and CD spectra of the complexes suggest that poly(dA) . isomer 1 duplex assumes a B-type geometry while isomer 2 . poly(dA) . isomer 2 triplex and the isomer 1 . poly(rA) complexes have an A-type geometry. Although there are no apparent differences between steric restrictions to rotation about the backbones of either isomer 1 or 2, or steric restrictions to complex formation, the results suggest that the configuration of the methylphosphate linkage controls: 1) interaction with nucleases, 2) oligomer conformation, and 3) interaction with polynucleotides. The latter effects may result from differences in solvation of the two isomers.

Preparation of a decadeoxyribonucleotide helix for studies by nuclear magnetic resonance

A self-complementary decadeoxyribonucleotide d-CpCpApApGpCpTpTpGpG was chemically synthesized by a procedure based on the phosphotriester approach. This procedure was carefully monitored and appropriately modified to ensure the purity of oligomer components at each step of the synthetic scheme. Extensive use was made of both analytical and preparative high-pressure liquid chromatography to purify and characterize the decamer and its constituent oligonucleotides. The final product (1318 A257 units or 16.5 mumol) was obtained in high purity and sufficient quantity for extensive physical studies by UV, CD, and NMR spectroscopy. Our preliminary results show that at a strand concentration of 1.3 X 10(-5) M and in 0.10 M sodium chloride and 0.01 M sodium phosphate buffer, pH 7.0, the decamer duplex has a Tm at 47 degrees C. The CD spectrum of this decamer duplex is similar to that of B-form DNA. All the resonances of the nonexchangeable base protons of the decamer are well resolved in the 1H NMR spectrum, when the single-stranded form was examined by using a 360-MHz spectrometer and when the duplex form was examined by using a 600-MHz spectrometer. These base proton resonances have been tentatively assigned by using the incremental assignment technique. Although the decamer duplex serves as a substrate for AluI restriction endonuclease, it is not cleaved by HindIII endonuclease.

Proton nuclear magnetic resonance studies on dideoxyribonucleoside methylphosphonates

A series of dideoxyribonucleoside methylphosphonates, d-ApA, d-ApT, d-TpA, and TpT, were synthesized chemically and the diastereoisomers of each dimer were separated [Miller, P. S., Yano, J., Yano, E., Carroll, C., Jayaraman, K., & Ts'o, P. O. P. (1979) Biochemistry 18, 5134]. The 1H NMR spectra of these compounds are similar to those of their parent diester compounds. Specifically, the assignments of the 1H resonances of the two diastereoisomers of d-ApA (designated as 1 and 2) were reaffirmed by comparing with the unmodified, parent d-ApA. The absolute configuration of the phosphonate methyl group of the two isomers (d-ApA)1 and (d-ApA)2 was determined by the NOE technique. The 1H NMR spectra of the diastereoisomers of d-ApA, as well as the corresponding monomer components dAp and CH3pdA, and TpT were analyzed by spectrum simulation techniques. Thus, all the coupling constants and chemical shifts of the proton resonances of the deoxyribofuranose ring and the phosphonate methyl group could be precisely determined. These data provide the information for an analysis of the sugar puckering and backbone conformations of these novel nonionic nucleic acid analogues. It was found that the conformations of the sugar-phosphate backbones of each isomer are similar to each other and are similar to the conformations of the parent dinucleoside monophosphates. The average adenine stacking conformations of (d-ApA)1 and (d-ApA)2 were described in numerical coordinates derived from a computer analysis which included both ring-current magnetic anisotropy and atomic diamagnetic anisotropy effects. The two computer-derived conformational models are similar to those derived from the graphic approximation based only on the ring-current effects. For each pair of dimer analogues, the base stacking mode of isomer 1 is similar to that of its parent diester while the extent of base overlap in isomer 2 is less than that in isomer 1. The results of the conformational analysis based on NMR data are consistent with the results obtained from ultraviolet and circular dichroism measurements on these dimers.

Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates

A series of dideoxyribonucleoside methylphosphonate analogues, dNpN and dNpNp, which contain a nonionic 3'--5' methylphosphonyl internucleoside linkage were prepared. The two diastereoisomers, designated isomers 1 and 2, of each dimer differ in configuration of the methylphosphonate group and were separated by column chromatography. The diastereoisomers of each dimer have different conformations in solution as shown by ultraviolet hypochromicity data and their circular dichroism spectra. For example, dApA isomer 1 is more highly stacked than isomer 2, although both isomers are less stacked than the dinucleoside monophosphate, dApA. The circular dichroism spectrum of isomer 1 is very similar to that of dApA, while the CD spectrum of isomer 2 shows a loss of molecular ellipticity, [theta], at 270 nm and a greatly diminished [theta] at 250 nm. These results suggest that the stacked bases of dApA isomer 1 tend to orient in an oblique manner, while those in isomer 2 tend to orient in a parallel manner. This interpretation is verified by the 1H NMR study of these dimers (L. S. Kan, D. M. Cheng, P. S. Miller, J. Yano, and P. O. P. Ts'o, unpublished experiments). Both diastereoisomers of dAaA form 2U:1A and 2T:1A complexes with poly(U) and poly(dT), respectively. The higher Tm (Tm of poly(U)--isomer 1, 15.4 degrees C; Tm of poly(U)--isomer 2, 19.8 degrees C; Tm of poly(dT)--isomer 1, 18.7 degrees C; Tm of poly(dT)--isomer 2, 18.4 degrees C) values of these complexes vs. those of the corresponding dApA--polynucleotide complexes (Tm of poly(U)--dApA, 7.0 degrees C; Tm of poly(dT)--DApA, 9.2 degrees C) result from decreased charge repulsion between the nonionic dimer backbone and the negatively charged polymer backbone. The difference in conformations between dApA isomer 1 and dApA isomer 2 is reflected in the Tm of the isomer 1-poly(U) complex which is 4.4 degrees C lower than that of the isomer 2-poly(U) complex. Since these nonionic oligonucleotide analogues are taken up by cells in culture, they show promise as molecular probes for the function and structure of nucleic acids inside living cells.

Effects of a trinucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, on mammalian cells in culture

The nonionic 2'-O-methyribooligonucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, is complementary to the...ApCpC...sequence found in the amino acid accepting stem of most tRNAs and the anticodon region of tRNAgly and to the threonine codon of mRNA. Gmp(Et)Gmp(EtU forms hydrogen-bonded complexes with the amino acid accepting stem of tRNApheyeast and unfractionated tRNA Escherichia coli under physiological salt conditions at 37 degrees C as determined by equilibrium dialysis. The extent of phenylalanine aminoacylation of tRNApheE.coli is inhibited 39% by Gmp(Et)Gmp(Et)U at 37 degrees C in solution. The triester is resistant to hydrolysis by serum nucleases and cell lysates. The triester is readily taken up by transformed Syrian hamster fibroblasts growing in monolayer. Within the cell, the triester is deethylated to give the trinucleotide species Gmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU and is also hydrolyzed to dimeric and monomeric units. Treatment of transformed fibroblasts in monolayer with 25 micronM Gmp(Et)Gmp(Et)U results in a 40% inhibition of cellular protein synthesis with a concurrent slight increase in cellular RNA synthesis during the first 4 h. After 4 h, the rate of cellular protein synthesis begins to recover while RNA synthesis returns to that of the control. Our biochemical studies suggest that inhibition of cellular protein synthesis might be expected if Gmp(Et)Gmp(Et)UGmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU, which have been taken up by or formed within the cell, physically bind to tRNA and mRNA and inhibit the function of these nucleic acids. The reversible inhibition of protein synthesis may be a consequence of further degradation of the trinucleotide species within the cell as well as to an increase in supply of RNA molecules involved in protein synthesis. The growth of the transformed fibroblasts is inhibited during the first 24 h of incubation with 25 micronM Gmp(Et)Gmp(Et)U after which growth proceeds at a normal rate. In cloning experiments, the number and size of colonies formed by the transformed fibroblasts after 5 days exposure to 25 micronM triester is decreased by 50% relative to untreated controls. The temporary inhibition of cell growth may reflect the transitory inhibition of cellular protein synthesis caused by the triester.

The Ghost Anomaly in the 9Be(p, d)8Be Reaction

The ghost of the 8Be ground state has been observed in the 9Be(p, d)8Be reaction, and fitted using a many-level R-matrix formalism.

Use of phosphorus oxychloride in synthesizing nucleotides and oligonucleotides

Procedures are described for phosphorylating protected nucleotides, oligonucleotides and phosphoramidate oligonucleotide derivatives at the 3'-hydroxyl group. The conditions (phosphorylation with phosphorus oxychloride and pyridine in dioxane followed by hydrolysis with aqueous pyridine) are sufficiently mild that base labile (trifluoroacetylamino; beta-cyanoethyl phosphotriester) and acid labile (O-monomethoxytrityl; phosphoramidate) functions are retained intact. Application of the technique is illustrated by the synthesis of dpT, dTp, d(CF(3)CONH)Tp, dTp(N)Tp, and dTp(N)Tp(N)Tp. In addition, the utilization of phosphorus oxychloride in joining thymidine derivatives and dinucleoside phosphotriester blocks via phosphodiester links is described.