A direct synthesis of pyrrolocytosine from 5-iodocytosine.

We have employed a tandem Sonogashira/annulation reaction between 5-iodocytosine derivatives and terminal alkynes to yield the fluorescent bicyclic nucleobase pyrrolcytosine. Pyrrolocytosine bearing substituents only on the pyrrole ring are conveniently synthesized from 5-iodocytosine. Water soluble pyrrolocytosines are being investigated as reporter groups in SNP analysis.

Synthesis and properties of PNA oligomers containing orotic acid derivatives.

We have investigated the incorporation of C6-derivatives of uracil into polypyrimidine peptide nucleic acid oligomers (PNA). Starting with orotic acid (uracil-6-carboxylic acid) we have prepared a PNA monomer containing the methyl orotate nucleobase which is compatible with Fmoc-based synthesis. Treatment of the resin-bound oligomers with hydroxide or amines cleanly converted the ester to an orotic acid or orotamide-containing PNA. Alternatively, the methyl orotate-containing PNA was liberated from the resin by standard acidolysis. PNA bearing a modified nucleobase was found to hybridize to both poly(rA) and poly(dA). Complexes with poly(rA) were more stable than those with poly(dA) but both were destabilized relative to an unmodified PNA. Modification of a terminal residue was tolerated better than modification of an internal position. The type of charge provided by the modification affected the complex stability. In the worst case, an internal modification was nearly as detrimental as a base mismatch.

Progress towards a submonomer synthesis of peptide nucleic acid.

We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the alpha-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.

Towards a circular bis-peptide nucleic acid.

En route to a circular bis-PNA molecule, we have synthesized and characterized the DNA binding of several "clamp"-type bis-PNAs. In order to incorporate charge into a circular PNA, a new linker based on the achiral 2-aminoethylglycine has been used.

Nucleobase modified peptide nucleic acid.

The Pd0/Cu1 catalyzed cross-coupling of terminal alkynes onto peptide nucleic acid monomers or submonomers bearing iodinated nucleobases has been utilized as a route to base-modified oligomers. Both 5-iodouracil and 5-iodocytosine derivatives undergo the cross-coupling to give the expected products in moderate to good yields. However, depending on the particular substrates and reaction conditions, the cross-coupling may be followed by a ring closing reaction to give the fluorescent furano- and pyrrolo-fused uracil and cytosine derivatives, respectively.

Optimization of a solid-phase synthesis of a PNA monomer.

A new scheme for the synthesis of peptide nucleic acid (PNA) is described. First, a resin-bound amino acid is alkylated under Fukuyama-Mitsunobu conditions. A nucleobase is then incorporated via an acid fluoride. Subsequently, oligomerization may be achieved by deprotection, coupling of another amino acid, and repetition of the cycle. Each step of the submonomer synthesis has been optimized to provide essentially quantitative yield. [reaction: see text]

Inhibition of in vitro pre-mRNA splicing in S. cerevisiae by branched oligonucleotides.

A series of V- and Y-shaped nucleic acids, related to the splicing intermediates derived from S. cerevisiae actin pre-mRNA, were prepared. The effects of such branched nucleic acids (bNAs) on the efficiency of in vitro pre-mRNA splicing in yeast were studied. The exogenous bNAs each effect the efficiency of splicing, yet to different degrees, depending on the sugar composition and topology of the molecules. Y-shaped RNAs inhibited the formation of mRNA (i.e. RNA splicing) to the greatest extent.

Radiation safety parameters following prostate brachytherapy.

PURPOSE: To determine the degree and variability of radiation exposure to the general public from patients after I-125 or Pd-103 prostate brachytherapy. METHODS AND MATERIALS: Radiation exposure measurements were made from 38 consecutive, unselected patients with stage T1 or T2 prostatic carcinoma who had transperineal I-125 or Pd-103 implants at the University of Washington in 1998. RESULTS: The exposure rate at the anterior skin surface following a I-125 implant ranged from 2.2 to 8.9 mrem/hour (average: 5.0). The exposure rate at the anterior skin surface from a Pd-103 implant ranged from 0.5 to 4.9 mrem/hour (average: 1.7). Based on the current Nuclear Regulatory Commission (NRC) regulations the time required to reach the annual limit at the anterior skin surface would be 20 hours for I-125 and 59 hours for Pd-103. For exposure at the lateral skin surface, the times would exceed 500 hours for either isotope. CONCLUSIONS: This data suggest that patients need not be concerned about being a radiation risk to the general public following their procedure.

A fiber optic biosensor for fluorimetric detection of triple-helical DNA.

A fiber optic biosensor was used for the fluorimetric detection of T/AT triple-helical DNA formation. The surfaces of two sets of fused silica optical fibers were functionalized with hexaethylene oxide linkers from which decaadenylic acid oligonucleotides were grown in the 3'to 5'and 5'to 3'direction, respectively, using a DNA synthesizer. Fluorescence studies of hybridization showed unequivocal hybridization between oligomers immobilized on the fibers and complementary oligonucleotides from the solution phase, as detected by fluorescence from intercalated ethidium bromide. The complementary oligonucleotide, dT10, which was expected to Watson-Crick hybridize upon cooling the system below the duplex melting temperature ( T m), provided a fluorescence intensity with a negative temperature coefficient. Upon further cooling, to the point where the pyrimidine motif T*AT triple-helix formation occurred, a fluorescence intensity change with a positive temperature coefficient was observed. The reverse-Hoogsteen T.AT triplex, which is known to form with branched nucleic acids, provided a corresponding decrease in fluorescence intensity with decreasing temperature. Full analytical signal evolution was attainable in minutes.

Fiber-optic DNA sensor for fluorometric nucleic acid determination.

Single-stranded deoxyribonucleic acid (ssDNA) thymidylic acid icosanucleotides (dT20) were synthesized on the surfaces of derivatized quartz optical fibers to create an optical DNA biosensor. The synthesis made use of an automated solid-phase synthesizer and phosphoramidite synthons. The covalently immobilized oligomers were found to hybridize with complementary ssDNA (cDNA) or ssRNA (cRNA) from solution, and the device was regenerable for multiple cycles of application. Hybridization on optical fibers was detected by the use of the fluorescent DNA stain ethidium bromide (EB). The procedure used hybridization assay techniques and provided a detection limit of 86 ng x mL(-1) cDNA and a sensitivity of 200% fluorescence intensity increase per 100 ng x mL(-1) of cDNA, with one cycle of hybridization analysis requiring 45 min. The sensor has been observed to be regenerable (minimum of five cycles) and to sustain full activity after prolonged storage times (1 year), harsh washing conditions (sonication), and sterilization (autoclaving). The extent of hybridization between the immobilized and complementary nucleic acid strands was determined by UV absorbance thermal denaturation studies wherein all 20 bases on each strand of the nucleic acid were found to be involved in duplex formation.

Yeast lariat debranching enzyme. Substrate and sequence specificity.

Yeast RNA lariat debranching enzyme has been purified to near homogeneity using a bacterial overproducer of the enzyme. The enzyme is capable of digesting a variety of branched nucleic acid substrates, including group II intron lariats, multicopy single-stranded DNAs (msDNAs), and a variety of synthetic branched RNAs. A trinucleotide release assay using radiolabeled msDNA substrates was developed and used to determine the basic biochemical parameters for the enzyme. The debranching enzyme shows a strong preference for purines at the 2'-position in both msDNA and synthetic branched RNA substrates, in accord with the structure of its native substrate, which always has a 2'-G residue. The use of small synthetic branched RNA substrates will allow systematic mechanistic and structural studies of this unique enzyme.

Association of branched nucleic acids.

Various branched nucleic acids (bNA's) of the general formula, 5'-(N)xrA[2'-(N)y], 3'-(N)y, have been prepared and their association with complementary linear oligonucleotides has been studied. The binding of complementary sequences to bNA's (for instance when N = dT, x = 0; y = 10 or x = y = 10 and the complement is dA10) yields transition temperatures (Tm's) equal to or greater than those of the corresponding linear complexes of similar base composition. Furthermore, a saturation of binding is observed when the number of mole-equivalents of complementary sequence equals the number of "arms" less one (n-1), i.e., for the "Y"-shaped molecule, 5'-T10-rA[(2'-T10), 3'-T10]; n = 3, saturation occurs at two equivalents of complementary sequence. The significance of these results is discussed in terms of possible triple helix formation.

Solid-phase synthesis of branched oligoribonucleotides related to messenger RNA splicing intermediates.

The chemical synthesis of oligoribonucleotides containing vicinal (2'-5')- and (3'-5')-phosphodiester linkages is described. The solid-phase method, based on silyl-phosphoramidite chemistry, was applied to the synthesis of a series of branched RNA [(Xp)nA2' (pN)n3'(pN)n] related to the splicing intermediates derived from Saccharomyces cerevisiae rp51a pre-messenger RNA. The branched oligonucleotides have been thoroughly characterized by nucleoside and branched nucleotide composition analysis. Branched oligoribonucleotides will be useful in the study of messenger RNA splicing and in determining the biological role of RNA 'lariats' and 'forks' in vivo.

Factors affecting the survival of bisected sheep embryos in vivo.

Two experiments were carried out to examine the effects of different factors on the survival of split sheep embryos. In Experiment 1, embryos collected on Day-6, Day-7 or Day-8 were bisected and transferred into recipient ewes in pairs. The proportions of Day-6, Day-7 and Day-8 demi-embryos developing to lambs were 26% (14/54), 30% (31/102) and 32% (24/74), respectively. Replacement of bisected late morula to expanded late blastocyst stage embryos into zonae did not affect their survival rate (P>0.5). The proportion of demi-embryos developing to lambs in recipients with two or more ovulations was higher (35%, 53/152) than in recipients with a single ovulation (21%, 16/78 ; P<0.05). In Experiment 2, Day-6 embryos were split with or without exposure to 0.25 M of sucrose and were transferred into recipients in pairs or singly. Exposure to 0.25 M of sucrose decreased the proportion of split embryos developing to lambs compared with that of the controls (31%, 22/70 vs 49%, 34/70 ; P<0.05). The effects of the number of demi-embryos transferred or the stage of development on the survival rate were not significant (P>0.05). The number of lambs born per original embryo was the highest when the embryos were split without exposure to sucrose and transferred into recipients singly (106%, 17/16).