Minor groove binder-conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence.

Here we describe the properties of a novel class of oligonucleotide probes capable of sensitive hybridization-triggered fluorescence. These fluorogenic probes, known commercially as MGB Eclipse probes, are characterized by having a conjugated minor groove binder (MGB) ligand at the 5'-end and a fluorophore at the 3'-end. Additionally, they have an efficient quencher moiety at the 5'-end that is useful with a wide variety of fluorescent dyes. Fluorescence of the single-stranded MGB Eclipse probe is efficiently quenched by the interaction of the terminal dye and quencher groups when not hybridized. Upon hybridization to a complementary target, the MGB molecule folds into duplex and hyper-stabilizes it, allowing the use of shorter, more specific probe sequences. The 5'-MGB-quencher group also prevents nuclease digestion by Taq DNA polymerase during PCR. Because of the hybridization-triggered fluorescence and the excellent specificity imparted by the MGB, these 5'-MGB Eclipse probes have great versatility for real-time PCR applications. The high sensitivity and specificity are illustrated using single nucleotide polymorphism detection, viral load determination, and gene expression analysis.

[An approach to isolating individual tRNA from the human placenta by affinity chromatography. Isolation of highly purified Phe-tRNA Phe]. / Podkhod k polucheniiu individual'nykh tRNK iz platsenty cheloveka, osnovannyi na metode affinnoi khromatografii. Vydelenie vysokoobogashchennogo preparata Phe-tRNK Phe.

A new approach to isolation of individual tRNAs from eukaryotes based on affinity chromatography is suggested. At first, using a sorbent with oligonucleotide pTGGT attached, the total tRNA with native CCA-ends was obtained. Then by means of a sorbent with oligonucleotide pTTCAG immobilized, which is complementary to a part of the tRNA(Phe) anticodon loop, tRNA(Phe) with the acceptor activity greater than 1000 pmole/unit was isolated.

[Immobilized oligonucleotides as affinity sorbents for restriction endonucleases]. / Immobilizovannye oligonukleotidy kak affinnye sorbenty dlia éndonukleaz restriktsii.

Affinity chromatography of IIS type restriction endonucleases is proposed. It is shown that endonucleases HgaI, FokI, and SfaNI have affinity to the matrix with immobilized oligonucleotides which contain the endonuclease's recognition sites resistant to the hydrolysis.

[Diastereomers of nonionic oligonucleotide analogs. VI. Isolation of diastereomers of ethyl phosphotriesters of the octanucleotide d(GCCAAACA) by high performance affinity chromatography]. / Issedovanie diastereomerov neionnykh analogov oligonukleotidov. VI. Razdelenie diastereomerov étilovykh fosfotriéfirov oktanukleotida d(GCCAAACA) metodom vysokoéffektivnoi affinnoi khromatografii.

Diastereomers of oligonucleotide ethyl phosphotriesters were separated by high-performance complementary (affinity) chromatography on a column with the immobilized complementary oligonucleotide. The elution buffer contained 0.18 M K2HPO4, pH 7.5, and 30% acetonitrile. The temperature of the separation was a few degrees lower than Tm of corresponding oligonucleotide complexes. The diastereomers separated completely or partially were: d[GCC(Et)AAACA], d[GCCA(Et)AACA], d[GCAA(Et)ACA], d[GCC(Et)A(Et)AACA], d[GCC(Et)AA(Et)ACA], d[GCCA(Et)A(Et)ACA], d[GCC(Et)A(Et)A(Et)ACA].

A new method for the postsynthetic generation of abasic sites in oligomeric DNA.

The abasic site is the most common lesion in DNA and is thought to play a critical role in mutagenesis. However, a general chemical method for the site-specific generation of true abasic sites in oligodeoxynucleotides has been lacking. We now describe a procedure which permits the postsynthetic generation of abasic sites in single- or double-stranded DNA oligomers without regard to their base composition. An appropriately protected 3-deoxyhexitol was synthesized and used as the monomer that was incorporated into DNA oligomers using the standard phosphoramidite method for automated DNA synthesis. The resulting stable diol-containing oligonucleotides were purified by HPLC and converted quantitatively into the corresponding abasic DNA sequences by mild periodate oxidation. The abasic site in DNA was found to be relatively stable at room temperature, but was completely cleaved when treated with putrescine at 95 degrees C. Identification of the major degradation products was accomplished by gel electrophoresis, HPLC isolation, and characterization by electrospray ionization mass spectrometry. The thermal stabilities of duplex oligonucleotides containing a natural abasic site were studied, and the results were compared with those from oligomers containing T/dA, F/dA, or the precursor diol opposite dA at the same site.

Affinity chromatography of DNA fragments and P-modified oligonucleotides.

The wide possibilities for use of affinity chromatography are demonstrated by two examples: (i) isolation of a single-stranded fragment of the tick-borne encephalitis virus DNA (302-mer) and an oligonucleotide (34 bases) from reaction mixtures and (ii) fractionation of mixtures of diastereoisomers of octathymidylates with modified internucleotide phosphates. All affinity sorbents are constructed by the covalent attachment of the oligonucleotides to solid supports and can be used repeatedly.