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M S Shchepinov

Publications and source records attributed to M S Shchepinov.

10 recordsLinked to original sources
PubMed2003

Recent applications of bifunctional trityl groups.

Triphenylmethyl derivatives represent an important class of dyestuffs as well as a useful family of protecting groups widely used in organic synthesis to transiently block various functional moieties. These applications are well documented and have been a subject of a number of reviews. Here we focus instead on some novel applications of a trityl which make good use of its ability to easily form a stabilised cation in combination with additional peripheral functionalities. Topics covered include applications in bioconjugation, cross-linking, mass-spectrometry, fluorescence and optics.

Combinatorial Chemistry Techniques↗
PubMed2001

Matrix-induced fragmentation of P3'-N5' phosphoramidate-containing DNA: high-throughput MALDI-TOF analysis of genomic sequence polymorphisms.

Chemical and enzymatic approaches were used to produce polynucleotide fragments containing acid-labile internucleotide P3'-N5' phosphoramidate bonds, either in a surface-bound form or in solution. The primer extension reaction utilizing 5'-amino-5'-deoxynucleoside 5'-triphosphates generates polynucleotides that can be fragmented into short, easy-to-analyze pieces simply by being premixed with the acidic matrices typically used for MALDI-TOF mass spectrometry of nucleic acids. This leads to detection procedures that are simple, robust and easy to automate. Utilizing this approach, a polymorphic site in the human ADRB3 gene was interrogated. Primer extensions with phosphoramidate analogs of dNTPs allowed for unambiguous discrimination of all possible genotypes.

Amides↗
PubMed1999

Oligonucleotide dendrimers: stable nano-structures.

DNA dendrimers with two, three, six, nine or 27 arms were reassociated as complementary pairs in solution or with an array of complementary oligonucleotides on a solid support. In all cases, duplex stabilities were greater than those of unbranched molecules of equal length. A theoretical treatment for the process of dissociation of dendrimers explains the major properties of the complexes. The favourable features of DNA dendrimers-their enhanced stability and the simple predictability of their association behaviour-makes them promising as building blocks for the 'bottom up' approach to nano-assembly. These features also suggest applications in oligonucleotide array/DNA chip technology when higher hybridisation temperatures are required, for example, to melt secon-dary structure in the target.

Base Sequence↗
PubMed1999

Trityl mass-tags for encoding in combinatorial oligonucleotide synthesis.

Combinatorial libraries of oligonucleotides on beads were synthesised by a split-and-mix strategy using 5'-DMTr- or 5'-Fmoc- nucleoside phosphoramidites. Trityl moieties with different masses were used to encode for the bases coupled at each step in the synthesis of oligonucleotides selected by hybridisation from the libraries. Tags orthogonal to the nucleotides added were produced by coupling amines of different MW to an activated carboxyl group(s) on the trityl moiety. Tags can be released from the support by laser irradiation and measured directly by TOF without matrix. Alternatively, they may be released by an acidic treatment and then analysed by (MA)LDI-TOF.

Combinatorial Chemistry Techniques↗
PubMed1997

Oligonucleotide dendrimers: synthesis and use as polylabelled DNA probes.

Oligonucleotide dendrimers were synthesized using a novel phosphoramidite synthon, tris-2,2,2-[3-(4,4'-dimethoxytrityloxy) propyloxymethyl]ethyl- N , N -diisopropylaminocyanethoxy phosphoramidite. Label, incorporated using [gamma-32P]ATP and polynucleotide kinase, was increased in proportion to the number of 5'-ends. There was a similar increase in signal when these multiply labelled oligonucleotides were used as probes to oligonucleotide arrays. A dendrimeric oligonucleotide was used successfully as a primer in the PCR. The strand bearing the dendrimer was resistant to degradation by T7 Gene 6 exonuclease making it easy to convert the double-stranded product of the PCR to a multiply-labelled, single-stranded probe.

Adenosine Triphosphate↗
PubMed1997

Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays.

We have investigated the use of spacer molecules to reduce steric interference of the support on the hybridisation behaviour of immobilised oligonucleotides. These spacers are built up from a variety of monomeric units, using phosphoramidite chemistry, by condensation onto an amine-functionalised polypropylene support. The optimal spacer length was determined to be at least 40 atoms in length, giving up to 150-fold increase in the yield of hybridisation. The effects of different charged groups in the spacer were also examined, and it was shown that both positively and negatively charged groups in the spacer diminish the yield of hybridisation. Steric hindrance in hybridisation can also be a problem if the oligonucleotides attached to the support are too close to each other. Surface coverage was varied using a combination of cleavable and stable linkers, giving the highest hybridisation yields for surfaces containing approximately 50% of the maximum concentration of oligonucleotides.

Base Sequence↗
PubMedDate not supplied

Design of multidye systems for FRET-based applications.

A new solid phase approach, based on orthogonal protective group strategy utilizing Fmoc and DMTr groups, was used to assemble linear polymeric chains with pending groups at desired locations. A compound synthesized using four different fluorophores with consequently overlapping absorption and emission spectra (pyrene, perylene, fluorescein and TAMRA) was shown to fluoresce at 570 nm when excited at 330 nm, demonstrating sequential energy transfer across four chromophores.

Energy Transfer↗
PubMedDate not supplied

[Selectively cleaved synthetic oligodeoxyribonucleotides for reverse immobilization of DNA].

A streptavidin-coated TSK-gel support, with the loading capacity of 50-70 nmol of biotinylated substance per gram of dry support, and biotinylated oligonucleotides, containing the 4,9-dithiadodecane-6,7-dihydroxy-1,12-diphosphate insert, were prepared for the reversible immobilization of DNA. A non-nucleotide link can be located either at 5'- or 3'-end of the DNA fragment between the biotin moiety and the nucleotide sequence and is subjected to the selective periodate cleavage at the glycol group, which takes 45 min in solution and 3 h in heterophase. For the incorporation of the cleavable and biotin moieties into synthetic oligonucleotides, the corresponding phosphoramidite reagents and biotinylated CPG support were synthesized.

Base Sequence↗
PubMedDate not supplied

[Characteristics of the pH2-42 probe for the D13S25 locus of human chromosome 13: nucleotide sequence, localization, and PCR markers].

The sequence of the HindIII-HindIII fragment of probe pH2-42 of locus D13S25 of human genome is given. Localization of the probe in q14-q21 of human chromosome 13 is confirmed by hybridization in situ. Seven oligonucleotide primers for the polymerase chain reaction are chosen so that amplified products almost completely cover the analyzed sequence. Reconstruction of localization of polymorphic SspI-sites in D13S25 was based on the data of Bowcock and Hebert [3] and this study. The results obtained make it possible to use the primer sets to screen cosmid libraries and to mark the D13S25 locus of human chromosome 13.

Base Sequence↗