Three Novel Spin-Labeled Substrates for Enzymatic Incorporation into Nucleic Acid Lattices

The synthesis of one C(4)-spin-labeled uridine-5′-diphosphate (C(4)-UDP) and two nitroxide-containing 2′-deoxyuridine-5′-triphosphate (dUTP) analogs are reported. The C(4)-UDP derivative was incorporated into copolymers by polynucleotide phosphoxylase (PNPase); one of the two dUTP analogs, substituted at position C(4), was a good substrate for TdT, whereas the other one, substituted at position C(5), served as substrate for E. coli DNA polymerase (Pol I).     

Incorporation of a minimal nucleotide into DNA

Abasic sites are amongst the most frequent DNA lesions and result from spontaneous hydrolysis of the glycosidic bond or from the removal of damaged nucleobases. These depurination events can also occur on free deoxyribonucleoside triphosphates present in cells and lead to the formation of an abasic site triphosphate of which very little is known. Herein, we report the synthesis and biochemical characterization of the minimal triphosphate dФTP. Unexpectedly, dФTP is tolerated by various DNA polymerases and the incorporation efficiency obeys the A-rule. Single incorporation of dФMP units were also observed opposite abasic sites and the addition of prosthetic molecules mimicking base-pairs do not seem to favor the process.     

Incorporation of 4'-C-aminomethyl-2'-O-methylthymidine into DNA by thermophilic DNA polymerases

The dual modified nucleotide 4'-C-aminomethyl-2'-O-methylthymidine 5'-triphosphate was synthesized and enzymatically incorporated into DNA by the thermophilic DNA polymerases Pfu and Therminator III. The dual ribose modification imparted increased exonuclease resistance to DNA compared to the well-known 2'-O-methyl modification.     

Synthesis of Muramyl dipeptide Analogs by Incorporation of 3,3,3-Trifluoroalanine

N-Acetylmuramyl-L-alanyl-D-isogl (Muramyl dipeptide, MDP), the smallestimmunoactive fragment of the cell wall peptidoglycans, which exhibits diverse biologicalactivities such as adjuvant property. enhancement of host defence ability againstmicrobial infection as wei] as antiviral and antitumor potency' =. In tJle last decades.studies on the synthesis of analogs and the relationship between structure and activity ofMDP analogs have emerged since its first synthesis in 1975" 3' '. Because of…     

Primer Extension Reaction Assays for Incorporation of Deoxynucleotide Analogue into DNA

Incorporation of deoxynucleotide analogues into DNA is important for the expansion of DNA functions. Primer extension reactions are commonly used for the assay of such reaction events. However, current assay protocols generally rely on radiolabeling, fluorescence reporter labeling, or removal of specific deoxynucleotide triphosphate in the reaction mixture. Herein we report on the design of two novel assay protocols that utilize a dideoxynucleotide‐terminated template strand and a phosphorothiolate‐modified deoxynucleotide‐terminated template strand. We designed and synthesized a deoxyuridine triphosphate analogue (dU*TP) containing 2‐bromoisobutyryl group and demonstrated that it could be well recognized by ?29DNA polymerase, E. coli DNA polymerase I Klenow Fragment, Bst DNA polymerase Large Fragment, and E. coli DNA polymerase I Klenow Fragment (exo⁽), which translated to effective incorporation of dU*TP into DNA. dU*TP was also successfully incorporated into extremely long single‐stranded DNA at high‐density using ?29 DNA polymerase by rolling circle amplification.     

Thymidine analogues for tracking DNA synthesis

Replicating cells undergo DNA synthesis in the highly regulated, S-phase of the cell cycle. Analogues of the pyrimidine deoxynucleoside thymidine may be inserted into replicating DNA, effectively tagging dividing cells allowing their characterisation. Tritiated thymidine, targeted using autoradiography was technically demanding and superseded by 5-bromo-2-deoxyuridine (BrdU) and related halogenated analogues, detected using antibodies. Their detection required the denaturation of DNA, often constraining the outcome of investigations. Despite these limitations BrdU alone has been used to target newly synthesised DNA in over 20,000 reviewed biomedical studies. A recent breakthrough in "tagging DNA synthesis" is the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU). The alkyne group in EdU is readily detected using a fluorescent azide probe and copper catalysis using 'Huisgen's reaction' (1,3-dipolar cycloaddition or 'click chemistry'). This rapid, two-step biolabelling approach allows the tagging and imaging of DNA within cells whilst preserving the structural and molecular integrity of the cells. The bio-orthogonal detection of EdU allows its application in more experimental assays than previously possible with other "unnatural bases". These include physiological, anatomical and molecular biological experimentation in multiple fields including, stem cell research, cancer biology, and parasitology. The full potential of EdU and related molecules in biomedical research remains to be explored.     

Polymerase‐Catalysed Incorporation of Glucose Nucleotides into a DNA Duplex

Active but unselective : Nucleoside triphosphates possessing glucose moieties (such as those depicted) instead of the natural furanose rings are recognised by the active sites of polymerases. Polymerases therefore seem to be very unspecific in their recognition patterns.

     

Incorporation of chlorine into hydroxy-apatite

Ca₅OH(PO₄)₃ and Ca₅Cl(PO₄)₃ readily form solid solutions Ca₅(OH_1−xCl_x)(PO₄)₃, if synthesized at 1000°C under p_H2O = 4 Torr from CaHPO₄, Ca(CH₃COOH)₂ and CaCl₂. The crystallographic a-axis expands from 9.418 to 9.634 Å, the c- axis contracts from 6.884 to 6.778 Å with increasing Cl content. A new OH stretching band appears in the IR spectrum at 3496 cm⁻¹ for x < 0.5. Two new OH bending bands appear at 755 and 795 cm⁻¹ for x > 0.5. By comparison with the corresponding IR bands in the hydroxy-fluoroapatite solid solution it is to be concluded that the OH…Cl hydrogen bond is stronger than the OH…F bond. This anomalous behavior reflects the difficulty encountered when Cl⁻ substitutes for OH⁻ in the (OH, Cl)-apatite. The large Cl⁻ prefers the halfway position between the Ca-triangles (as in pure Cl-apatite) whereas the OH⁻ sits slightly above or below the plane of the three Ca²⁺ (as in pure OH-apatite). Geometrically this is unfavorable leading to the a-axis contraction and to the OH…Cl compression. The seemingly strong hydrogen bond found in (OH, Cl)-apatite solid solutions destabilizes the structure and explains why, under biological conditions, the OH-apatite discriminates against Cl⁻.     

Structural Requirements in the Transmembrane Domain of GLIC Revealed by Incorporation of Noncanonical Histidine Analogs

1. Download : Download high-res image (186KB)
2. Download : Download full-size image

     

Incorporation of fluorescent probes into PAMAM dendrimers

Interactions of two fluorescent probes 1-(trimethylammoniumphenyl)-6-phenyl-1,3,5 hexatriene p-toluenesulfonate (TMA-DPH) and 12-(9-anthroyloxy) stearic acid (12-AS) with polyamidoamine (PAMAM) dendrimers were studied. Changes in fluorescence intensity and steady-state fluorescence anisotropy of TMA-DPH and 12-AS were monitored. It was found that 12-AS molecules incorporated into dendrimer cavities whereas TMA-DPH molecules aggregated on the surface of polymer. Dendrimer size had not significant impact on its host properties.     

Incorporation of quadruply-bonded units into solid-state materials

The thirtieth anniversary of the quadruple bond marks a time in science when synthetic inorganic chemists are exploring molecular routes to new solid-state materials. Dinuclear transition metal complexes possessing , , and components to their M-M bonding present exciting opportunities for the design of macromolecular compounds with interesting optical, electronic, and magnetic properties. This brief review reports recent progress in the area of ordered molecular arrays incorporating quadruply bonded and other multiply bonded M₂ units.     

Incorporation of nonadiabatic transition into wave-packet dynamics

Nonadiabatic wave-packet dynamics is factorized into purely adiabatic propagation and instantaneous localized nonadiabatic transition. A general formula is derived for the quantum-mechanical local nonadiabatic operator which is implemented within the framework of the R-matrix method. The operator can be used for incorporating the nonadiabatic transition in semiclassical wave-packet dynamics.     

Incorporation of trifluoroisoleucine into proteins in vivo

Two fluorinated derivatives of isoleucine: d,l-2-amino-3-trifluoromethyl pentanoic acid (3TFI, 2) and d,l-2-amino-5,5,5-trifluoro-3-methyl pentanoic acid (5TFI, 3) were prepared. 5TFI was incorporated into a model target protein, murine dihydrofolate reductase (mDHFR), in an isoleucine auxotrophic Escherichia coli host strain suspended in 5TFI-supplemented minimal medium depleted of isoleucine. Incorporation of 5TFI was confirmed by tryptic peptide analysis and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) of the protein product. Amino acid analysis showed that more than 93% of the encoded isoleucine residues were replaced by 5TFI. Measurement of the rate of activation of 5TFI by the E. coli isoleucyl-tRNA synthetase (IleRS) yielded a specificity constant (k(cat)/K(m)) 134-fold lower than that for isoleucine. 5TFI was successfully introduced into the cytokine murine interleukin-2 (mIL-2) at the encoded isoleucine positions. The concentration of fluorinated protein that elicits 50% of the maximal proliferative response is 3.87 ng/mL, about 30% higher than that of wild-type mIL-2 (EC(50) = 2.70 ng/mL). The maximal responses are equivalent for the fluorinated and wild-type cytokines, indicating that fluorinated proteins can fold into stable and functional structures. 3TFI yielded no evidence for in vivo incorporation into recombinant proteins, and no evidence for activation by IleRS in vitro.     

Incorporation of guanosine gels into sieving matrices for length- and sequence-based separation of DNA in capillary electrophoresis

Sieving gels are used in capillary gel electrophoresis to resolve DNA strands of different lengths. For complex samples, however, such as those encountered in metagenomic analysis of microbial communities or biofilms, length-based separation may mask the true genetic diversity of the community since different organisms may contribute same-length DNA with different sequences. There is a need, therefore, for DNA separations based on both the length and sequence. Previous work has demonstrated the ability of guanosine gels (G-gels) to separate four single-stranded DNA 76-mers that differ by only a few A/G base substitutions. The goal of the present work is to determine whether G-gels could be combined with commercial sieving gels in order to simultaneously separate DNA based on both length and sequence. The results are given for the four 76-mers and for a standard dsDNA ladder. Commercial sieving gels were used alone and in combination with G-gels. For the 76-mers, the combined medium was less efficient than the G-gel alone but was able to achieve partial resolution. The combined medium was at least as effective as the sieving gel alone at resolving the denatured DNA ladder and showed indications of sequence-based resolution as well, as supported by MALDI-MS. The results show that the combined sieving gel/G-gel medium retains the selectivity of the individual media, providing a promising approach to simultaneous length- and sequence-based DNA separation for metagenomic analysis of complex systems.