(<i>R</i>)- and (<i>S</i>)-2-(4-Bromophenyl)-2-oxoethyl 2-Methoxymethylpyrrolidine-1-dithiocarboxylate

Biedermann, M.; Hartung, H.; Dölling, W.; Verjus, P.

doi:10.1107/s0108270197016570

Cited by 3 publications

(5 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…39 Like 6-Cl-2APTP, sulfur-substituted analogs 2-thio-dTTP and 2-thio-dCTP also form larger base pairs due to the increased bond length of the thiocarbonyl. 40 The single-molecule experiments carried out in this study illustrate and shed new light on the well-appreciated plasticity of DNA polymerases like KF. This class of enzymes can accommodate even dramatically modified incoming dNTPs.…”

Section: ■ Discussionmentioning

confidence: 68%

“…39 Like 6-Cl-2APTP, sulfur-substituted analogs 2-thio-dTTP and 2-thio-dCTP also form larger base pairs due to the increased bond length of the thiocarbonyl. 40 …”

Section: Discussionmentioning

confidence: 99%

“…In this case, replacement of oxygen with chlorine dramatically decreases the strength of the hydrogen bonding . Like 6-Cl-2APTP, sulfur-substituted analogs 2-thio-dTTP and 2-thio-dCTP also form larger base pairs due to the increased bond length of the thiocarbonyl …”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits

et al. 2015

View full text Add to dashboard Cite

DNA polymerases exhibit a surprising tolerance for analogs of deoxyribonucleoside triphosphates (dNTPs), despite the enzymes’ highly evolved mechanisms for the specific recognition and discrimination of native dNTPs. Here, individual DNA Polymerase I Klenow Fragment (KF) molecules were tethered to a single-walled carbon nanotube field-effect transistor (SWCNT-FET) to investigate accommodation of dNTP analogs with single-molecule resolution. Each base incorporation accompanied a change in current with its duration defined by τclosed. Under Vmax conditions, the average time of τclosed was similar for all analog and native dNTPs (0.2 to 0.4 ms), indicating no kinetic impact on this step due to analog structure. Accordingly, the average rates of dNTP analog incorporation were largely determined by durations with no change in current defined by τopen, which includes molecular recognition of the incoming dNTP. All α-thio-dNTPs were incorporated more slowly, at 40 to 65% of the rate for the corresponding native dNTPs. During polymerization with 6-Cl-2APTP, 2-thio-dTTP, or 2-thio-dCTP, the nanocircuit uncovered an alternative conformation represented by positive current excursions that do not occur with native dNTPs. A model consistent with these results invokes rotations by the enzyme’s O-helix; this motion can test the stability of nascent base pairs using non-hydrophilic interactions, and is allosterically coupled to charged residues near the site of SWCNT attachment. This model with two opposing O-helix motions differs from the previous report in which all current excursions were solely attributed to global enzyme closure and covalent bond formation. The results suggest the enzyme applies a dynamic stability-checking mechanism for each nascent base pair.

show abstract

Section: ■ Discussionmentioning

confidence: 68%

“…39 Like 6-Cl-2APTP, sulfur-substituted analogs 2-thio-dTTP and 2-thio-dCTP also form larger base pairs due to the increased bond length of the thiocarbonyl. 40 …”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Thus we turned to the thiocarbonyl group as a way to increase size by a small increment. This substitution, 0.45 Å longer than the carbonyl group, has previously been used on several nucleoside analogues but has not yet been generally studied for its effects on DNA base pairing and replication. Here we report the results of base-pairing studies and of polymerase kinetics studies of 2-thio- and 4-thio-thymidine .…”

mentioning

confidence: 99%

Enhanced Base Pairing and Replication Efficiency of Thiothymidines, Expanded-size Variants of Thymidine

Sintim

Kool

2005

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Here we test the steric effects of added size on DNA base pairing and replication by the use of thiocarbonyl group replacements for natural nucleoside thymidine. The 2-thioT (2S) and 4-thioT (4S) nucleosides were reported previously, but their pairing specificity and replication fidelity were unknown. We find that 2S pairs with higher specificity than thymidine, and both 2S and 4S nucleoside triphosphates are replicated with higher efficiency than natural dTTP. The results indicate possible biotechnological uses for these analogues and have implications in the ongoing use of thionucleobases in cancer treatment.

show abstract

“…In order to modify the size and hydrogen-bonding ability of the substrates, we substituted the carbonyl functionalities in thymidine for thiocarbonyl groups. Thiolated thymidines have an enlarged steric demand, due to the 0.45 longer doublebond length, [31] and additionally decreased H-bonding abilities compared to the native carbonyl groups. We found that primer probes bearing a 4'-C-methoxymethylene modification and thio modification placed at the 3'-terminal nucleotide displayed greatly increased discrimination properties in allele-specific PCR.…”

Section: Introductionmentioning

confidence: 99%

Increased Single‐Nucleotide Discrimination in Allele‐Specific Polymerase Chain Reactions through Primer Probes Bearing Nucleobase and 2′‐Deoxyribose Modifications

Kranaster

Marx

2007

Chemistry A European J

View full text Add to dashboard Cite

The diagnosis of genetic dissimilarities between individuals is becoming increasingly important due to the discovery that these variations are related to complex phenotypes like the predisposition to certain diseases or compatibility with drugs. The most common among these sequence variations are single-nucleotide polymorphisms (SNPs). The availability of reliable and efficient methods for the interrogation of the respective genotypes is the basis for any progress along these lines. Many methods for the detection of nucleotide variations in genes exist, in which amplification of the target gene is required before analysis can take place. The allele-specific polymerase chain reaction (asPCR) combines target amplification and analysis in a single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes. The most important parameter in asPCR is the discrimination of these matched or mismatched pairs. In recent publications we have shown that the reliability of SNP detection through asPCR is increased by employing chemically modified primer probes. In particular, primer probes that bear a polar 4'-C-methoxymethylene residue at the 3' end have superior properties in discriminating single-nucleotide variations by PCR. Here we describe the synthesis of several primer probes that bear nucleobase modifications in addition to the 4'-C-methoxymethylenated 2'-deoxyriboses. We studied the effects of these alterations on single-nucleotide discrimination in allele-specific PCR promoted by a DNA polymerase and completed these results with single-nucleotide-incorporation kinetic studies. Moreover, we investigated thermal denaturing of the primer-probe-template complexes and recorded circular dichroism (CD) spectra for inspecting the thermodynamic and photophysical duplex behaviour of the introduced modifications. In short, we found that primer probes bearing a 4'-C-methoxymethylene residue at the 2'-deoxyribose moiety in combination with a thiolated thymidine moiety have synergistic effects and display significantly increased discrimination properties in asPCR.

show abstract

(R)- and (S)-2-(4-Bromophenyl)-2-oxoethyl 2-Methoxymethylpyrrolidine-1-dithiocarboxylate

Cited by 3 publications

References 3 publications

Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits

Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits

Enhanced Base Pairing and Replication Efficiency of Thiothymidines, Expanded-size Variants of Thymidine

Increased Single‐Nucleotide Discrimination in Allele‐Specific Polymerase Chain Reactions through Primer Probes Bearing Nucleobase and 2′‐Deoxyribose Modifications

Contact Info

Product

Resources

About