Publisher Summary This chapter discusses the sequencing end-labeled DNA with base-specific chemical cleavages. In the chemical DNA sequencing method, one end-labels the DNA, partially cleaves it at each of the four bases in four reactions, orders the products by size on a slab gel, and then reads the sequence from an autoradiogram by noting which base-specific agent cleaved at each successive nucleotide along the strand. This technique sequences the DNA made in and purified from cells. No enzymatic copying in vitro is required, and either single- or double-stranded DNA can be sequenced. Most chemical schemes that cleave at one or two of the four bases involve three consecutive steps: modification of a base, removal of the modified base from its sugar, and DNA strand scission at that sugar. Base-specific chemical cleavage is only one step in sequencing DNA. The chapter presents techniques for producing discrete DNA fragments, end-labeling DNA, segregating end-labeled fragments, extracting DNA from gels, and the protocols for partially cleaving it at specific bases using the chemical reactions. The chapter also discusses the electrophoresis of the chemical cleavage products on long-distance sequencing gels and a guide for troubleshooting problems in sequencing patterns.

Sequencing end-labeled DNA with base-specific chemical cleavages.

https://www.cell.com/cell/pdf/0092-8674(93)90530-4.pdf

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans

3.7. Palladium Nanoparticles as Catalysts 888 3.8. Other Transition-Metal Complexes 888 3.9. Transition-Metal-Free Reactions 889 4. Applications 889 4.1. Alkynylation of Arenes 889 4.2. Alkynylation of Heterocycles 891 4.3. Synthesis of Enynes and Enediynes 894 4.4. Synthesis of Ynones 896 4.5. Synthesis of Carbocyclic Systems 897 4.6. Synthesis of Heterocyclic Systems 898 4.7. Synthesis of Natural Products 903 4.8. Synthesis of Electronic and Electrooptical Molecules 906

https://www.chem.ccu.edu.tw/~joyce/referance/ericyang/Chem.%20Rev/Chem.%20Rev.%202007,%20107,%20874-922.pdf

The Sonogashira Reaction: A Booming Methodology in Synthetic Organic Chemistry†

Antibodies, the most popular class of molecules providing molecular recognition needs for a wide range of applications, have been around for more than three decades. As a result, antibodies have made substantial contributions toward the advancement of diagnostic assays and have become indispensable in most diagnostic tests that are used routinely in clinics today. The development of the systematic evolution of ligands by exponential enrichment (SELEX) process, however, made possible the isolation of oligonucleotide sequences with the capacity to recognize virtually any class of target molecules with high affinity and specificity. These oligonucleotide sequences, referred to as "aptamers", are beginning to emerge as a class of molecules that rival antibodies in both therapeutic and diagnostic applications. Aptamers are different from antibodies, yet they mimic properties of antibodies in a variety of diagnostic formats. The demand for diagnostic assays to assist in the management of existing and emerging diseases is increasing, and aptamers could potentially fulfill molecular recognition needs in those assays. Compared with the bellwether antibody technology, aptamer research is still in its infancy, but it is progressing at a fast pace. The potential of aptamers may be realized in the near future in the form of aptamer-based diagnostic products in the market. In such products, aptamers may play a key role either in conjunction with, or in place of, antibodies. It is also likely that existing diagnostic formats may change according to the need to better harness the unique properties of aptamers.

Aptamers: An Emerging Class of Molecules That Rival Antibodies in Diagnostics

Publisher Summary This chapter reviews the current state of the knowledge of transcription and translation in Caenorhabditis elegans. Transcription in eukaryotes is accomplished by three RNA polymerases, each transcribing a particular type of RNA; RNA polymerase I transcribes ribosomal RNA, RNA polymerase II transcribes mRNAs and snRNAs, and RNA polymerase III transcribes tRNAs and other low-molecular-weight RNAs. The chapter focuses on RNA polymerase II transcription. The C. elegans gene for the large subunit of RNA polymerase II has been cloned, and has shown to encode a protein that resembles its vertebrate counterparts. For most polymerase II transcribed genes in C. elegans, a sequence fitting the consensus TATA element about 30 bp upstream of the transcriptional start site is found. Recently, a cDNA encoding the TATA box binding protein, or TATA binding protein (TBP) subunit of transcription factor II D (TFIID), has been identified in the nematode. This protein shows extended regions of sequence similarity to vertebrate TBP, binds to a TATA box sequence and can substitute for vertebrate TFIID basal activity in in vitro extracts. These results illustrate a high degree of evolutionary conservation in the basic transcription machinery.

Transcription and translation.

Chemistry directed to the synthesis of the tricyclic ring system 3, a purine analogue with degenerate hydrogen-bonding potential, has been investigated and has resulted in the synthesis of several novel pyrrolo[2,3-d]pyrimidine derivatives as potential precursors. The known analogue 2-amino-7H-pyrrolo[2,3-d]pyrimidin-4-one (7-deazaguanine) is converted by the Vilsmeier reagent into 4-chloro-2-dimethylaminomethyleneamino-6-formyl-7H-pyrrolo[2,3-d]pyrimidine 10. Formylation at the α-position of the pyrrole ring was determined by the comparison of 13C NMR data of the corresponding alcohol and the unsubstituted derivative and is in agreement with the regiospecificity reported for the Mannich reaction of this compound. In contrast, base-catalysed hydroxymethylation of 4-chloro-2-methylsulfanyl-7H-pyrrolo[2,3-d]pyrimidine with formaldehyde in aqueous THF occurs at the desired β-position to afford the 5-hydroxymethyl product 17. 7-Methylation of the ButMe2Si-protected alcohol 17 led to several potential precursors of the desired tricyclic structure. The 5-phthalimidooxymethyl derivatives of either 2-methylsulfanyl- or 4-chloro-7-methyl-2-methylsulfonyl-7H-pyrrolo[2,3-d]pyrimidine with ammonia gave the aminooxymethyl derivatives but these subsequently failed to cyclise. Several approaches to cyclise 4-hydroxyamino-5-hydroxymethyl-7-methyl-2-methylsulfonyl-7H-pyrrolo[2,3-d]pyrimidine 27 afforded the corresponding 4-amino compound as the major component. Both the experimental and modelling results show that considerable strain is associated with the formation of 3.

Some Pyrrolopyrimidine Chemistry Directed to the Synthesis of Tricyclic Purine Analogues.

On decrit des analogues de nucleosides contenant l'analogue P de base degenere, ainsi que leurs derives, lesquels comportent des fractions de marqueurs comprenant, de preference, des fractions de signal. Ces analogues de nucleosides sont utiles pour marquer l'ADN ou l'ARN ou pour etre incorpores dans des oligonucleotides.

Analogues de nucleosides

Synth. und eigenschaften von 1-(2-aethino-oxy-aethyl)-cytosinen


 The efficacy of selection programs in sheep depends on accurate evaluation of genetic merit. Globally, genetic evaluations are based on best linear unbiased prediction (BLUP) in which fixed effects and breeding values are estimated simultaneously. With genotyping becoming increasingly routine, pedigree, performance, and genomic data are being combined in single-step genomic BLUP (ssGBLUP) evaluations to generate genomic enhanced estimated breeding values (GEBV). Since GEBV are more accurate, younger animals can be selected more reliably; a corollary benefit is a shortened generation interval. Traits that are lowly heritable, expressed in one sex, measured late in life, or difficult and/or expensive to measure benefit most from genomic evaluation. Adoption of this technology has lagged in sheep most likely due to the higher cost of genotyping compared to the value of an animal. Nevertheless, genomics has been successfully incorporated in sheep breeding programs in several countries (e.g., Australia, France, New Zealand). Increases in accuracy of EBV of up to 60% have been reported. In 2021, the efficacy of genomic selection in a U.S. sheep breed (Katahdin) was tested by comparing predictive ability and bias of EBV using ssGBLUP and pedigree BLUP for weight and fecal egg counts at weaning. Approximately 5,000 animals, most born within the last 5 years, were genotyped with a 50k array. Nearly 70k body weights and 14k fecal egg counts were available. Genomic information improved predictive ability for both traits by as much as 10%, and reduced bias in the evaluation of fecal egg counts. Accuracies of EBV improved appreciably in younger genotyped animals (by as much as 1.81 times). An outcome was release of GEBV in the evaluation of U.S. Katahdin sheep. With integration of genomics into genetic evaluation, there is clear opportunity to augment the reliability of genetic evaluation and thereby rates of selection response in sheep.

/pdf/377-derivation-and-use-of-genomic-enhanced-estimated-2ub6ipoh.pdf

Daniel M. Brown

Papers

Some Pyrrolopyrimidine Chemistry Directed to the Synthesis of Tricyclic Purine Analogues.

Analogues de nucleosides

Synth. und eigenschaften von 1-(2-aethino-oxy-aethyl)-cytosinen

377 Derivation and Use of Genomic Enhanced Estimated Breeding Values for Selection in Sheep

Use of 5‐Nitroindole‐2′‐deoxyribose‐5′‐triphosphate for Labeling and Detection of Oligonucleotides.