化学生物学实验技术

In vitro selection or systematic evolution of ligands by exponential enrichment is a combinatorial procedure that allows the identification of oligonucleotides showing properties of interest—so-called aptamers—through iterative selection/amplification rounds. ...

Since the early 1990s, combinatorial deoxyribonucleic acid and ribonucleic acid libraries have been used to isolate specific ligands for a variety of target molecules, as well as nucleic acid-based catalysts for different reactions. These iterative procedures are based on the fact th ...

This chapter outlines seven synthetic and molecular biology techniques that allow the controlled synthesis of nucleic acid libraries. Specifically: (1) The high-diversity chemical synthesis of point mutations; (2) the high-diversity chemical synthesis of point deletions; (3) ...

A brief overview of the properties of the deoxyribonucleic acid mimic peptide nucleic acid (PNA) is given, and the recent progress in cellular delivery of PNA and of using PNA oligomers for antisense and antigene gene targeting is presented.

Nuclease footprinting techniques were initially developed to investigate protein-deoxyribonucleic acid (DNA) interactions but these tools of molecular biology have also become instrumental for probing sequence-selective binding of small molecules to DNA. Here, the met ...

The aim of this chapter is to provide reliable protocols for the study of nonenzymatic oligomerization reactions of ribonucleic acid and its analogs. Traditional radioactive labels are replaced by fluorescent dyes. Product analysis is either based on reversed-phase high-pressure ...

Fimers are specifically modified primers selected to inhibit nonspecific interactions occurring in cycle sequencing. They are postsynthetically derived from 2′-methoxyoxalamido or 2′-succinimido precursor oligonucleotides by treatment with appropriate small mo ...

During the last few years, several innovative technologies have become available for performing sensitive and accurate genetic analyses. These techniques use fluorescent detection strategies in combination with nucleic acid amplification protocols. Most commonly used is ...

In this chapter, we present methods for denaturing and native gel electrophoresis of nucleic acids based on fluorescently labeled probes and automatic signal detection by a deoxyribonucleic acid sequencer. Specific examples are given for the determination of ribonucleic acid (RN ...

The design of molecules that recognize specific sequence on the deoxyribonucleic acid (DNA) double helix would provide interesting tools to interfere with DNA information processing at an early stage of gene expression. This chapter describes in detail the protocol of conjugation be ...

An efficient strategy for nucleic acid labeling and analysis on deoxyribonucleic acid (DNA) chips has been developed. This approach, which combines the fragmentation and the labeling steps, is based on the reactivity of the phosphates of DNA and ribonucleic acid (RNA) fragments and is using ...

We describe synthesis of four novel biotin phosphoramidites with tethering arms ranging from 20 to 74 atoms in length. One of these phosphoramidites is a uridine derivative with a biotin moiety attached through the 2′-position. The biotin phosphoramidites were synthetized based on robu ...

Methods of peptide-oligonucleotide conjugate synthesis are presented that may be useful in the study of cell targeting and delivery of oligonucleotides and their analogs. The first method involves total stepwise solid-phase synthesis on a single support. The second involves prepa ...

The anticodon domain of lysine transfer ribonucleic acid (tRNA) is a model system for investigation of the structural and biochemical effects of nucleoside posttranscriptional modification. To enable detailed study of the biophysical and structural effects of hypermodified n ...

Oligonucleotides incorporating 8-aza-7-dazapurines (pyrazolopyrimidines) were synthesized. The corresponding nucleosides were prepared and were converted into phosphoramidites. The oligonucleotide duplex stability was studied and was compared to that of the par ...

The methods for the synthesis and purification of negatively charged peptide nucleic acid (PNA)-relative deoxyribonucleic acid (DNA) mimics containing alternating residues of phosphono peptide nucleic acid (pPNA) monomers and PNA-like monomers on the base of trans-4-hydroxy ...

Methods and protocols for automated synthesis and purification of locked nucleic acid (LNA), a class of oligonucleotides obeying the Watson-Crick base-pairing rules but displaying unprecedented binding affinities toward complementary deoxyribonucleic acid (cDNA) and r ...

A protocol for the straightforward preparation of small circular oligodeoxyribonucleotides (2–28 nt) is reported. The assembly of the oligonucleotide chain (standard phosphoramidite chemistry) and cyclization by the phosphotriester method take place on a tailor-made nuc ...

In this chapter, a concise account of the synthesis of oligonucleotides using the H-phosphonate methodology is given. It includes various methods for the preparation of the starting material, nucleoside 3′-H-phosphonate monoesters, their conversion into dinucleoside H-phosp ...

Ribonucleases H are complex enzymes whose functions are not clearly understood, further compounded by the fact that multiple forms of the enzyme are present in various organisms. They are known to recognize and degrade the ribonucleic acid (RNA) strand of numerous deoxyribonucleic acid ...