P. E. Vorobjev

Oligonucleotide Conjugated to Linear and Branched High Molecular Weight Polyethylene Glycol as Substrates for RNase H

Two conjugates of an anti-HIV oligonucleotide (ODN) with different high molecular weight monomethoxy polyethylene glycols (MPEGs) have been tested for their activity as substrate towards RNase H. The MPEG does not impede the formation of the regular hybrid duplex with the target RNA sequence as pointed out by the persistence of the RNase H activity; thus, these derivatives stimulate the hydrolysis of RNA by the enzyme at the same site and with the same extent of cleavage as the native sequence.

Cleavage of RNA in hybrid duplexes by theE. coli ribonuclease H: II. Substrate properties of oligonucleotides containing nonnucleotide linkers

The 20-mer bridged oligodeoxynucleotides containing short oligomers joined by the hexamethylenediol and hexaethylene glycol linkers were shown to form complementary DNA/DNA and RNA/DNA complexes whose thermostability depends on the length and number of the nonnucleotide linkers. Hybrid complexes of the bridged oligonucleotides proved to be substrates for theE. coli ribonuclease H. The presence of one-three nonnucleotide linkers in a 20-mer decreased the hydrolysis efficacy only 1.2–1.4-fold. It is the composition of the RNA cleavage products that was influenced the most significantly by the nonnucleotide linkers. RNase H simultaneously hydrolyzed the RNA 3′-ends of each hybrid duplex involving a bridged oligonucleotide. The presence of an inverted 3′-3′-phosphodiester bond at the 3′-end of the oligodeoxyribonucleotide only slightly affected the RNase H activity.

A NEW APPROACH TO POTENTIATE SITE-SPECIFIC HYBRIDIZATION: A SET OF HYDROPHOBIC HETEROBIFUNCTIONAL SHORT OLIGODEOXYRIBONUCLEOTIDES

Abstract An effective approach to enhance the short oligonucleotide reagent to attack ssDNA based on the use of a set of short oligonucleotide heterobifunctional derivatives bearing steroid residues is proposed.

Key Aspects of Nucleic Acid Library Design for in Vitro Selection

Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.

Efficient Cleavage of DS DNA by Bleomycin Conjugated via Hexaethylene Glycol Linker to Triplex‐Forming Oligonucleotides

New conjugates of bleomycin A5 with oligonucleotides are synthesized. The bleomycin residue was attached to the 3′‐ or 5′‐ terminus of hexadecathymidilate via a hexaethylene glycol phosphate linker. Newly designed conjugates were shown to cleave site‐specifically both strands of a dsDNA fragment within a triplex. The maximum extent of cleavage for individual strand amounts to 61%.

Multilayer associates based on oligonucleotides and gold nanoparticles

The development of nanodevices for the efficient transport of therapeutic molecules is one of the most urgent problems of modern molecular medicine. Noncovalent agents for the delivery of nucleic acids (NA) including those based on gold nanoparticles (GNPs) represent an attractive alternative to covalent systems, since it is easier in this case to provide the controlled release of NA. We have demonstrated the possibility to create potentially biocompatible associates of GNPs containing alternating layers of oligonucleotides and other polymers as a promising platform for the delivery of oligonucleotides into living cells. The multilayer (five layers) coated GNPs can be assembled by the sequential treatment of gold nanoparticles with nonthiolated oligonucleotide (ON), thiolated carboxyl-polyethylene glycol (SH-PEG3000-COOH), and linear polyethyleneimine (PEI). We have developed an algorithm for the analysis of multilayer coated GNPs by gel electrophoresis, photon correlation spectroscopy, and transmission electron microscopy. The assembly of associates bearing two oligonucleotide layers and having a net positive surface charge has been described. Multilayer coated GNPs were shown not to degrade in the presence of a high concentration of the major blood protein, serum albumin.

Correlated target search by uracil-DNA glycosylase in the presence of bulky adducts and DNA-binding ligands

Many proteins specific for rare targets in DNA, such as transcription factors, restriction endonucleases, and DNA repair enzymes, search for their targets by one-dimensional diffusion along DNA. One of these proteins is uracil-DNA glycosylase (Ung), which excises the uracil bases formed by rare events of cytosine deamination. We have studied the ability of Ung to move along DNA with its path hindered by bulky DNA covalent adducts (fluorescein) or ligands blocking the major or minor DNA groove. The fluorescein adduct strongly inhibits translocation only along double-stranded DNA, whereas noncovalently bound ligands partly inhibit DNA cleavage but barely affect translocation. The ability of uracil-DNA glycosylase to search for its targets in the presence of molecules competing for DNA binding may be important for DNA repair in the intracellular environment.

Cleavage of RNA in Hybrid Duplexes by E. coli Ribonuclease H: III. Substrate Properties of RNA Duplex Complexes with Oligodeoxyribonucleotides Containing a Bleomycin A5 Residue

The effect of bleomycin A5 residue linked to four-, eight-, and twelve-mer oligodeoxyribonucleotides on the substrate properties of their tandem and continuous (with or without unmodified octanucleotide effectors) hybrid duplexes was studied using E. coli RNase H. The bleomycin derivatives of oligodeoxyribonucleotides were shown to form hybrid duplexes with practically the same thermostability as those formed by unmodified oligodeoxyribonucleotides. The RNA in the bleomycin-containing hybrid duplexes is cleaved by E. coli RNase H; however, the initial hydrolysis rate (v0) is 2.6–3.4-fold reduced for the continuous duplexes. In the case of tandem hybrid complexes, the effect of bleomycin on v0 was less pronounced. We hypothesized that steric factors play a key role in the bleomycin inhibition and effectors probably determine the substrate properties of such hybrid complexes. Of all the tandem systems studied, the RNA duplex with the bleomycin-containing tetranucleotide flanked with two effectors displayed the best substrate properties.