Synthesis of Circular Oligonucleotide Conjugates

Abstract

A new approach to the non-template synthesis of circular oligodeoxyribonucleotides containing flexible non-nucleotidic linkers has been developed. Using this technique a set of circular molecules representing triple helix forming, antisense and guanosine tetrad containing oligonucleotides has been obtained.     

Aldehydic Oligonucleotide: A Key Intermediate for the Preparation of Oligonucleotide Conjugates Through Oxime Bond Formation

Oligonucleotides functionalized with an aldehyde group are the key intermediates used for the preparation of peptide-oligonucleotide conjugates through the formation of an oxime linkage. Herein, we describe a brief overview of various synthetic protocols developed in our laboratory for the preparation of aldehyde containing oligonucleotides and their subsequent conjugation with peptides.     

Oligonucleotide Conjugates Derived from an Electrophilic Site: Conjugation to Baseless Carbohydrate Residue. Synthesis,Hybridization and Modeling Studies

Abstract

Conjugation of electrophiles to oligonucleotides via tethers camying nucleophilic sites well-known. However, for the rever.se reaction, the availahlc methods to generate electrophilic sites in oligonucleotides are not many: (e.g., periodate oxidation of terminal rihose sugar followed by reductive amination).     

Use of Oligonucleotide Conjugates in Creating Self-Assembling Supramolecular Systems

Abstract

The chemistry of two types of oligonucleotide conjugates containing novel chromophores are described. One, containing a stilbenedicarboxamide bridge, generates unusually stable hairpin structures that are useful in assessing rates of electron transfer through the π system of a DNA double helix. The other, containing gold nanoparticle conjugates, provides a highly selective system for detecting nucleotide sequences in oligonucleotides.     

Novel Short Oligonucleotide Conjugates as Inhibitors of Human Telomerase

Abstract

A series of oligonucleotide conjugates were designed and synthesized as novel inhibitors of human telomerase. These compounds contain a relatively short (6–7-mer) oligonucleotide domain, with an N3′ → P5′ phosphoramidate (np) or thio-phosphoramidate (nps) backbone, targeted to the template region of the RNA component of the enzyme and various pendant groups attached to either their 5′- or preferably to the 3′- termini. The most potent compounds in the series inhibited telomerase with low nM IC₅₀ values in biochemical assays whereas the cognate oligonucleotides without the pendant groups were significantly less active having IC₅₀ values 100-1000-fold higher.     

Visible Light Activatable Binary System of Oligonucleotide Conjugates for Nucleic Acids Modification

Abstract

A binary system of oligonucleotides conjugated to perfluoroarylazide and perylene for sequence-specific photomodification of nucleic acids has been developed. The system can be activated by visible light (450-580 nm), reacts 300000 times faster than azide in the absence of perylene and provides highly efficient (up to 99%) photomodification of target ssDNA.     

Synthesis and Hybridization Characteristics of Oligodeoxynucleotide-Alkaline Phosphatase Conjugates

Abstract

Modified oligodeoxynucleotides, 20 to 30 bases in length and containing “linker arm” bases, are chemically synthesized, then attached covalently to alkaline phosphatase in a 1:1 conjugate through a 19 atom spacer. Such conjugates hybridize rapidly and selectively to complementary sequences similar to unmodified oligomers, and allow colorimetrlc and fluorogenic detection of hybrids.     

Fluorescent Labeling of Oligonucleotide Probes for Double Indicator Microarray Hybridization Analysis

Russian Journal of Bioorganic Chemistry - Herein, we present a synthesis of a molecular construct based on the polysulfonated indocarbocyanine dye and the lysine. The chemical structure of the...     

DNA Sequencing by Hybridization to Oligonucleotide Matrix. Calculation of Continuous Stacking Hybridization Efficiency

Abstract

In this paper we consider the efficiency of additional rounds of “continuous stacking” hybridization in DNA sequence reconstruction by hybridization with oligonucleotide matrix (SHOM). After the initial hybridization of target DNA with the matrix of oligonucleotides of fixed length L some additional hybridizations should be carried out in the presence of fluorescently labeled oligonucleotides of another length l. These additional oligonucleotides can hybridize in tandem with matrix tuples (continuous stacking hybridization) thus forming an extended duplex with the target DNA strand. The additional data obtained allows resolutions of branching points arising in the reconstruction procedure. Multiple rounds of continuous stacking hybridization considerably increase the efficiency of the sequencing method, eventually approaching the power of (L+l)-matrix. We develop here an algorithm that allows us to minimize the number of additional hybridization steps, by assembling sets of l-tuples to be added together in each round of continuous stacking hybridization. For SHOM using a matrix of octanucleotides, continuous stacking hybridization with pen- tanucleotides increases the length of unambiguously sequenced DNA from 200 to several thousands of base pairs.     

Perylene-Labeled Oligonucleotide as a Probe in Homogeneous Hybridization Assay

Abstract

An oligodeoxynucleotide bearing a 3′-terminal perylene-containing pseudonucleoside unit was synthesized and used as a probe in homogeneous hybridization. The fluorescence anisotropy of the perylene dye rose upon hybridization of the modified conjugate with the complementary nucleotide sequence. These results provide for designing efficacious hybridization probes.     

New Photoreactive Oligoribonucleotide Conjugates: Hybridization and Modification Assays

An evaluation of hybridization and modification abilities of new types of photoactivatable oligoribonucleotide conjugates bearing p‐azidotetrafluorobenzamide group at the N4 of cytosine is presented.     

一种基于寡核苷酸微阵列芯片的多重可扩增探针杂交技术

多重可扩增探针杂交技术(multiplex amplifiable probe hybridization,MAPH)是近年来发展起来的一种用于基因组中DNA拷贝数检测的新技术。并发展了一种基于寡核苷酸微阵列芯片的MAPH技术。该方法根据所检测的DNA序列,制备若干具有通用引物的FCR产物作为可扩增探针组,与固定在尼龙膜上待测的基因组DNA杂交。用磁珠回收特异性杂交的探针,经生物素标记的通用引物扩增后,与相应的寡核苷酸微阵列芯片杂交。该特异性的寡核苷酸微阵列芯片包括10个抗肌营养不良基因的外显子探针和阴性、阳性探针。杂交清冼后,链霉亲和素-Cy3染色用芯片扫描仪得到杂交的荧光图像。分析荧光信号的强度差异给出特定基因片段拷贝数的变化。该方法用微阵列技术代替MAPH中的电泳检测技术,可大幅度增加检测的通量。选择了一个正常男性、一个正常女性和一个肌营养不良症患者的基因组DNA来进行验证。结果表明,该方法能够同时给出抗肌营养不良基因多个外显子中的基因片段拷贝数差异信息。     

Synthesis of Oligonucleotide Conjugates with the Aid of N-Chloroacetamidohexyl Phosphoramidite Reagent

Abstract

A novel phosphoramidite building block derived from N-chloroacetyl-6-aminohexanol is attached at the 5′-terminus on the last step of oligonucleotide synthesis. Postsynthetic treatment of support-bound modified oligonucleotides with a variety of amines and mercaptanes affords oligonucleotide conjugates in a high yield.     

Oligonucleotide Conjugates: Alteration of the Pharmacokinetic Properties of Antisense Agents

Abstract

Cholic acid, cholesterol, several polyamines and polyethylene glycols were conjugated to antisense oligonucleotides targeted to human or murine intercellular adhesion molecule-1 (ICAM-1) mRNA to study their effects on cellular absorption.     

Finding a Most Likely Clone Ordering from Oligonucleotide Hybridization Data

Using an extension of a statistical model given by E. Lander and M. Waterman, we define the a posteriori probability of a clone ordering based upon oligonucleotide hybridization data. We give algorithms for computing the likelihood of a clone ordering and for finding a clone ordering of maximum likelihood. The dynamic programming algorithm for computing likelihoods runs in time O(mnc), where m is the number of oligonucleotide probes, n is the number of clones, and c is the coverage of the clone library. We use the Expectation-Maximization technique to maximize likelihoods.     

寡核苷酸阵列比较基因组杂交技术及其应用

阵列-比较基因组杂交技术（array comparative genomic hybridization, array CGH）能在全基因组水平和/或高分辨率基础上检测染色体拷贝数的变化,主要应用于遗传学和肿瘤学研究。Array CGH中微阵列探针通常是PCR扩增的BAC克隆或cDNA分子。最近几年,寡核苷酸阵列比较基因组杂交（oligonucleotide array CGH, oaCGH）逐渐开始应用。oaCGH与BAC array CGH比较,具有操作更简便、探针设计更灵活、分辨率更高等多项优点,预计oaCGH将逐步取代利用BAC克隆片段或cDNA分子的array CGH。oaCGH的应用及其与其它高通量检测技术的结合将促进新的癌症相关基因、肿瘤耐药基因的发现。本文综述了现有主要oaCGH平台在空间分辨率、探针长度、灵敏度、特异性等方面的特点及其应用,概括了oaCGH近年来的进展。     

5-Deazaflavins: New Very Efficient DNA Photosensitisers,Synthesis of Oligonucleotide Conjugates

Abstract

In order to study electron transfer processes through the DNA double helix, we have synthesised a series of 5-deazaflavin derivatives 1–4 and demonstrated their ability to induce very efficiently 2′-deoxyguanosine and DNA oxidations by electron transfer from guanine. 5-Deazaflavin-oligonucleotide adducts were also synthesised for the study of electron transfers through double or triple helix formed with their complementary sequence.