Two improvements that greatly enhance the rate of phosphotriester oligonucleotide synthesis are described: 1) use of hindered primary amines, e.g. t-butyl amine for decyanoethylation of oligonucleotide triester intermediates, and 2) a simplified isolation procedure that eliminates the tedious bicarbonate extraction after each condensing reaction. Using the improved procedures, oligonucleotide f...

To cluster and characterize DNA sequences focusing on the oligonucleotide frequency, we developed a novel method and program package designed designated as Self-Organizing Clustering (SOC) [4]. Being based on Self-Organizing Map (SOM) [1, 2, 3], the algorithm of SOC made use of K-means with modification. In the SOC, the oligonucleotide frequency was regarded as a series of oligonucleotide patte...

PURPOSE Signal transducer and activator of transcription 3 (STAT3) has shown to play a critical role in head and neck squamous cell carcinoma (HNSCC) and we have recently completed clinical trials of STAT3 decoy oligonucleotide in patients with recurrent or metastatic HNSCC. However, there is limited understanding of the role of STAT3 in modulating other aspects of tumorigenesis such as angioge...

While most molecular reactions involving synthetic oligonucleotides, notably PCR and DNA sequencing, are carried out in liquid phase, a rapidly growing number of important applications utilize synthetic oligonucleotides attached to solid supports. In general, the purpose for using a solid support-attached oligonucleotide is to capture something, hold on to it, enrich it, and identify and/or pur...

The photoreactions of HMT [4'-(hydroxymethyl)-4,5',8-trimethylpsoralen] monoadducts in double-stranded DNA have been studied with complementary oligonucleotides. The HMT was first attached to the thymidine residue in the oligonucleotide 5'-GAAGCTACGAGC-3' as either a furan-side monoadduct or a pyrone-side monoadduct. The HMT-monoadducted oligonucleotide was then hybridized to the complementary ...