5-Hydroxymethyl-dC (hm-dC) has long been postulated as the oxidative product formed from 5-methyl-dC by hydroxyl radicals and ionizing radiation. Recently, hm-dC has also been identified as a component of nuclear DNA in the brain that has not been formed by oxidative damage. A potential role has been proposed for hm-dC in epigenetic control of neuronal function. This finding stimulated us to offer the phosphoramidite of hm-dC for the synthesis of oligonucleotides containing hm-dC at defined positions to allow researchers to study the biological function of this newly discovered, naturally occurring nucleoside.

Glen UnySupport is a version of UnyLinker™, developed at Isis Pharmaceuticals, and is preferred for high throughput oligonucleotide synthesis. Glen UnySupport is compatible with most deprotection strategies from gas phase deprotection with methylamine to UltraMild deprotection with potassium carbonate in methanol. We now offer Glen UnySupport under license from Isis Pharmaceuticals. Glen UnySupport™ Frits We now offer high density polyethylene (HDPE) frits with embedded Glen UnySupport to allow customers to make their own inexpensive columns. The frits contain 40 nanomoles of Glen UnySupport and fit directly into empty MerMade and AB3900 columns. They can also be used on ABI 394 and Expedite instruments when fitted into an inexpensive female-female luer adapter. tC and tCo - Tricyclic Fluorescent Nucleoside Analogues These tricyclic dC base analogues have been shown to base pair faithfully with dG with virtually no disruption of the normal duplex structure. This means that the stability of the DNA duplex is not compromised as compared to the control regardless of the DNA sequence. The fluorescence quantum yield of tC is essentially unchanged between single stranded and double stranded DNA - 0.21 for single stranded DNA and 0.19 for duplex DNA. Also, the fluorescence characteristics of tC are not sensitive to neighboring base combinations. tCo has been shown to be the brightest fluorescent nucleoside analogue in duplex context reported so far and even retains the majority of its fluorescence when surrounded by guanine residues. Indeed, tCo has been reported to be 25-50 times brighter than 2-aminopurine. 3'-Cap for Improved Target Affinity and Specificity 3'-Uaq Cap CPG, a Uridine support modified with a 2'-anthraquinone residue, is the most effective oligonucleotide cap known to date. For short hybrid duplexes between DNA probes and RNA target strands, the increase in Tm is up to 18 °C and the modification is effective in increasing the Tm of DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. 3'-Uaq Cap also increases probe specificity by depressing the melting point of terminal mismatches.

Professor Asanuma and his group at Nagoya University have designed an azobenzene phosphoramidite for incorporation into oligonucleotides that can subsequently be photo-regulated. For example, using UV or visible light for photo-regulation, the azobenzene residue's conversion from trans to cis and back can lead to dissociation and reformation of DNA duplexes. and recovery and suppression of transcription by T7-RNA polymerase. Other applications in regulating bioprocesses and in nanotechnology can be easily envisaged.

This article, prepared by authors from TriLink BioTechnologies, describes the advantages of CleanAmp™ Primers over existing procedures for Hot Start PCR. CleanAmp™ Primers have a thermally labile protecting group on one (fast releasing - Turbo Primers) or two (slow releasing - Precision Primers) phosphate groups adjacent to the 3' terminus. The relative merits of Turbo and Precision Primers are discussed in detail. Glen Research is delighted to make monomers available for the synthesis of CleanAmp™ Primers to the research community under license from TriLink BioTechnologies. Please see the Updated Purification Procedure.

New technologies that require oligonucleotides modified with chelated metallobases, like transition metals, have recently emerged. We are happy to offer 2,2'-Dipicolylamine Phosphoramidite as a modification reagent readily leading to chelated metal oligonucleotide complexes. This product was developed by Syntrix Biosystems, Inc., Auburn, WA.

Phosphonoacetate modified oligonucleotides show great potential as biological modifiers in a wide variety of research applications. They have been shown to be active in siRNA duplexes and accelerate the initial rate of cleavage by RNase H-1 when incorporated with phosphorothioates. However, the most interesting observation to date is that they exhibit an unprecedented enhancement in penetration of cultured cells. Oligonucleotides containing this modification are quite simple to prepare using PACE monomers.

Although PACE chemistry works reasonably well with iodine oxidizers, we recommend a non-aqueous oxidizer for optimal performance. (1R)- or (1S)-(+)-(10-Camphorsulfonyl) oxaziridine (CSO) dissolved in acetonitrile is a suitable alternative oxidizer and we now offer a 0.1M solution specifically for PACE chemistry.

We have expanded our popular Glen-Pak DNA cartridge line to include the Glen-Pak DNA Cartridge 3g, a large cartridge capable of purifying 10-20 µmole oligonucleotide syntheses using the standard DMT-on procedure and Glen-Pak DNA 30mg 96-Well Plates for parallel purification of up to 50 nmole scale syntheses.

Nanoparticle-based bio-barcode assay redefines "undetectable" PSA and biochemical recurrence after radical prostatectomy.
C. Shad Thaxton, Robert Elghanian, Audrey D. Thomas, Savka I. Stoeva, Jae-Seung Lee, Norm D. Smith, Anthony J. Schaeffer, Helmut Klocker, Wolfgang Horninger, Georg Bartsch, and Chad A. Mirkin
PNAS October 19, 2009 doi: 10.1073/pnas.0904719106
(PDF VERSION)

New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Förster resonance energy transfer probes in 5'-nuclease assays.
Igor V. Kutyavin
Nucleic Acids Res. published 7 December 2009, 10.1093/nar/gkp1138

NEW PRODUCTS

5',8-Cyclo-dA CE Phosphoramidite: Cyclo-dA is a critical lesion formed in radiation-damaged DNA and repaired by Nucleotide Excision Repair.

Alkyne Modifiers: We offer two new products for Click Chemistry to expand the alkyne side. 3'-Alkyne-Modifier Serinol CPG can be used to insert an alkyne group at the 3' terminus and Alkyne-NHS Ester can be used for labelling of amino-modified oligonucleotides and other biomolecules.

CPR II CPG: This 3'-phosphate support is compatible with ß-elimination prior to oligonucleotide cleavage and deprotection.

RECENT HIGHLIGHTS

Fluorescent Phosphoramidites

Unnatural Base Pair System

Serinol-Based Reagents

Click Chemistry

Thiophosphoramidites

5'-CholesterylTEG Phosphoramidite

Solid Chemical Phosphorylation Reagent

Formylindole

8-D-dG-CE Phosphoramidite

Universal Support III

A Comparative Study of Universal Supports

Pyrrolidine CE Phosphoramidite

Pyrene-dU, Perylene-dU

Fmoc-Amino-Modifier:C6-dT

AP-dC (G-clamp) UPDATE

Technical Briefs

Synthesis of Long Oligonucleotides

Preparation of Oligos Containing Abasic Sites

Deprotection-Volume 2-RNA Deprotection

LNA vs 2'-F-RNA

Deprotect to Completion

Glen-Pak purification: 6-FAM

New application: 5-Me-iso-dC and iso-dG

New application-5'-OMe-dT