PRODUCT OVERVIEW - emp Biotech · 2017. 11. 30. · 4,5-Dicyanoimidazole (DCI) is an efficient...

Synthesis Reagentsemp BIOTECH 1

Synthesis ReagentsFor Automated Oligonucleotide Syntheses

P R O D U C T O V E R V I E W

excellence made possible

emp BIOTECH 3

Synthesis ReagentsFor Automated Oligonucleotide Syntheses

P R O D U C T O V E R V I E W

Deblocking Solutions 5

Activators 7

Capping Solutions 11

Oxidizer Solutions 15

Cleavage Solutions 17

Solvents, Molecular Sieves and other Reagents 19

Purification 25

Redox Labels 29

Packaging Specifications 34

Terms and Conditions 35


DetritylationDeblocking solutions, used for the cleavage of the 5‘-DMTr group at the last building block of

nucleotide chain, can consist either of dichloroacetic or trichloroacetic acid in dichloromethane,

dichloroethane or toluene. Our Hyacinth Deblocking solution (3 % dichloroacetic acid in toluene

at


Activationemp BIOTECH manufactures three different activators for use on various DNA

and RNA synthesizers. They are available either in dry solid form for dissolution into

anhydrous acetonitrile or as a prepared solution of various molarities.

A C T I VAT O R S

BO

O

HO

P

BO

O

OP

O

O

O

O

B

NC

P

DMTr

N P

O

O

O

O

BDMTr

CN

+

activator solution

emp BIOTECHSynthesis Reagents8

Hyacinth BMT

A C T I VAT O R S

Catalog No. Description Unit Size

NC-0101Hyacinth BMT Crystals

(5-Benzylmercaptotetrazole, BTT)1.5 g to 50 kg

NC-01020.25 M Hyacinth BMT Solution

(BMT in anhydrous acetonitrile)100 mL to 200 L





Hyacinth BMT activator (also known as 5-Benzylmercapto-1H-tetrazole or BTT)

demonstrates important advantages in the syntheses of oligonucleotides:

•Couplingefficienciesof99%withimpeccablequality

•Lowerpercentageofn-1sequences

•Dramaticreductionofcouplingtimes

to under 3 minutes in RNA syntheses

•EfficientRNAsynthesisusing50%orless

TBDMS, TOM®orACE® monomer

•Excellentbatchtobatchconsistency

for reproducible and stable oligo production

S NH

NNN

Ordering Hotline +49 30 [email protected]


ETT

DCI

A C T I VAT O R S


NC-0107 ETTCrystals(5-Ethylmercaptotetrazole) 1.5 g to 50 kg

NC-01080.25MEthylmercaptotetrazoleSolution

(ETTinanhydrousacetonitrile)100 mL to 200 L






NC-0112 DCI Crystals (4,5-dicyanoimidazole) 1.5 g to 50 kg

NC-01050.25 M 4,5-dicyanoimidazole solution

(DCI in anhydrous acetonitrile)100 mL to 200 L

5-Ethylthiotetrazole(ETT)isanefficientactivatorforusein

chemicalsynthesisofeitherDNAorRNA.ETThasexcellent

performance with respect to coupling times, coupling

efficiency,consumptionofphosphoramiditesandreduction

ofn-1impurities.ETTcanbeusedforRNAsynthesiswith

TBDMS, O-Methyl, TOM®orACE® amidites.

4,5-Dicyanoimidazole(DCI)isanefficientactivator

for use in chemical synthesis of DNA.

N

HN CN

CN

NN

N

HN

S CH2

CH3



Capping Reagents

Foreachsynthesiscycle,upto1to2%offree5’-hydroxygroupsremain

after the phosphoramidite coupling step has been completed. By running

asubsequent„Capping“stepusingananhydride,thesefreehydroxylgroups

are converted to acetates and are hindered from further chain elongation

and formation of long oligonucleotides with incorrect sequences. For optimal

acetylation, a solution of acetic anhydride in THF or acetonitrile (Capping A)

willbemixedinsituduringreactionwithacatalyticactingsolutionof

N-methylimidazole (Capping B). Additives such as pyridine, lutidine or collidine

functionasmildbasestoenhancetheefficiencyofthecappingreaction.

C A P P I N G S O L U T I O N S

BO

O

OP

BO

O

HO

RO

O O

CH3

O

CH3

BO

O

OP

BO

O

O

RO

H3CO

capping solution


Capping A



NC-0701Capping A (THF / lutidine / acetic anhydride,

V / V / V = 80 / 10 / 10)100 mL to 200 L

NC-0702Capping A (THF / acetic anhydride,

V/V=90/10)100 mL to 200 L

NC-0703Capping A (acetonitrile / lutidine /

acetic anhydride, V / V / V = 80 / 10 / 10)100 mL to 200 L

NC-0704Capping A (acetonitrile / acetic anhydride,

V/V=90/10)100 mL to 200 L

NC-0705Capping A (20 % N-methylimidazole

in acetonitrile, for ÄKTA oligopilot™)100 mL to 200 L

NC-0706Capping A (THF / pyridine / acetic anhydride,

V / V / V = 80 / 10 / 10)100 mL to 200 L

NC-0707Capping A Ultramild (THF / pyridine /

phenoxyaceticanhydride,(V/V/V=85/10/5)100 mL to 200 L



Capping B



NC-0801 Capping B (16 % N-methylimidazole in THF) 100 mL to 200 L

NC-0802 Capping B (10 % N-methylimidazole in THF) 100 mL to 200 L

NC-0803Capping B (10 % N-methylimidazole in THF /

pyridine, V / V = 80 / 10)100 mL to 200 L

NC-0804Capping B (10 % N-methylimidazole

in acetonitrile / pyridine, V / V = 80 / 10)100 mL to 200 L

NC-0805 Capping B (6,5 % DMAP in THF) 100 mL to 200 L

NC-0806Capping B1 (40 % acetic anhydride

in acetonitrile, for ÄKTA oligopilot™)100 mL to 200 L

NC-0807Capping B2 (60 % lutidine in acetonitrile,

for ÄKTA oligopilot™)100 mL to 200 L



OxidationOxidizersolutionspromotetheoxidationoftrivalentphosphotriesterintopentavalent

phosphatetriesterusingiodineasamildoxidizingagent.Theyareavailableinstandard0.02M

or0.05MiodineconcentrationswithdifferentmixturesofTHF,pyridineandwater.Custom

mixturesarealsoavailable.TheHyacinthOxidizersolution[0.05Miodineinpyridine/water

(V/V=90/10)]isapplicableforthesynthesesofhighquality,large-scaleoligonucleotides.

O X I D I Z E R S O L U T I O N S

BO

O

OP

I2

BO

O

ODMTr

RO

BO

O

OP

BO

O

ODMTr

OR

O


NC-05010.1 M Iodine in THF / pyridine / water

(V / V / V = 78 / 20 / 2)100 mL to 200 L

NC-0502HyacinthOxidizer

0.05Miodineinpyridine/water(V/V=90/10)100 mL to 200 L


(V / V / V = 66 / 22 / 12)100 mL to 200 L


(V/V/V=90.6/0.4/9)100 mL to 200 L

NC-05050.01 M Iodine in acetonitrile / pyridine / water

(V / V / V = 64 / 6 / 30)100 mL to 200 L


(V/V/V=89.6/0.4/10)100 mL to 200 L


(V / V / V = 70 / 20 / 10)100 mL to 200 L

oxidizersolution



Cleavage & DeprotectionCleavage of the oligonucleotide from its solid support and subsequent removal of

all protecting groups from the nucleobases and phosphates close the cycle of automated

oligonucleotide synthesis and bring it to completion. For this purpose, three different

Cleavage solutions from emp BIOTECH are available. The correct choice will depend on

your requirements for standard, fast or mild cleavage conditions.

C L E AVA G E S O L U T I O N S


NC-0901 Ammoniumhydroxide,concentrated(≥ 28 %) 100 mL to 200 L

NC-0902AMA (conc. ammonia /

40 % aqueous methylamine, V / V = 1 / 1)100 mL to 200 L

NC-0903 0.05 M potassium carbonate in dry methanol 100 mL to 200 L

Standard: Usageofonevolumeofconc.ammoniumhydroxide(≥ 28 %) under sealed

conditions appropriate for removal of the protecting groups an the nucleobases

Fast: Usage of one volume of AMA under sealed conditions at 65 °C for 10 min

Mild: VersionA–Usageofonevolumeofconc.ammoniumhydroxide(≥ 28 %)

under sealed conditions for 8 h at room temperature

Version B – Cleavage from the support with 0.05 M potassium carbonate

in methanol for 30 min at room temperature; following removal of the

protecting groups under sealed conditions over night at room temperature

BO

O

OP

O

O

O

O

O

B

NC

BO

OH

OP

O

O

O

O

O

B

P

cleavage solution



Solvents

Molecular Sieves

S O LV E N T S , M O L E C U L A R S I E V E S A N D O T H E R R E A G E N T S


NC-0601 Methylene chloride (Water content < 12 ppm) 100 mL to 200 L

NC-0602 Acetonitrile (Water content < 20 ppm) 100 mL to 200 L

NC-0603 Ethylacetate(Watercontent<20ppm) 100 mL to 200 L

NC-0604 Pyridine (Water content < 30 ppm) 100 mL to 200 L

NC-0605 Toluene (Water content < 20 ppm) 100 mL to 200 L

NC-060610 % Tetrahydrofurane in acetonitrile

(Water content < 20 ppm)100 mL to 200 L

NC-0609 Acetonitrile (Water content < 10 ppm) 100 mL to 200 L


HR-0101-E100.0-001Molecular Sieves, spheres, 2.5-5.0 mm,

3Å pore size, dust reduced100 g


3Å pore size, dust reduced500 g

HR-0101-F001.0-001Molecular Sieves, spheres, 2.5-5.0 mm,

3Å pore size, dust reduced1 kg


3Å pore size100 g


3Å pore size500 g

HR-0102-F001.0-001Molecular Sieves, spheres, 2.5-5.0 mm,

3Å pore size1 kg



EZ Dry Moisture Traps•Formaintainingwater-freeconditionsinanhydroussolventsandreagents

•Forremovalofwaterfromsolvents



HR-0103-Z005.0-001 EZDryMiniMoistureTrap,activatedmolecular

sieve sachets. For volumes up to 100 mL.

Smallest bottleneck: 12mm.

5 packs

HR-0103-Z010.0-001 10 packs

HR-0104-Z005.0-001 EZDry1LMoistureTrap,activatedmolecular

sieve sachets. For volumes up to 1000 mL.


5 packs

HR-0104-Z010.0-001 10 packs

HR-0105-Z005.0-001 EZDry2.5LMoistureTrap,activatedmolecular

sieve sachets. For volumes up to 2.5 L.


5 packs

HR-0105-Z010.0-001 10 packs


sieve sachets. For volumes up to 4 L.


5 packs

HR-0106-Z010.0-001 10 packs


sieve sachets. For volumes up to 20 L.


5 packs

HR-0107-Z010.0-001 10 packs

EZDryMoistureTrapsareusedforefficientremovalofwaterfromsolventsandreagents.

The traps will maintain anhydrous conditions of 30 ppm or less while resisting increases in

water content due to routine or repeated opening of reagent containers.

EZDryMoistureTrapsensureyourphosphoramiditeandactivatorsolutionsremaindryand

water-freefromthefirstdaytothelastdayofuse.EachEZDRYbatchistestedaccordingto

strictqualityassurancespecifications.Thisenablesoptimalcouplingconditionsandhighquality

nucleic acids.

EZDryMoistureTrapsarevacuumsealed,fullyactivated,andready-to-use.Thepouchmaterialis

inert to acetonitrile, pyridine and toluene. Five sizes are available for any bottle size and volume.



CE-ß-Elimination



NC-030220 % Diethylamine in acetonitrile

(water content < 20 ppm)100 mL to 200 L

NC-030320 % t-Butylamine in acetonitrile

(water content < 20 ppm)100 mL to 200 L

Alkylation of the N3-position of thymidine by acrylnitrile, which is liberated during

ß-elimination of the cyanoethyl group from the phosphates, is a well-known side

reaction during simultaneous cleavage of the protecting groups and the oligonucleotide

from the support.

This side reaction can be avoided by use of diethylamine in acetonitrile for the

ß-elimination. The oligonucleotide is subsequently cleaved from the support using

any standard cleavage conditions.

BO

O

OP

O

O

O

O

O

NH

N

O

O

NC

BO

O

OP

O

O

O

O

O

N

N

O

O

CN

conc. NH3

CN



Sulphurizing Reagent



NC-0304-E005.0-001 Phenylacetyldisulfide(PADS),solid 5 g

NC-0304-E025.0-001 Phenylacetyldisulfide(PADS),solid 25 g

The phosphite triester formed in the coupling step can be converted

to the corresponding phosphorothioate triester by treatment with 0.2 M solution

ofphenylacetyldisulfide(PADS)inacetonitrileand3-picoline(1:1=V:V).

Typically, a 1.5-column volume of PADS solution is used, and sulphurization

iscompletewithin3minutes,atwhichtimeexcessreagentisrecoveredfrom

the reaction vessel by washing with acetonitrile.

BO

O

OP

BO

O

ODMTr

RO

BO

O

OP

BO

O

ODMTr

OR

S

PADS solution



Gel Filtration – Columns

P U R I F I C AT I O N


CP-0109-Z002.0-001 CentriPure N2 Columns 2 columns








CP-0112-Z001.0-001 CentriPure N50 Columns 1 column


CP-0118-Z001.0-001 CentriPure N100 Columns 1 column


Simple,fastandreliable.CentriPurecolumnsareusedfordesaltingandpurification

of oligonucleotides (≥10 bp) after removal of protecting groups or after post-synthetic

labeling reactions. CentriPure is available for a variety of sample volumes. The columns

arereadytouseandpackedwithapre-swollenmatrixcontainingKathon™CGas

preservative.



Gel Filtration – Zetadex Desalting Resin

P U R I F I C AT I O N


TM-0101-E100.0-001 Zetadex-25Superfine 100 g


TM-0101-F001.0-001 Zetadex-25Superfine 1 kg

TM-0102-E100.0-001 Zetadex-25Fine 100 g


TM-0102-F001.0-001 Zetadex-25Fine 1 kg

TM-0103-E100.0-001 Zetadex-25Medium 100 g


TM-0103-F001.0-001 Zetadex-25Medium 1 kg



TM-0104-F001.0-001 Zetadex-50Superfine 1 kg



TM-0105-F001.0-001 Zetadex-50Fine 1 kg



TM-0106-F001.0-001 Zetadex-50Medium 1 kg



Amidite Fluorophores and Labels

R E D O X L A B E L S

TAMRA-DMTr-phosphoramidite is used

for convenient covalent labeling of nucleic

acids at the 5‘- or 3‘-end as well as at any

desired position during automated chemical

synthesis of oligonucleotides. Due to the

presence of the DMTr group, TAMRA-DMTr-

phosphoramidite is readily soluble in

acetonitrile and can be used in standard

oligonucleotide synthesis coupling protocols.

TAMRAhasahighextinctioncoefficient

andanexcellentfluorescentquantumyield.

For this reason, dual-labeled TAMRA/Fluorescein

oligonucleotides are commonly used as probes

with Real-Time-PCR devices.

When using TAMRA-DMTr-phosphoramidite,

deprotectionconditionsareMILDERthan

standard conditions and should be selected

for use from the following list:

PAC-protection:

•4hoursconc.ammoniaatroomtemperature

•90minAMA(conc.ammonia:methylamine=1:1)atroomtemperature

•3hourst-butylamine:methanol:water=1:1:2at90°C

•4hours0.05Mpotassiumcarbonateindrymethanolatroomtemperature

Standard-protection:

•20hourst-butylamine:water=1:3at65°C

Standardprocedurescanbeusedifadditionalpurificationisrequired.

P

O

NO

NH

CN

DMTrO

ON

COO

N

OC

CH3

CH3

H3C

H3C


Amidite Fluorophores and Labels


PF-0102-C100.0-001

5-Carboxytetramethylrhodamine

DMTr-CE-phosphoramidite

(5-TAMRA-DMTr-phosphoramidite)

100 μmol

PF-0102-D250.0-001

5-Carboxytetramethylrhodamine



250 mg

PF-0103-C100.0-001

6-Carboxytetramethyl-rhodamine



100 μmol

PF-0103-D250.0-001

6-Carboxytetramethyl-rhodamine



250 mg

PF-0104-C100.0-0016-Carboxyfluorescein-dipivaloylCE-phosphoramidite

(6-FAM-phosphoramidite)100 μmol

PF-0104-D250.0-0016-Carboxyfluorescein-dipivaloylCE-phosphoramidite

(6-FAM-phosphoramidite)250 mg

PF-0104-E001.0-0016-Carboxyfluorescein-dipivaloylCE-phosphoramidite

(6-FAM-phosphoramidite)1 g


PF-0301-C100.0-001 Dabcyl-5'-phosphoramidite 100 μmol

PF-0301-D250.0-001 Dabcyl-5'-phosphoramidite 250 mg

PF-0302-C100.0-001 Dabcyl-3'-phosphoramidite 100 μmol

PF-0302-D250.0-001 Dabcyl-3'-phosphoramidite 250 mg




Fluorophore Activated Esters


AF-0401 MANT-NHSester Exc.:325nm Em.:412nm 5 mg to 100 g

AF-0105 5-FAM-NHSester Exc.:496nm Em.:519nm 5 mg to 1 kg

AF-0106 6-FAM-NHSester Exc.:497nm Em.:519nm 5 mg to 1 kg

AF-0107 5-TAMRA-NHSester Exc.:550nm Em.:575nm 5 mg to 1 kg

AF-0108 6-TAMRA-NHSester Exc.:549nm Em.:572nm 5 mg to 1 kg

AF-0110 6-ROX-NHSester Exc.:587nm Em.:599nm 5 mg to 1 kg

Amino-functionalized oligonucleotides react with succinimidyl ester activated dyes

to form conjugates having stable amide bonds.

TECHNICALNOTE:Beforestartingthecouplingreaction,theoligonucleotidemustbe

lyophilized once with 0.1 M sodium bicarbonate in order to remove residue ammonia ions!

BO

O

OPO

O-

O

NH

(CH2)6

BO

O

OPO

O-

BO

OH

OPO

O-

n

BO

O

OPO

O-

O

H2N (CH2)6

BO

O

OPO

O-

BO

OH

OPO

O-

n

+

OO OH

ClCl

O OH3C CH3

HOOC

O

O

N

O

O

OO OH

ClCl

O OH3C CH3

HOOC

O



32

BiosensoricFor electrochemical applications, emp BIOTECH now offers a wide variety

ofElectroActivebiosensorsforlabelingofbiomolecules,specificallynucleicacids,

toformlabeledprobesequippedwithredox-activereportergroups.

Pro

du

ctC

od

e

Cla

ss o

fR

edo

x La

bel

Elec

tro

de*

Pote

nti

al E

f (V

) vs

. A

g/A

gC

l (1M

KC

l)

Peak

Sep

arat

ion

∆

Ep (

mV

) [∪

= 0

.1 V

/s]

Stab

ility

of

Elec

tro

chem

istr

y[2

0 C

ycle

s]

Cyclic Voltamogram Au Electrode (black) Au-dsDNA-Electrode (blue)

AF-0405 Quinone

Au - 0.425 68 stable

Au-dsDNA - 0.428 79 stable

AF-0201 Phenothiazine

Au - 0.216 31 stable


AF-0202 Phenothiazine

Au -0.198 29 stable


AF-0402MetalComplex

Au +0.292 55 stable

Au-dsDNA +0.292 58 stable

AF-0403MetalComplex

Au +0.390 59 stable

Au-dsDNA +0.390 57 stable

*Auelectrode–goldwire;Au-dsDNAelectrode–goldwiremodifiedwithdsDNA(18basepairs)


potential (V, vs. AglAgCl)

curr

ent

(A)


curr

ent

(A)


curr

ent

(A)


curr

ent

(A)


curr

ent

(A)



Biosensoric


AF-0201-D005.0-001 DicarboxymethyleneBlueNHSester(DCMB-SE) 5 mg

AF-0202-D005.0-001 MonocarboxymethyleneBlueNHSester(MCMB-SE) 5 mg

AF-0402-D005.0-001 FerrocenecarboxylicacidNHSester(Ferrocene-SE) 5 mg

AF-0403-D005.0-001Ferrocene-amidopentylcarboxylicacidNHSester

(Ferrocene-C6-SE)5 mg

AF-0405-D005.0-001Anthraquinone-2-amidopentylcarboxylicacid

NHSester(AQI-C6-SE)5 mg

Amino-functionalizedoligonucleotidesarereactedwithsuccinimidylesteractivatedredox

labels to form conjugates having stable amide bonds.

TECHNICALNOTE:Beforestartingthecouplingreaction,theoligonucleotidemustbe

lyophilized once with 0.1 M sodium bicarbonate in order to remove residue ammonia ions!

AdditionalnovelElectroActivebiosensorsarecurrentlyunderdevelopment.


BO

O

OPO

O-

O

HN (CH2)6

BO

O

OPO

O-

BO

OH

OPO

O-

n

BO

O

OPO

O-

O

H2N (CH2)6

BO

O

OPO

O-

BO

OH

OPO

O-

n

+OOCN

O

O

e-

e-O



Packaging Specifications

Glass bottles

•100mLamberglassbottlewith20mmcrimp/septum

•200mLamberglassbottlewith24-405thread




•1LamberglassbottlewithGL45thread

•2.5LamberglassbottlewithGL45thread

•4LamberglassbottlewithGL45thread

•4Lamberglassbottlewith38-430thread

Stainless steel drums

1.4404 (AISI 316L) for corrosive and non-corrosive reagents

withUN1A1W/X2.0/900certification

Drumsize(max.fillingvolume):

•22.4Liters(20Liters)

•33Liters(30Liters)





Threadedconnection:G2Tri-SureClosurewithPTFEseal

Operating pressure: up to 1.5 bar

Any required adapters and connections are available from emp BIOTECH.


Terms and Conditions

For conducting business with emp BIOTECH, please review our general terms and

conditions as listed on our website www.empbiotech.com.

emp BIOTECH GmbH

Robert-Rössle-Str. 10

13125Berlin·Germany

Tel.+49(0)3094892201

Fax+49(0)3094893201

[email protected]

emp BIOTECH isanISO9001:2008certifiedcompany·Registrationnumber011001300789(TÜVRheinland)

We will deliver any requested packing size and / or will customize all packaging

tosuityourspecificapplicationsandrequirements.Ifyoudonotseewhatyouare

looking for, please contact us.

emp BIOTECHSynthesis Reagents36 www.empbiotech.com 10.2

017

PRODUCT OVERVIEW - emp Biotech · 2017. 11. 30. · 4,5-Dicyanoimidazole (DCI) is an efficient...

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Transcript of PRODUCT OVERVIEW - emp Biotech · 2017. 11. 30. · 4,5-Dicyanoimidazole (DCI) is an efficient...