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Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l www.genelink.com QUALITY CONSISTENCY CONFIDENCE Gene Link oligos are for demanding applications and consistent results. We believe that investigators who value time and have no room for an experiment to fail due to oligo quality should consider Gene Link. Our numerous quality control steps for each oligo assure confidence. An actual gel photo of each oligo is affixed on the oligo report. An absolute testimony of quality. Gene Link has raised the standard since inception over a decade ago. We have the pictures to prove it! Actual Gel Photo GOLD STANDARD

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Page 1: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

P r e m i u m O l i go nuc l e o t i de S y n t he s i s

1 Gene Link l 1-800-GENE LINK l www.genelink.com

QUALITY • CONSISTENCY • CONFIDENCE

Gene Link oligos are for demanding applications

and consistent results. We believe that investigators who

value time and have no room for an experiment to fail due to

oligo quality should consider Gene Link. Our numerous

quality control steps for each oligo assure confidence.

An actual gel photo of each oligo

is affixed on the oligo report. An

absolute testimony of quality.

Gene Link has raised the standard

since inception over a decade ago.

We have the pictures to prove it!

Actual Gel Photo

G O L D STAN D A R D

Page 2: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

G O L D STAN D A R D

Gene Link l 1-800-GENE LINK l www.genelink.com 2

The Gene Link Advantagen Stringent Quality Control

Measures

n Specializing in Long Oligos up to 250 mer

n Trityl Monitoring of All Oligos

n Polyacrylamide Gel Photograph of Each Oligo

n All Modifications Available

n All Oligo Types Available

n Easy Online Ordering System

n Online Design and Analysis Tools

n Knowledgeable Technical Support

n Personalized, Friendly Customer Service

250

100%

100%

100%

Oligo size

Yiel

dYi

eld

Yiel

d

Coupling efficiency 99.50%

Coupling efficiency 99.00%

Coupling efficiency 98.00%

Coupling Efficiency and Full Length Oligo Yield

Oligo Size 99.50% 99.00% 98.00%

20 90.916 82.617 68.12340 82.243 67.573 45.4860 74.398 55.268 30.36380 67.301 45.204 20.27

100 60.881 36.973 13.533120 55.074 30.24 9.034140 49.821 24.734 6.031160 45.068 20.23 4.027180 40.769 16.546 2.688200 36.88 13.533 1.795220 33.36 11.07 1.19240 30.18 9.05 0.8250 28.7 8.19 0.65

Superior to “Mass-Produced Factory Oligos”Gene Link is not an oligo factory.Each oligo is synthesized, processedand quality assured to Gene Link’sabsolute standards. This includescoupling efficiency monitoring ofeach base during synthesis and electrophoretic analysis of each oligo on a polyacrylamide gel to visually assess quality.

Coupling EfficiencyWe maintain a coupling efficiencythreshold of greater than 99.5% forall oligos by using premium reagentsof exacting specifications, membranesynthesis, state-of-the-art instrumentsand optimized software-driven protocols. This may not be evidentwhen comparing short oligos, asPCR and sequencing reactions arevery robust and can tolerate up to50% failure/truncated sequence oligos. However, you are clearly taking a chance by using long oligossynthesized at anything below99.5% coupling efficiency.

Trityl MonitoringAll Gene Link DNA synthesizers areequipped with trityl monitors formonitoring coupling efficiency ofeach added base. The instrumentsare programmed to halt when it fallsbelow the threshold.

See example of routine trityl bars.

Long Oligos

Ask our competitors how oftenthey synthesize 200 to 250 mer

oligonucleotides. Gene Link specializes in long oligos.

You are invited to compare.

Sequence length

Routine Trityl Coupling Efficiency

Actual trityl coupling efficiency of a 210 mer.

Page 3: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

Oligo Design and Analysis Tools

3 Gene Link l 1-800-GENE LINK l www.genelink.com

Gene Link has been leading theway by providing the most userfriendly online experience inoligo ordering. From oligo designand analysis, to the convenientordering system and the assur-ance of a secured transaction,Gene Link provides the mostcomprehensive web resource inthe industry.

Features include convenientNCBI blasting and secondarystructure analysis, simple importtools for large orders in spread-sheet or text file format, andthree levels of review and editing.

Applications include RNAiExplorer™, a robust siRNAsearch and design tool, and astandalone Oligo Explorer™application for online acquisitionof sequences and oligo design.

Custom Oligo Ordering System• Classic ordering system with

extensive analysis features

• Timesaver multi oligo import fromspreadsheet and text files

• Ability to handle mixed oligo types,purity and modifications in a singleorder

• Selection of oligo type (DNA, RNA,Phosphorothioate, Chimeric, etc.)

• Simple drop down menu selectionfor 5', internal or 3' modifications

• Analyze for oligo hairpin and loops

• Integrates with NCBI Blast forhomology checks

• Flip 3' to 5' and reverse complement

Online Oligo Analysis• Simulate annealing, loops and

hairpin formations

• Calculate MW, EC, Tm, A260, etc.

Too busy to order all of your oligos in

one session? Gene Link’s answer to

the multitasking researcher with end-

less interruptions is the “Save Session“

feature. Enter as many oligos as you

wish, click the “Save Session“ button

and resume at your will. Your oligos

will be saved. What’s more, you'll save

money on shipping by consolidating

your multiple orders into one.

Save Session

Page 4: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

C u s t o mO l i go nuc l e o t i de

S y n t he s i s

Gene Link l 1-800-GENE LINK l www.genelink.com 4

Multiple Oligo NCBI BlastClick to ascertainhomologies to other sequences.

Perform NCBI Blast of multiplesequences at once by using GeneLink’s online MultiBlast application.Import all the sequences using aspreadsheet or a text file. All of yoursequences will be blasted and resultsretrieved. Gene Link offers a veryconvenient approach to perform multiple blast searches.

Molecular BiologyConvenience AppletsGene Link has numerousonline applets for quick calculations. The BioCalculatoris a series of applets for sim-plifying the routine laboratory calculations. Thefollowing convenient calcula-tors are available:

• Oligo Resuspension

• Oligo Dilution

• Oligo Tm

• Reagent Dilution

• Molarity Determination

• Ligation

• Base/Dye Ratio

Oligo Explorer™A PC-based application for standaloneDNA sequence retrieval and oligo design.

Oligo Explorer™ was developed todesign PCR and sequencing primers.Oligo Explorer™ is an efficient easy-to-use tool to determine primer prop-erties like Tm, GC%, primer loops andprimer dimers.

Oligo Explorer™ also includes a pow-erful “Primer Wizard” tool that helpsyou to find suitable primer pairs. Youcan set your own parameters for theprimer pair search engine or use thedefault parameters. “Primer Wizard”suggests primer pairs that amplifyPCR products of the given length.Individual primer pairs are suggestedthat theoretically will not form stableprimer dimers or primer loops.

Page 5: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

Oligo Specifications Report

Custom Oligo SpecificationsGene Link custom oligonucleotidesare supplied desalted and lyophilized.They are ready to use after appropri-ate reconstitution. Dry oligonu-cleotides are stable at roomtemperature for an extended periodof time.

Storage & ReconstitutionThe oligonucleotide should preferablybe frozen upon receipt. TE buffer (10 mM Tris, 1 mM EDTA, pH 7.5) isrecommended for dissolving theoligonucleotides. After reconstitutionstore the stock solution at –80°C or–20°C.

Purity & UsageThe crude, desalted oligonucleotidesupplied is suitable for all amplifica-tion and sequencing protocols. Gelpurification is advised for all oligosused for cloning applications and foroligos longer than 50 mer.

Biophysical DataEach oligo after desalting is quanti-fied by recording A260. Exact nmolsand µg are determined by the extinc-tion coefficient and molecular weightof the oligo.

Gel Photo DocumentationAn actual gel picture of the synthe-sized custom oligonucleotide is supplied. A major single band represents high purity of the crudeoligonucleotide.

5 Gene Link l 1-800-GENE LINK l www.genelink.com

Gene Link’s CustomOligonucleotide SynthesisReport specifies each oligoname and sequence alongwith its pertinent physicalproperties such as MW,%GC, Tm, A260 units, etc.Our report is also unique inthat we affix an actual poly-acrylamide gel electrophore-sis photograph onto eachreport, so that you also mayvisually attest to the qualityof our product.

From your custom oligo tothe presentation of our oligosynthesis report, not a stepof quality is overlooked. Youare invited to compare.

Page 6: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

C u s t o mO l i go nuc l e o t i de

S y n t he s i s

Gene Link l 1-800-GENE LINK l www.genelink.com 6

Unmodified DNA Oligo Synthesis*

Scale of Synthesis Catalog No. Price ($)

50 nmol 26-6400-05 0.90

200 nmol 26-6400-02 2.00

1 µmol 26-6400-01 3.75

2 µmol 26-6400-03 6.50

10 µmol 26-6400-10 32.00

15 µmol 26-6400-15 38.00

*minimum charge for 15 mer applies. Please visit www.genelink.comfor current list prices. Call for institutional discount pricing structure.

Oligo Scale of Synthesis and Typical Yield

Crude Desalted RPC Purified** Gel Purified20 mer oligo* 30 mer oligo* 50 mer oligo*Typical yield Typical yield Typical yield

Scale A260 Units nmols mg A260 Units nmols mg A260 Units nmols mg

50 nmol 8-10 30+ 0.2-0.3 4-5 12+ 0.1-0.16 NR* [1-2] NR* [2-4] NR* [0.03-0.06]

200 nmol 20-25 80+ 0.6-0.8 8-12 24+ 0.26-0.4 4-6 8+ 0.13-0.2

1 µmol 100-120 400+ 3-4 40-50 30+ 1.3-1.6 20-25 40+ 0.6-0.8

Purity & Yield

*Yield of 30 µg/A260 unit for oligos is calculated for an ~equimolar base composition. Long stretches of a single base or homopolymers will have variable yields. Example for homopolymeric 50 mer: A(50) = ~20/A260 Unit; G(50) = ~28/A260 Unit; T(50) = ~35/A260 Unit and C(50) = ~39/A260 Unit.

Purity is greater than 80% depending on oligo sequence andstructure. Refer to coupling efficiencytable for oligo length dependent purityand yield.

No further purification required forPCR and sequencing applications.

Gel purification recommended for oli-gos above 50 mer and all applicationsinvolving cloning and mutagenesis.

Purity 85% to 95% depending on oligo sequence andstructure.

Yield and purity will be lower forsequences with high GC content.

Not recommended for oligos longerthan 35 mer.

**RPC is reverse phase purification using acartridge; a substitute for HPLC.

Purity 98% to ~100% depending on oligo sequence and struc-ture.

Yield will gradually decrease as length ofoligo increases. Palindromes, hairpins andhigh GC content oligos and oligos con-taining stretches of 3 or more G’s inducesstrong secondary structure and basestacking thus decreasing purity and yield.

NR* Not Recommended

Purification

Scale of Synthesis Price ($)/purification

Product Catalog No. 50 nmol 200 nmol 1 µmol 2 µmol 10 µmol 15 µmol

Gel Purification 26-6400-XX 75.00 75.00 150.00 280.00 1500.00 1800.00

Reverse Phase Cartridge 26-6400-XX 30.00 30.00 90.00 170.00 750.00 900.00

Design your oligos today and use them tomorrow

morning! Investigators who just can not wait order

our rush service (order by 12 noon EST). We ship the

same day for next early morning delivery in the US

and 72 hours for most international destinations.

* Turn-around time stated is for unmodified oligos.

Please inquire about purified and modified oligos

Same Day Oligo*

Page 7: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

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Page 8: Premium Oligonucleotide Synthesis - Gene Link · Premium Oligonucleotide Synthesis 1 Gene Link l 1-800-GENE LINK l QUALITY • CONSISTENCY • CONFIDENCE Gene Link oligos are for

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0/A 2

60Un

it;

G(50

)=~2

8/A 2

60Un

it;

T(50

)=~3

5/A 2

60Un

it a

nd C

(50)

=~3

9/A 2

60Un

it.

*** R

PC i

s re

vers

e ph

ase

purif

icat

ion

usin

g a

cart

ridge

; a

subs

titu

te f

or H

PLC.

NR*

Not

Reco

mm

ende

d.Purit

y is

mor

e th

an 8

0% d

epen

ding

on o

ligo

sequ

ence

and

str

uctu

re.

Purit

y 85

% t

o 95

% d

epen

ding

on

olig

ose

quen

ce a

nd s

truc

ture

. No

t re

com

men

ded

for

olig

os lo

nger

tha

n 35

mer

.

Purit

y 98

% t

o ~1

00%

dep

endi

ng o

n ol

igo

sequ

ence

and

str

uctu

re.

Yiel

d w

ill g

radu

ally

decr

ease

as

leng

th o

f ol

igo

incr

ease

s.

Gen

e Li

nk™

Hai

rpin

Loo

p Fo

rmat

ion

and

Prim

er D

esig

n*

Seq

uenc

e5'

-CA

GC

GC

AC

TA

CA

GG

CAT

GA

CG

T-3'

5'-G

TC

CG

CA

CG

TA

CG

GA

CAT

-3'

5'-G

TC

AG

CC

GC

AC

GTA

CG

GA

CAT

-3'

5'-A

GTA

AC

GC

AC

TAC

GG

AC

TTA

CG

AC

-3'

22m

er;

dG=

-47.

5; T

m(N

N)=

61.6

°C18

mer

; dG

=-3

8.4;

Tm

(NN)

:57.

0°C

21m

er;

dG:-

46.3

; Tm

(NN)

:61.

70°C

24m

er;

dG=

-47.

1; T

m(N

N)=

58.8

°C

* Dim

ers

5' C

AG

CG

CA

CT

AC

AG

GC

AT

GA

CG

T3'

5' G

TC

CG

CA

CG

TAC

GG

AC

AT3'

5' G

TC

AG

CC

GC

AC

GTA

CG

GA

CAT

3'5'

AG

TA

AC

GC

AC

TAC

GG

AC

TT

AC

GA

C 3

'|

||

|+

||

||

||

++

||

||

||

+|

| |

|+

++

++

++

+3'

TG

CA

GTA

CG

GA

CA

TC

AC

GC

GA

C 5

'3'

TA

CA

GG

CAT

GC

AC

GC

CT

G 5

'3'

TA

CA

GG

CA

TG

CA

CG

CC

GA

CT

G 5

'

3' C

AG

CA

TT

CA

GG

CA

TC

AC

GC

AA

TG

A5'

STAC

K AT

3 I

S 4

BP L

ONG.

STAC

K AT

8 I

S 6

BP L

ONG.

STAC

K AT

11

IS 6

BP

LONG

.ST

ACK

AT 2

IS

4 BP

LON

G.dG

=-4

.8;

Tm=

-58.

4°C

dG=

-5.7

; Tm

=-4

2.4°

CdG

=-4

.65;

Tm

=-2

8.2°

CdG

=-2.

05;

Tm=-

47.3

°C

Hai

rpin

None

5'G

TC

CG

CA

C5'

GT

CA

GC

CG

CA

C5'

AG

TA

AC

GC

AC

TLo

ops

||

||

|]

| |

|]

||

||

]3'

TAC

AG

GC

ATG

3'TA

CA

GG

CA

TG

3' C

AG

CA

TT

CA

GG

CA

STEM

AT

1 IS

5 B

P LO

NG.

LOOP

=6.

STEM

AT

6 IS

3 B

P LO

NG.

LOOP

=6

STEM

AT

2 IS

4 B

P LO

NG.

LOOP

=12

.dG

=-5

.3;

Tm=

87.3

°CdG

=-2

.4;

Tm=

68.9

°CdG

=0.

8; T

m=

13.8

°C

*Sec

onda

ry s

truc

ture

res

ults

are

tru

ncat

ed t

o sh

ow t

he m

ost

stab

le s

truc

ture

s. A

ll th

erm

odyn

amic

val

ues

incl

udin

g Tm

and

sec

onda

ry s

truc

ture

s ca

lcul

ated

and

dis

play

ed s

olel

y in

dica

te t

he r

elat

ive

stab

ility

of

the

seco

ndar

y st

ruct

ures

. Th

ey s

houl

d on

ly b

e us

ed t

o co

mpa

re t

he r

elat

ive

stab

ility

of

the

stru

ctur

es.

dG v

alue

uni

t is

kca

l/m

ol.

Visi

t w

ww.

gene

link.

com

/too

ls/g

l-SO

D.as

p to

des

ign

olig

os o

r cl

ick

on t

he ‘A

naly

ze’ b

utto

n w

hile

on

the

onlin

e ol

igo

orde

ring

pag

e.

Stor

age

& Re

cons

titu

tion

Th

e ol

igon

ucle

otid

e sh

ould

pre

fera

bly

befr

ozen

upo

n re

ceip

t. T

E bu

ffer

(10

mM

Tris

,1

mM

EDT

A, p

H 7

.5)

is r

ecom

men

ded

for

diss

olvi

ng t

he o

ligon

ucle

otid

es.

Afte

rre

cons

titu

tion

sto

re t

he s

tock

sol

utio

n at

-80

°C o

r -2

0°C.

Gel

Phot

o Do

cum

enta

tion

An a

ctua

l gel

pic

ture

of

the

synt

hesi

zed

cust

om o

ligon

ucle

otid

e is

sup

plie

d. A

maj

or s

ingl

e ba

nd r

epre

sent

s hi

gh p

urit

yof

the

cru

de o

ligon

ucle

otid

e.

Puri

ty &

Usa

geTh

e cr

ude,

des

alte

d ol

igon

ucle

otid

e su

pplie

d is

sui

tabl

e fo

r al

l am

plif

icat

ion

and

sequ

enci

ng p

roto

cols

. Ge

l pur

ific

atio

nis

adv

ised

for

all

olig

os u

sed

for

clon

ing

appl

icat

ions

and

for

olig

os lo

nger

tha

n50

mer

.

Biop

hysi

cal

Data

Each

olig

o af

ter

desa

ltin

g is

qua

ntif

ied

byre

cord

ing

A 260

. Ex

act

nmol

s an

d µg

is

dete

rmin

ed b

y th

e ex

tinc

tion

coe

ffic

ient

an

d m

olec

ular

wei

ght

of t

he o

ligo.

Succ

essf

ul u

se o

f ol

igos

as

prim

ers

for

ampl

ifica

tion

and

sequ

enci

ng s

tart

s w

ith

func

tiona

l prim

er d

esig

n fo

llow

ed b

y op

tim

ized

PCR

am

plifi

catio

n co

ndit

ions

.Fo

rtun

atel

y, b

oth

PCR

and

sequ

enci

ng r

eact

ions

are

in

here

ntly

‘rob

ust’

and

have

bee

n ob

serv

ed t

o to

lera

te w

ide

varia

tions

in q

ualit

y of

prim

ers

whe

n us

ing

uniq

ue t

em-

plat

es.

The

sam

e ‘to

lera

nce’

can

als

o le

ad t

o fa

lse

prim

ing,

poor

res

ults

and

fru

stra

ting

tim

e lo

ss w

ith

tem

plat

es o

fhi

gher

com

plex

ity.

Prim

er s

peci

ficit

y al

one

does

not

gua

rant

ee a

n op

tim

umam

plifi

cati

on y

ield

. Nu

mer

ous

com

pute

r ap

plic

atio

ns a

reav

aila

ble

for

prim

er s

earc

h an

d de

sign

. M

ost

of t

hese

appl

icat

ions

do

not

cons

ider

the

eff

ect

of h

airp

in s

truc

-tu

res

whi

ch t

end

to b

e qu

ite

stab

le t

herm

odyn

amic

ally

.Ge

nera

l gui

delin

es f

or p

rimer

des

ign

are

give

n be

low

fol

-lo

wed

by

a br

ief

acco

unt

of s

tabl

e ha

irpin

str

uctu

re

form

atio

n an

d no

n-W

atso

n-Cr

ick

base

pai

ring

indu

ced

by

a st

retc

h of

G’s

and

G’s

inte

rspe

rsed

wit

h A’

s or

C’s

(1-3

).

Gene

ral G

uide

lines

1. S

peci

fici

ty:

Sele

ct a

n 18

to

24m

er s

tret

ch w

ith

perf

ect

spec

ifici

ty.

2. B

ase

Com

posi

tion

:Pr

efer

ably

mai

ntai

n GC

con

tent

bel

ow60

% w

ith

no s

tret

ches

of

mor

e th

an 3

G’s

or 4

run

s of

the

sam

e ba

se.

3. T

m:

Sele

ct p

rimer

Tm

wit

hin

a fe

w d

egre

es o

f th

e pa

ir.

4. C

ross

Hom

olog

ies:

Perf

orm

NCB

I bl

ast

to d

eter

min

eex

tent

of

cros

s ho

mol

ogie

s.

5. S

econ

dary

Str

uctu

re:

Perf

orm

com

pute

r as

sist

ed a

naly

sis

to v

iew

for

mat

ion

of s

tabl

e di

mer

s, lo

ops

and

hairp

ins.

Prim

er D

esig

n