Oligo Synthesis

*: Remember that the scale in nmol does NOT refer to the final yield of the oligo. It refers to the starting material for synthesis. FINAL yield is always measured in OD.

It is not always obvious to determine how many micrograms of oligos you may need for your assays. It is even more complicated to select the right synthesis scale.

How many reactions will I be able to do with 25 nmol PCR primers?

Most PCR reactions use 0.1−0.5 μM primer. Assuming a maximum concentration of 0.5 μM and a reaction volume of 20 μL, each reaction will require 10 pmol oligonucleotide primer.

For a typical 25mer oligonucleotide, 1 OD is equivalent to approximately 4 nmol, or 4000 pmol. Guaranteed yield for a 20 base PCR primer on the 25 nmol scale is 12 nmol.

Therefore, with even the minimum yield from a 25 nmol synthesis, you should be able to perform 1200 PCR reactions.

In summary: minimum guarantee for a 20mer ≈ 12 nmol = 12,000 pmol = 1200 reactions.

 

Competitive Advantages of Our Oligos synthesis

High-Quality: ISO 9001 & ISO 13485 quality certifications, extremely low mutation and low error rates, in accordance with the stringent quality control standards for oligo synthesis.
Good Stability: Unrivaled control of oligo specifications ensures batch-to-batch consistency and traceability.
Highly-Customizable: Flexible synthesis scales are available; four alternative purification options include Desalt, RPC, PAGE, and HPLC.
Technical Support: Professional teams experienced in oligo synthesis and various modifications offer support throughout the entire production progress.
Cost-Effective: Competitive prices and affordable services.

1. Unmodified DNA Oligo synthesis:

Oligo Length
Purification
Amount(OD)

 

15-59 bp

 

RPC

1-5 OD

6-10 OD

11-20 OD

>20 OD

 

PAGE

1-5 OD

6-10 OD

11-20 DO

>20 OD

HPLC

1-2 OD

2. Unmodified DNA Oligo synthesis:

Oligo Length

Purification

Amount(OD)

 

61-90 bp

 

PAGE

1-2 OD

3-5 OD

6-10 OD

11-20 OD

 

91-120 bp

 

PAGE

1 OD

2 OD

>2 OD

121-150 bp

PAGE

1 OD

OD and nmol:

Purification

50 nmol

100 nmol

200 nmol

1 µmol

5 µmol

10 µmol

Desalt

3 OD

6 OD

10 OD

45 OD

200 OD

400 OD

RPC

2 OD

5 OD

8 OD

45 OD

200 OD

400 OD

PAGE

1 OD

2 OD

3 OD

10 OD

45 OD

100 OD

HPLC

1 OD

2 OD

4 OD

20 OD

100 OD

200 OD

Custom DNA Oligos Modifications

Below Scales are available:

2 OD

5 OD

10 OD

20 OD

Fluorescent Dyes Labels

The most important fluorescent compounds used to label oligonucleotides are fluorescein and various fluorescein analogs. Fluorescein is a multi-ring aromatic compound that is strongly fluorescent.

* The fluorescent color was calculated with the maximum emission wavelength, for your reference only.

Label Name
Purifications
Positions
Excitation
Maximum (nm)
Emission
Maximum (nm)

Cy3

HPLC

5′, 3’End

549

566

Cy5

HPLC

5′, 3’End

646

669

FAM

HPLC

5′, 3’End

495

520

HEX

HPLC

5’End

535

556

TET

HPLC

5’End

521

536

FITC

HPLC

5′, 3’End

492

515

6-JOE

HPLC

5′, 3’End

529

555

ROX

HPLC

5′, 3’End

586

610

TAMRA

HPLC

5′, 3’End

557

583

Helix Fluor555

HPLC

5′, 3’End

542

558

Helix Fluor575

HPLC

5′, 3’End

546

575

Texas Red

HPLC

5′, 3’End

588

601

Quasar 570

HPLC

5′, 3’End

548

566

Quasar 670

HPLC

5′, 3’End

647

670

Cy3.5

HPLC

5′, 3’End

581

596

Cy5.5NS

HPLC

5′, 3’End

678

701

Cy7NS

HPLC

5′, 3’End

750

780

CAL Fluor Red 590

HPLC

5′, 3’End

569

591

CAL Fluor Red 610

HPLC

5′, 3’End

590

610

DABCYL

HPLC

5′, 3’End

453

0

AMCA

HPLC

5′, 3’End

353

455

DEAC

HPLC

5′, 3’End

411

471

MCA

HPLC

5′, 3’End

322

390

LRB Red

HPLC

5′, 3’End

568

583

CR6G

HPLC

5′, 3’End

524

556

Bodi Fluor R6G

HPLC

5′, 3’End

528

547

NBD-X

HPLC

5′, 3’End

467

539

California Red

HPLC

5′, 3’End

583

603

iFluor™ 647

HPLC

5′, 3’End

649

664

iFluor™ 660

HPLC

5′, 3’End

662

678

iFluor™ 680

HPLC

5′, 3’End

676

695

iFluor™ 700

HPLC

5′, 3’End

685

710

iFluor™ 710

HPLC

5′, 3’End

712

736

iFluor™ 750

HPLC

5′, 3’End

749

775

iFluor™ 800

HPLC

5′, 3’End

801

820

VIC

HPLC

5’End

538

554

LC RED-610

HPLC

3’End

590

610

LC RED-640

HPLC

3’End

625

640

LC RED-705

HPLC

3’End

685

705

Bodipy 493/503

HPLC

3’End

493

503

Bodipy 564/570

HPLC

3’End

564

570

Bodipy 581/591

HPLC

3’End

581

591

Bodipy 630/650

HPLC

3’End

630

650

Bodipy 650/665

HPLC

3’End

650

665

BODIPY R6G

HPLC

3’End

528

547

SIMA

HPLC

5’End

533

557

Yakima Yellow Epoch

HPLC

5′, 3’End

530

549

Dual Labels

Dual-labeled fluorescent probes typically contain a 5′ fluorophore and a 3′ quencher. The probes are often designed to anneal between the upstream and the downstream primer in a PCR reaction. These are commonly used with quantitative PCR, mutation detection, allele determination, and SNP detection.

Label Name

Purifications

Positions

5’FAM-3’TAMRA

HPLC

5′, 3’End

5’HEX-3’TAMRA

HPLC

5′, 3’End

5’TET-3’TAMRA

HPLC

5′, 3’End

5’JOE-3’TAMRA

HPLC

5′, 3’End

5’VIC-3’TAMRA

HPLC

5′, 3’End

5’FAM-3’BHQ1

HPLC

5′, 3’End

5’VIC-3’BHQ1

HPLC

5′, 3’End

5’HEX-3’BHQ1

HPLC

5′, 3’End

5’JOE-3’BHQ1

HPLC

5′, 3’End

5’TET-3’BHQ-1

HPLC

5′, 3’End

5’Cy5-3’BHQ2

HPLC

5′, 3’End

5’Cy3-3’BHQ2

HPLC

5′, 3’End

5’ROX-3’BHQ2

HPLC

5′, 3’End

5’TET-3’BHQ2

HPLC

5′, 3’End

5’JOE-3’BHQ2

HPLC

5′, 3’End

5’HEX-3’BHQ2

HPLC

5′, 3’End

5’TAMRA-3’BHQ2

HPLC

5′, 3’End

5’Texas Red-3’BHQ2

HPLC

5′, 3’End

5’Quasar 670-3’BHQ2

HPLC

5′, 3’End

5′-FAM and 3′-BHQ2

HPLC

5′, 3’End

5’Quasar 670-3’BHQ3

HPLC

5′, 3’End

5’CY5-3’BHQ3

HPLC

5′, 3’End

5’FAM-3’ECLIPS

HPLC

5′, 3’End

5’HEX-3′ ECLIPS

HPLC

5′, 3’End

5’TAMRA-3’Eclipse

HPLC

5′, 3’End

5’ROX-3’Eclipse

HPLC

5′, 3’End

5’TET-3’Eclipse

HPLC

5′, 3’End

5’JOE-3’Eclipse

HPLC

5′, 3’End

5’FAM-3’MGB

HPLC

5′, 3’End

5’HEX-3’MGB

HPLC

5′, 3’End

5’TET-3’MGB

HPLC

5′, 3’End

5’JOE-3’MGB

HPLC

5′, 3’End

5’ROX-3’MGB

HPLC

5′, 3’End

5’Texas Red-3’MGB

HPLC

5′, 3’End

5’Quasar 670-3’MGB

HPLC

5′, 3’End

5’VIC-3’MGB

HPLC

5′, 3’End

5’FAM-3’DABCYL

HPLC

5′, 3’End

5’HEX-3’DABCYL

HPLC

5′, 3’End

5’TET-3’DABCYL

HPLC

5′, 3’End

5’JOE-3’DABCYL

HPLC

5′, 3’End

5’TAMRA-3’DABCYL

HPLC

5′, 3’End

5’Texas Red-3’Dabcyl

HPLC

5′, 3’End

5’ROX-3’Dabcyl

HPLC

5′, 3’End

5’CY3-3’DABCYL

HPLC

5′, 3’End

5’Cy5-3’DABCYL

HPLC

5′, 3’End

5’Phos and 3’FAM

HPLC

5′, 3’End

5’TAMRA and 3’Phos

HPLC

5′, 3’End

5’C6-Biotin,3’Biotin

HPLC

5′, 3’End

5’C6-Biotin,3’Cy5

HPLC

5′, 3’End

5’C6-NH2,3’C3-Fam

HPLC

5′, 3’End

5’C6-NH2,3’Cy3

HPLC

5′, 3’End

5’Cy5,SS,

HPLC

5′, 3’End

5’Cy5,3’C7-NH2

HPLC

5′, 3’End

5’Cy5,3’SH

HPLC

5′, 3’End

5’Dabcyl,3’C3-Fam

HPLC

5′, 3’End

5’DlG,3’Digoxin

HPLC

5′, 3’End

5’SH,3’Cy3

HPLC

5′, 3’End

5’Fam,3’C3-Fam

HPLC

5′, 3’End

5’TAMRA,3’C3-Fam

HPLC

5′, 3’End

Quenchers:

FRET quenching depends on the ability of the fluorophore to transfer energy to the quencher. For this to happen, the emission spectrum of the fluorophore must overlap with the absorption spectrum of the quencher. For a quencher to quench fluorescence from several different fluorophores, it must therefore have a wide absorption spectrum and a high extinction coefficient.

Label Name

Purifications

Positions

DABCYL

HPLC

3’End

TAMRA

HPLC

3’End

BHQ 1

HPLC

3’End

BHQ 2

HPLC

3’End

BHQ 3

HPLC

3’End

MGB

HPLC

3’End

BBQ-650

HPLC

3’End

TQ1

HPLC

3’End

TQ2

HPLC

3’End

TQ3

HPLC

3’End

TQ4

HPLC

3’End

TQ5

HPLC

3’End

TQ6

HPLC

3’End

QSY 7 carboxylic acid

HPLC

3’End

TQ7

HPLC

3’End

Affinity Ligands:

Oligo nucleotides can be labeled with biotin or digoxigenin or directly labeled with alkaline phosphatase. A variety of linker arms are available as spacers to minimize steric hindrance.

Label Name

Purifications

Positions

Biotin dT

HPLC

5′, 3’End, Internal

Biotin

HPLC

5′, 3’End, Internal

Biotin-TEG

HPLC

5′, 3’End, Internal

DIG

HPLC

5′, 3’End

Spacers:

Spacer modifications C3, 9, C12 and 18 are used to insert a spacer arm in an oligonucleotide. These modifications can be added in multiple additions when a longer spacer is required.

Label Name

Purifications

Positions

Spacer C6

HPLC

5′, 3’End, Internal

Spacer 9

HPLC

5′, 3’End, Internal

Spacer C12

HPLC

5′, 3’End, Internal

Spacer C3

HPLC

5′, 3’End, Internal

Spacer C18

HPLC

5′, 3’End, Internal

D Spacer

HPLC

5′, 3’End, Internal

Attachment moieties:

A primary amino group or a thiol group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface.

Label Name

Purifications

Positions

5’-Amino-Modifier-C6

HPLC

5’End

3’-Amino-Modifier-C7

HPLC

3’End

5’-Amino-Modifier-C12

HPLC

5’End

Thiol-Modifier C6 S-S

HPLC

5′, 3’End, Internal

Thiol-Modifier-C3 S-S

HPLC

5′, 3’End, Internal

TM increase

The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases. Slight variations in the DNA sequence can have profound implications on the stability of the DNA duplex.

Label Name

Purifications

Positions

2’ OMe-rA

PAGE

5′, 3’End, Internal

2’ OMe-rC

PAGE

5′, 3’End, Internal

2’ OMe-rG

PAGE

5′, 3’End, Internal

2’ OMe-rU

PAGE

5′, 3’End, Internal