Duplex Stability - Introduction

Introduction to Duplex Stability

Duplex Stability Applications

Duplex Stability Design/Protocol

Duplex Stability Literature

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Introduction to Duplex Stability

Many molecular biology applications require oligonucleotide primers and/or probes with enhanced duplex stability, that is, a higher affinity for their complementary sequences. Examples include antisense, siRNA, and SNP detection experiments. For these and other applications, enhancing primer/probe-target duplex stability increases both the selectivity and sensitivity of the oligo for its target. An oligo's binding affinity for its target can be manipulated by incorporating various modifications into it, either on the ends or at an internal position (1). Examples include 2'-OMethyl base, 2-Amino-dA, 5-methyl-dC and 2'-Fluoro bases. Changes in duplex stability incurring from such modifications is indicated by changes in the melting temperature (Tm) of the duplex formed between the modified oligo and its target over that formed by the unmodified oligo. Depending on the modification, Tm can be increased over a range of 0.5C to 3.0C per base substitution.

Duplex Stability Modifications						View PDF	Excel Mods & Code List
Product	Code	Catalog No.	50 nmol scale (XX=05)	200 nmol scale (XX=02)	1 mmol scale (XX=01)	2 mmol scale (XX=03)	10 mmol scale (XX=10)	15 mmol scale (XX=15)
2'-Fluoro deoxyadenosine (2'-F-A)	[fA]	26-6692	$42.00	$42.00	$50.00	$70.00	$265.00	$340.00
2'-Fluoro deoxycytosine (2'-F-C)	[fC]	26-6463	$27.00	$27.00	$39.00	$49.00	$214.00	$321.00
2'-Fluoro deoxyguanosine (2'-F-G)	[fG]	26-6693	$42.00	$42.00	$50.00	$70.00	$265.00	$340.00
2'-Fluoro deoxyuridine (2'-F-U)	[fU]	26-6462	$27.00	$27.00	$39.00	$49.00	$214.00	$321.00
2'-O methyl adenosine A	[mA]	27-6410A	$9.72	$9.72	$19.00	$30.00	$110.00	$160.00
2'-O methyl cytosine C	[mC]	27-6410C	$9.72	$9.72	$19.00	$30.00	$110.00	$160.00
2'-O methyl guanosine G	[mG]	27-6410G	$8.64	$9.72	$19.00	$30.00	$110.00	$160.00
2'-O methyl uridine U	[mU]	27-6410U	$9.72	$9.72	$19.00	$30.00	$110.00	$160.00
2-Amino dA	[Am-dA]	26-6525	$176.00	$176.00	$228.00	$342.00	$1,825.00	$2,282.00
5-Carboxy dC	[5-ca-dC]	26-6891	$594.00	$594.00	$772.00	$1,158.00	$5,728.00	$7,160.00
5-methyl deoxycytosine [5mdC]	[5mdC]	26-6413	$67.00	$67.00	$82.00	$145.00	$473.00	$629.00
Anthraquinone-C2-dT	[AQ-dT]	26-6613	$1,064.00	$1,064.00	$1,307.00	$1,474.00	$9,521.00	$13,068.00
AP-dC G-Clamp (Aminoethyl-Phenoxazine-dC (AP-dC))	[AP-dC]	26-6920	$497.00	$497.00	$969.00	$969.00	$5,167.00	$6,458.00
d5SICS	[d5SICS]	26-6562	$1,588.00	$1,588.00	$1,804.00	$2,707.00	$14,435.00	$18,044.00
dDs (7-(2-thienyl)-imidazo[4,5-b]pyridine)	[dDs]	26-6565	$265.00	$265.00	$335.00	$427.00	$2,117.00	$2,647.00
dDss	[dDss]	26-6566	$0.00	$0.00	$0.00	$0.00	$0.00	$0.00
dNaM	[dNaM]	26-6561	$782.00	$782.00	$874.00	$1,311.00	$6,992.00	$8,740.00
dPa pyrrole-2-carbaldehyde (Pa)	[dPa]	26-6564	$183.00	$183.00	$237.00	$356.00	$1,898.00	$2,373.00
Locked Analog A (LNA-A)	[+A]	26-6517	$41.00	$41.00	$49.00	$81.00	$340.00	$443.00
Locked Analog G (LNA-G)	[+G]	26-6518	$41.00	$41.00	$49.00	$81.00	$340.00	$443.00
Locked Analog mC (LNA-mC)	[+mC]	26-6519	$41.00	$41.00	$49.00	$81.00	$340.00	$443.00
Locked Analog T (LNA-T)	[+T]	26-6520	$41.00	$41.00	$49.00	$81.00	$340.00	$443.00
MGB 3' CDPI3	[MGB-CDPI3-3]	26-6456	$348.00	$348.00	$443.00	$589.00	$1,782.00	$2,145.00
MGB-5' CDPI3	[MGB-CDPI3-5]	26-6457	$880.00	$880.00	$1,782.00	$1,901.00	$8,532.00	$10,260.00
N4-Ethyl dC [N4-Et-dC]	[N4-Et-dC]	26-6685	$378.00	$378.00	$459.00	$688.00	$3,672.00	$4,590.00
N6-Methyl dA (m6dA)	[m6dA]	26-6601	$345.00	$345.00	$415.00	$535.00	$1,825.00	$2,282.00
propyne dC	[pdC]	26-6501	$140.00	$140.00	$216.00	$286.00	$1,728.00	$2,160.00
propyne dU	[pdU]	26-6502	$105.00	$105.00	$137.00	$205.00	$1,095.00	$1,369.00
5'-Pyrene Cap (5')	[Pyr-Cap]	26-6949	$274.00	$274.00	$356.00	$534.00	$2,847.00	$3,559.00
Spermine Oligo Cationic Tail (ZNA-Oligos)	[Spm]	26-6454	$350.00	$350.00	$455.00	$682.00	$3,639.00	$4,549.00
Stilbene Cap: Trimethoxystilbene Cap (5')	[Stb-Cap]	26-6989	$274.00	$274.00	$356.00	$534.00	$2,847.00	$3,559.00
2-Thio-dT (S2dT)	[S2dT]	26-6537	$382.00	$382.00	$497.00	$746.00	$3,976.00	$4,970.00
Uaq Cap (3')	[Uaq-Cap]	26-6950	$253.00	$253.00	$329.00	$493.00	$2,628.00	$3,285.00

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Duplex Stability - Introduction

Introduction to Duplex Stability

Duplex Stability Modifications