Definitions and Physical Models
Complement
The complementary sequence to the entered oligonucleotide, which is shown in 5' to 3' orientation and in DNA format. Modifications are ignored when the complementary base is determined. However, for modifications that are native base analogs, the complementary base is the native base. Complementary base to inosine is cytosine.
GC ContentThe molar percentage of guanine and cytosine bases in an oligonucleotide sequence. LengthNumber of bases in the analyzed oligonucleotide sequence. Melting Temperature (ANALYZE function)
Melting temperature (T_{M}) is the temperature at which an oligonucleotide duplex is 50% in singlestranded form and 50% in doublestranded form. The Oligo Analyzer estimates T_{M} from the nearestneighbor twostate model, which is applicable to short DNA duplexes,
where H° (enthalpy) and S° (entropy) are the melting parameters calculated from the sequence and the published nearest neighbor thermodynamic parameters, R is the ideal gas constant (1.987 calK^{1}mole^{1}), [oligo] is the molar concentration of an oligonucleotide, and the constant of 273.15 converts temperature from Kelvin to degrees of Celsius. The most accurate, nearestneighbor parameters were obtained from the following publications for DNA/DNA base pairs
(Allawi,H., SantaLucia,J.,Jr., Biochemistry, 36, 10581), RNA/DNA base pairs (Sugimoto,N. et al., Biochemistry, 34, 11211), RNA/RNA base pairs (Xia,T. et al., Biochemistry, 37, 14719), and LNA/DNA base pairs (isolated LNA bases follow McTigue,P.M. et al., Biochemistry, 43, 5388, consecutive LNA bases follow Owczarzy,R et al., Biochemistry, 50, 9352).
T_{M} calculations for oligonucleotides containing nonconsecutive, isolated LNA nucleotides hybridized to a DNA template utilize LNA energetic parameters from McTigue,P.M. et al. Consecutive LNA bases on a DNA template use parameters from Owczarzy,R et al. LNA nucleotides on an RNA template are approximated because nearestneighbor parameters for these specific combinations are not yet available.
T_{M} depends on the monovalent and divalent salt concentrations ([Na^{+}] and [Mg^{++}], respectively) of the solvent.
Linear T_{M} corrections were previously used to model the effects of cations on DNA hybridization. However, scientists at IDT determined that these linear functions are inaccurate. We have developed new functions from several thousand ultraviolet and calorimetric melting experiments for over 100 short DNA duplexes in a variety of sodium, potassium, and magnesium buffers.
OligoAnalyzer employs the improved T_{M} salt correction function for monovalent (Na^{+}) ions (Owczarzy,R. et al., Biochemistry, 43, 3537),
and for divalent (Mg^{++}) ions (Owczarzy, R. et al., Biochemistry, 47, 5336),
where f_{GC} is the fraction of GC base pairs and N_{bp} is the number of base pairs.
The monovalent ion or the divalent ion correction equations are used depending on the following ratio R of [Mg^{++}] and [Na^{+}].
If R < 0.22, the monovalent ion correction is employed otherwise the divalent correction is used, including the case when [Na^{+}] is zero.
If R value is in the range from 0.22 to 6.0, the divalent ion correction is applied using a, d, and g
coefficients that varies with Na^{+} concentration. These coefficients are constant for higher values of R (the second column of the following table).
Variables adjusted to account for monovalent effects 

Constants 



Deoxynucleoside triphosphates (dNTPs) affects the concentration of free divalent ions that enters into the above correction functions and the calaculations of the ratio R. Free magnesium concentration is predicted from total Mg^{++} concentration, [tMg^{++}], using relationships developed from the equilibrium binding constant of Mg^{++} and dNTPs.
The association constant K_{a} is about 3x10^{4} in biological buffers. These new parameters and methods are implemented within the OligoAnalyzer and improve the melting temperature accuracy, especially for standard PCR conditions. In the current version, however, these new parameters (Mg^{++} and dNTP concentrations) are defaulted to 0.0 mM, so that predicted melting temperature are identical to values predicted by the previous version of the OligoAnalyzer. To take advantage of these new, more accurate methods, the values for [Mg^{++} ] and [dNTP] concentrations must be specified.
Target Type list has two possibilities DNA or RNA. Default type is DNA.
Oligo Conc box is used to enter oligo concentration ([oligo]) and has a range from 10^{4} µM (100 pM) to 10^{5} µM (100 mM). Default [oligo] is 0.25 µM, which is typically used in biological applications. Oligo concentration is assumed to be significantly larger (at least 6x) than concentration of the complementary target, which is true in majority of molecular biology experiments. If this is not a case, concentrations of both strands of the duplex must be considered and you should enter in the Oligo Conc box,
[oligo] = [strand1] – [strand2]/2 when [strand1] [strand2]
[oligo] = ([strand1] + [strand2])/4 when [strand1] = [strand2]
If the oligo sequence is selfcomplementary, enter total oligo concentration in the Oligo Conc box and T_{M} will be accurately predicted. Because target and the oligo are the same chemical species, target concentration is unnecessary to consider for selfcomplementary oligomers.
Na^{+} Conc box is used to enter total monovalent ions concentrations (Na^{+}, K^{+}, Tris^{+}) in the range from 5 mM to 1500 mM (1.5 M). Default concentration is 50.0 mM.
Mg^{++} Conc box is used to enter total divalent ions concentration [tMg^{++} ] in the range from 0.01 mM to 600 mM; however this concentration cannot be lower than the oligo concentration multiplied by the number of base pairs. Default Mg^{++} concentration is 0.0 mM.
dNTPs Conc box is used to enter total deoxynucleoside triphosphate concentrations (dNTPs) and in the range from 0.0 mM to 1000 mM (1.0 M); however the [dNTP] may not exceed 120% of the Mg^{++} concentration. Default dNTP concentration is 0.0 mM.
See mixed bases and modifications below for their effects on T_{M}.
Click here for further information regarding melting temperature.
Mismatch Melting Temperature (TM MISMATCH function)
A TM MISMATCH function predicts thermodynamics of DNA molecules containing a single base mismatch and compares the result with the perfectly matched duplex. This is useful for estimating the mismatch discrimination and design of probes to detect single nucleotide polymorphisms (SNPs) where the allelic forms of a gene sequence might differ at only a single base position.
The most accurate nearestneighbor parameters are applied to predict melting temperature of a DNA oligo that is hybridized to a DNA template with and without a single base mismatch (SantaLucia and Hicks, Annu. Rev. Biophys. Biomol. Struct, 33, 415–440). Overhangs (dangling ends) of the target strand are explicitly considered and this improves predictions for the annealing of oligo to a long DNA target sequence (Bommarito,S. et al., Nucleic Acids Res., 28, 19291934).
The melting temperatures of the exactly complementary target and the single base mismatch target are calculated using a twostate model,
where [strand1] and [strand2] are concentrations of single strands entered in the Oligo Conc box and the Target Conc box, and [strand1] ≥ [strand2]. The Target Conc box accepts values from 0 µM to 10^{5} µM (100 mM). Default target concentration is 0 µM, which should be used for hybridization of oligo its genomic target of unknown low concentrations. The exact complement T_{M} reported by the TM MISMATCH function could be slightly different from the T_{M} calculated by the ANALYZE function because of additional dangling end interactions and nonzero target concentration, which are not accounted in the standard T_{M} reported by the ANALYZE function.
Hybridization Temperature is the temperature, in degrees of Celsius, at which the percent of the single strand bound to the target is calculated.
Hybridization Percent Bound reports the percent of the exact complement and the single base mismatch sequences, which are expected to be annealed to target at the specified hybridization temperature. Percent bound () is calculated from the following equation (Owczarzy,R. Biophys. Chem., 117, 207215),
where K_{a} is the association equilibrium constant obtained from predicted thermodynamic parameters,
The T is the hybridization temperature in Kelvins. If the hybridization temperature is chosen to be the T_{M} of the exact complement then its percent bound () will always be 50% because that is set in the definition of melting temperature.
Mixed Bases DefinitionsMixed bases, which are also known as degenerate or wobble bases, can be introduced at any position of oligomer sequence. For example, mixed base composition at a single position can include all 4 bases ("N"), C or T bases, ("Y"), A or G bases ("R"), etc. Since there are 11 different possible combinations of 2, 3 or 4 bases, a universal nomenclature has been established that must be used when specifying nucleic acid content at a mixed base site.
Oligo Analyzer and IDT ordering system use standard definitions (IUB codes):
Symbol 
Mixed bases 
R 
A, G 
Y 
C, T 
M 
A, C 
K 
G, T 
S 
C, G 
W 
A, T 
H 
A, C, T 
B 
C, G, T 
V 
A, C, G 
D 
A, G, T 
N 
A, C, G, T 
Oligomer orders synthesized using mixed base sites result in a product that is a heterogeneous mixture of distinct oligomeric species. Species have different bases at the mixed sites. Therefore, they have different
molecular weight, melting temperature (T_{M}), and extinction coefficient (_{260}) values. Rather than reporting the various values for each of the component species, a single value is given that estimates the population average from all species present. Molecular weight calculations are made using the average base content. Melting temperature is calculated by averaging nearestneighbor enthalpy (H°) and entropy (S°) values at each mixed site. Extinction coefficient is similarly predicted by averaging nearestneighbor values at mixed sites.
Further, the minimum and maximum T_{M} of the oligomer mixture is also derived using the IDT proprietary T_{M}Extreme algorithm. The method uses the nearestneighbor thermodynamic model and the unified set of parameters (Allawi,H., SantaLucia,J.,Jr., Biochemistry, 36, 10581), however, it avoids the slow calculations of each possible oligomer. The T_{M} range is calculated in 5  10 msec. Predictions of T_{M} range are accurate with an average deviation of 0.5 °C in comparison with the complete T_{M} calculations for all possible oligomers in the mixture.
Modifications
Modified oligonucleotides also need special consideration to ensure accuracy when calculating molecular weight, extinction coefficient (_{260}), and melting temperature (T_{M}). Modifications can change oligo mass, and sometimes alter UV absorbance or T_{M}.
Examples:
Molecular Weight of an oligo containing an NHS Ester modification (such as 5' Texas Red NHS ester) is a sum of molecular weights of native oligo, the fluorophore group, and an amino modifier.
Extinction Coefficients (_{260}) of modifications, such as fluorophores and base analogs, are usually added to the
_{260} of the native oligonucleotide. Calculations for base analogs (e.g., 5bromo dC) and conjugated bases (e.g., fluorescein dT) are more complex. First,
_{260}of an oligo containing the unmodified base are calculated. Adjustment is later added for the contribution of the modification (fluorophore). Unfortunately,
_{260} values are not known for all modifications.
Melting Temperature (T_{M}) can be changed when nucleotides are modified or additional chemical groups are added. For example, introduction of phosphorothioated residues decreases T_{M} significantly. In contrast, LNA nucleotides increase T_{M}. Unfortunately, nearest neighbor thermodynamic parameters have not been determined for majority of these modifications. Therefore, no accurate parameters and physical models exist that would allow us to calculate melting temperatures for many modified oligonucleotides. Internal base modifications, e.g. biotindT, could collide and interfere with the duplex structure. Because the quantitative effects of interference are unknown, they are neglected. If thermodynamic parameters are not available, Oligo Analyzer reports T_{M} values for the unmodified sequence. Melting temperature changes caused by modifications may be approximated from the published literature. If needed, a precise T_{M} can be measured experimentally.
Click Here for further information regarding Modifications.
Molar Extinction Coefficient
Optical absorbance at 260 nm is routinely used to measure the concentration of nucleic acids present in a solution. Approximate conversion factors estimate that duplex DNA is about 50 µg/OD_{260}, singlestranded RNA is approximately 40 µg/OD_{260}, and singlestranded DNA is approximately 33 µg/OD_{260}. While this is true for randomized sequence, these conversion factors are less accurate for short oligonucleotides and repeating sequences. Since the absorbance of each base is different, base composition and sequence context influence the absorbance. For example, 1.0 OD_{260} of d(CCCCCCCCCCCC) (homopolymeric deoxycytidine) has a mass of 39 µg while 1.0 OD_{260} of d(AAAAAAAAAAAA) (homopolymeric deoxyadenosine) has a mass of 25 µg. The extinction coefficient (_{260}) describes the relationship between concentration and UV absorbance and can be calculated for any sequence. Greatest accuracy is therefore achieved when the exact value of _{260} is calculated for each oligo. Further, it is possible to take into account the presence of modified groups, such as fluorescent dyes, that have significant absorbance at 260nm.
The molar extinction coefficient is a physical constant that is unique for each sequence and describes the amount of absorbance at 260nm (A_{260}) of 1 mole/L DNA solution measured in 1 cm pathlength cuvette. This definition is derived from the BeerLambert law,
A = log(I_{O} / I) = * c * p
where A is the absorbance, I_{O} and I are, respectively, the intensities of incident and transmitted light, c is the molar concentration of an oligonucleotide (mole/L), p is the length of the light path through the sample (cm), and
is the molecule molar extinction coefficient (L/(mole
cm)). The
_{260} value of an oligonucleotide is calculated from the following equation
(Cantor,C.R. et al., Biopolymers, 9, 10591077., Cavaluzzi,M.J. and Borer,P.N. Nucleic Acids Res., 32, e13),
where _{Nearest Neighbor} is the nearest neighbor coefficient for a pair of bases,
_{Individual} is the coefficient for an individual base, and N is the length of the oligonucleotide.
See Mixed Base Definitions and Modifications for their effects on _{260}.
Click Here for further information regarding Molar Extinction Coefficient.
Molecular Weight (Anhydrous)
Molecular weight (MW) is the sum of the atomic masses of the constituent atoms for 1 mole of oligonucleotide. The anhydrous molecular weight represents the pure oligo free of any of the counter ions or water molecules that are normally weakly bound to an oligo after synthesis. This calculation gives with the molecular weight measured by mass spectroscopy.
Molecular weight of an oligomer is a sum of the weights of individual bases and chemical modifications. Oligos are typically synthesized without 5’phosphate group, which must be subtracted.
Anhydrous MW = _{Individual Base MW} + _{Individual Mod MW }  PO_{2}H + H_{2}
where PO_{2}H = 63.980 and H2 = 2.016
Molecular weights of DNA bases:
MW_{dA} 
313.209 
MW_{dC} 
289.184 
MW_{dG} 
329.208

MW_{dT} 
304.196

MW_{dU} 
290.169

MW_{dI} 
314.194

RNA bases: The molecular weight of an RNA nucleotide is the weight of a DNA nucleotide + 15.999, accounting for the additional oxygen atom present (Example: rA is dA (313.209) + 15.999 = 329.208). When determining the weight of uracil (rU) start with dU and not thymine (dT).
2'OMethyl bases: The molecular weight of an 2'Omethyl RNA nucleotide is the weight of a DNA nucleotide + 30.026, accounting for the additional methoxy group (OCH_{3}) present (For example, mA is dA (313.209) + 30.026 = 343.235). When determining the weight of uracil (mU) start with dU and not thymine (dT).
LNA bases: The molecular weight of an LNA nucleotide is the weight of a DNA nucleotide + 28.011, accounting for the bridging oxygen and carbon from the 2’ carbon to the 4’ carbon (OCH_{2}) present (For example, +A is dA (313.209) + 28.011 = 341.220). The exception is LNA C which contains an additional methyl group off of the 5carbon (14.026).
Phosphorothioated bases: The molecular weight of a phosphorothioate nucleotide is the weight of a nucleotide (DNA, RNA, 2’Omethyl, LNA) + 16.061, accounting for the substitution of one sulfur atom for a nonbridging oxygen atom in the phosphodiester backbone (For example, A* is A (313.209) + 16.061 = 329.270). Phosphorothioate modification refers to substitutions affecting the internucleoside linkages and does not involve the free 3' or 5' ends. Thus a 20mer phosphorothioate oligonucleotide has 19 phosphorothioate linkages.
See mixed base definitions and modifications for their effects on molecular weight.
nmole/OD_{260}
The amount of oligonucleotide in nanomoles that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm pathlength cuvette. nmole/OD_{260} is calculated from oligonucleotide's molar extinction coefficient. OD_{260} is calculated from the following equation,
OD_{260} = (A_{260} * V) / p
where A_{260} is the absorbance at 260 nm, V is the solution volume in mL, and p is the length of the light path through the sample (cm). Thus, OD_{260} has the units mL/cm. Starting from the oligo molar extinction coefficient,
_{260},
_{260} = L/(mol cm) = 10^{3} mL/(mol cm)
Since OD_{260} has the units of mL/cm, the equation can be written as,
10^{3} OD_{260}/mol = 10^{3} OD_{260} / 10^{9} nmol = OD_{260} / 10^{6} nmol
Combination of both equations yields,
_{260} = OD_{260} / 10^{6} nmol
and this can rearranged as,
nmole/OD_{260} = 10^{6} / _{260}
Problem
Invalid inputs in the oligonucleotide sequence box are listed in the order from 5' to 3' end of the oligo. The reason for error is displayed. The invalid items are highlighted in
red
for ease of identification within the sequence.
Secondary SequenceThe formatted input of the oligonucleotide sequence used to hybridize to the primary sequence of interest in the HETERODIMER function, shown in 5' to 3' orientation. SequenceThe formatted input oligonucleotide sequence, which is shown in 5' to 3' orientation.
µg/OD_{260}
The amount of oligonucleotide in micrograms that, when dissolved in 1 mL volume, results in 1 unit of absorbance at 260 nm with a standard 1 cm pathlength cuvette. µg/OD_{260} is derived using molecular weight and
nmole/OD_{260} values:
µg/OD_{260} = nmole/OD_{260} * molecular weight (g/mol) * 10^{3}
The definition of OD_{260} can be found within the nmole/OD_{260} definition.
