oligoprop
Calculate sequence properties of DNA oligonucleotide
Syntax
SeqProperties
= oligoprop(SeqNT
)
SeqProperties
= oligoprop(SeqNT
,
...'Salt', SaltValue
, ...)
SeqProperties
= oligoprop(SeqNT
,
...'Temp', TempValue
, ...)
SeqProperties
= oligoprop(SeqNT
,
...'Primerconc', PrimerconcValue
, ...)
SeqProperties
= oligoprop(SeqNT
,
...'HPBase', HPBaseValue
, ...)
SeqProperties
= oligoprop(SeqNT
,
...'HPLoop', HPLoopValue
, ...)
SeqProperties
= oligoprop(SeqNT
,
...'Dimerlength', DimerlengthValue
, ...)
Input Arguments
SeqNT  DNA oligonucleotide sequence represented by any of the following:

SaltValue  Value that specifies a salt concentration in moles/liter for
melting temperature calculations. Default is 0.05 moles/liter. 
TempValue  Value that specifies the temperature in degrees Celsius for
nearestneighbor calculations of free energy. Default is 25 degrees
Celsius. 
PrimerconcValue  Value that specifies the concentration in moles/liter for melting
temperature calculations. Default is 50e6 moles/liter. 
HPBaseValue  Value that specifies the minimum number of paired bases that
form the neck of the hairpin. Default is 4 base
pairs. 
HPLoopValue  Value that specifies the minimum number of bases that form
the loop of a hairpin. Default is 2 bases. 
DimerlengthValue  Value that specifies the minimum number of aligned bases between
the sequence and its reverse. Default is 4 bases. 
Output Arguments
SeqProperties  Structure containing the sequence properties for a DNA oligonucleotide. 
Description
returns
the sequence properties for a DNA oligonucleotide as a structure with
the following fields:SeqProperties
= oligoprop(SeqNT
)
Field  Description 

GC  Percent GC content for the DNA oligonucleotide. Ambiguous N characters
in SeqNT are considered to potentially
be any nucleotide. If SeqNT contains ambiguous N characters, GC is
the midpoint value, and its uncertainty is expressed by GCdelta . 
GCdelta  The difference between GC (midpoint value)
and either the maximum or minimum value GC could
assume. The maximum and minimum values are calculated by assuming
all N characters are G/C or not G/C, respectively.
Therefore, GCdelta defines the possible range of
GC content. 
Hairpins  H bylength( matrix
of characters displaying all potential hairpin structures for the
sequence SeqNT . Each row is a potential
hairpin structure of the sequence, with the hairpin forming nucleotides
designated by capital letters. H is the number
of potential hairpin structures for the sequence. Ambiguous N characters
in SeqNT are considered to potentially
complement any nucleotide. 
Dimers  D bylength( matrix
of characters displaying all potential dimers for the sequence SeqNT .
Each row is a potential dimer of the sequence, with the selfdimerizing
nucleotides designated by capital letters. D is
the number of potential dimers for the sequence. Ambiguous N characters
in SeqNT are considered to potentially
complement any nucleotide. 
MolWeight  Molecular weight of the DNA oligonucleotide. Ambiguous N characters
in SeqNT are considered to potentially
be any nucleotide. If SeqNT contains ambiguous N characters, MolWeight is
the midpoint value, and its uncertainty is expressed by MolWeightdelta . 
MolWeightdelta  The difference between MolWeight (midpoint
value) and either the maximum or minimum value MolWeight could
assume. The maximum and minimum values are calculated by assuming
all N characters are G or C ,
respectively. Therefore, MolWeightdelta defines
the possible range of molecular weight for SeqNT . 
Tm  A vector with melting temperature values, in degrees Celsius,
calculated by six different methods, listed in the following order:
Ambiguous 
Tmdelta  A vector containing the differences between Tm (midpoint
value) and either the maximum or minimum value Tm could
assume for each of the six methods. Therefore, Tmdelta defines
the possible range of melting temperatures for SeqNT . 
Thermo 
The rows correspond to nearestneighbor parameters from:
The columns correspond to:
N characters in SeqNT are
considered to potentially be any nucleotide. If SeqNT contains
ambiguous N characters, Thermo is
the midpoint value, and its uncertainty is expressed by Thermodelta . 
Thermodelta  4 by3 matrix containing
the differences between Thermo (midpoint value)
and either the maximum or minimum value Thermo could
assume for each calculation and method. Therefore, Thermodelta defines
the possible range of thermodynamic values for SeqNT . 
calls SeqProperties
= oligoprop(SeqNT
,
...'PropertyName
', PropertyValue
,
...)oligoprop
with optional properties
that use property name/property value pairs. You can specify one or
more properties in any order. Each PropertyName
must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
specifies
a salt concentration in moles/liter for melting temperature calculations.
Default is SeqProperties
= oligoprop(SeqNT
,
...'Salt', SaltValue
, ...)0.05
moles/liter.
specifies
the temperature in degrees Celsius for nearestneighbor calculations
of free energy. Default is SeqProperties
= oligoprop(SeqNT
,
...'Temp', TempValue
, ...)25
degrees Celsius.
specifies
the concentration in moles/liter for melting temperatures. Default
is SeqProperties
= oligoprop(SeqNT
,
...'Primerconc', PrimerconcValue
, ...)50e6
moles/liter.
specifies
the minimum number of paired bases that form the neck of the hairpin.
Default is SeqProperties
= oligoprop(SeqNT
,
...'HPBase', HPBaseValue
, ...)4
base pairs.
specifies
the minimum number of bases that form the loop of a hairpin. Default
is SeqProperties
= oligoprop(SeqNT
,
...'HPLoop', HPLoopValue
, ...)2
bases.
specifies
the minimum number of aligned bases between the sequence and its reverse.
Default is SeqProperties
= oligoprop(SeqNT
,
...'Dimerlength', DimerlengthValue
, ...)4
bases.
Examples
Create a random sequence.
seq = randseq(25) seq = TAGCTTCATCGTTGACTTCTACTAA
Calculate sequence properties of the sequence.
S1 = oligoprop(seq) S1 = GC: 36 GCdelta: 0 Hairpins: [0x25 char] Dimers: 'tAGCTtcatcgttgacttctactaa' MolWeight: 7.5820e+003 MolWeightdelta: 0 Tm: [52.7640 60.8629 62.2493 55.2870 54.0293 61.0614] Tmdelta: [0 0 0 0 0 0] Thermo: [4x3 double] Thermodelta: [4x3 double]
List the thermodynamic calculations for the sequence.
S1.Thermo ans = 178.5000 477.5700 36.1125 182.1000 497.8000 33.6809 190.2000 522.9000 34.2974 191.9000 516.9000 37.7863
Calculate sequence properties of the sequence ACGTAGAGGACGTN.
S2 = oligoprop('ACGTAGAGGACGTN') S2 = GC: 53.5714 GCdelta: 3.5714 Hairpins: 'ACGTagaggACGTn' Dimers: [3x14 char] MolWeight: 4.3329e+003 MolWeightdelta: 20.0150 Tm: [38.8357 42.2958 57.7880 52.4180 49.9633 55.1330] Tmdelta: [1.4643 1.4643 10.3885 3.4633 0.2829 3.8074] Thermo: [4x3 double] Thermodelta: [4x3 double]
List the potential dimers for the sequence.
S2.Dimers ans = ACGTagaggacgtn ACGTagaggACGTn acgtagagGACGTN
References
[1] Breslauer, K.J., Frank, R., Blöcker, H., and Marky, L.A. (1986). Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Science USA 83, 3746–3750.
[2] Chen, S.H., Lin, C.Y., Cho, C.S., Lo, C.Z., and Hsiung, C.A. (2003). Primer Design Assistant (PDA): A webbased primer design tool. Nucleic Acids Research 31(13), 3751–3754.
[3] Howley, P.M., Israel, M.A., Law, M., and Martin, M.A. (1979). A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. The Journal of Biological Chemistry 254(11), 4876–4883.
[4] Marmur, J., and Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. Journal Molecular Biology 5, 109–118.
[5] Panjkovich, A., and Melo, F. (2005). Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21(6), 711–722.
[6] SantaLucia Jr., J., Allawi, H.T., and Seneviratne, P.A. (1996). Improved NearestNeighbor Parameters for Predicting DNA Duplex Stability. Biochemistry 35, 3555–3562.
[7] SantaLucia Jr., J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics. Proceedings of the National Academy of Science USA 95, 1460–1465.
[8] Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996). Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research 24(22), 4501–4505.
[9] http://www.basic.northwestern.edu/biotools/oligocalc.html for weight calculations.