SREL
DNA Lab
All Possible Microsatellite Probes Available
Microsatellite DNA loci, also known as short tandem repeats (STRs), are
short, interspersed, repetitive elements with core repeat units of 1-6 bp.
Because the sequence ACACACACACACACACACAC could either be referred to as
"AC" or "CA" repeats, and the complementary DNA strand
TGTGTGTGTGTGTGTGTGTG as "TG" or "GT" repeats, they are all
really the same thing. Thus, it is generally desirable to simply refer to this
type of repeat by a single name, the lowest alphabetical designation being as
good a choice as any - which means "AC".
Below is a list of the lowest alphabetical designation for all unique
non-complementary di-, tri-, and tetra- nucleotide repeats. We have made probes
from most of these. By adjusting the length of the oligos (number of repeats),
we have matched the melting temperatures so that they can be combined in a
small number of "Mixes" for enrichment.
The 3 biotinylated oligo mixes we
generally use for enrichments.
Mix 2 - (AG)12, (TG)12, (AAC)6, (AAG)8, (AAT)12, (ACT)12,
(ATC)8;
Mix 3 - (AAAC)6, (AAAG)6, (AATC)6, (AATG)6, (ACAG)6,
(ACCT)6, (ACTC)6, (ACTG)6;
Mix 4 - (AAAT)8, (AACT)8, (AAGT)8, (ACAT)8,
(AGAT)8.
|
Core Repeat Unit |
Number of Repeats |
TM - 1 |
TM - 2 |
Oligo Mix |
|
AC |
13 |
|
60.6 |
1 |
|
AG |
12 |
58.6 |
|
2, 5 |
|
|
|
|
|
|
|
AAC |
6 |
65.4 |
|
2,7 |
|
AAG |
8 |
59.8 |
|
2, 7 |
|
AAT |
12 |
58.8 |
|
2, 5, 7 |
|
ACC |
8 |
63.9 |
|
x |
|
ACG |
6 |
67.6 |
|
x |
|
ACT |
12 |
57.6 |
|
2, 7 |
|
AGC |
6 |
67.6 |
|
|
|
AGG |
6 |
61.7 |
|
x |
|
ATC |
8 |
62.9 |
|
2, 7 |
|
CCG |
|
|
|
|
|
|
|
|
|
|
|
AAAC |
6 |
63.0 |
|
3 |
|
AAAG |
6 |
60.3 |
|
3 |
|
AAAT |
8 |
59.9 |
|
4, 5 |
|
AACC |
5 |
66.1 |
66.5 |
1, 6 |
|
AACG |
5 |
67.8 |
68.3 |
1, 6 |
|
AACT |
8 |
59.2 |
|
4 |
|
AAGC |
5 |
|
68.3 |
1, 6 |
|
AAGG |
5 |
63.5 |
64.1 |
1, 6 |
|
AAGT |
8 |
59.2 |
|
4 |
|
AATC |
6 |
62.2 |
|
3 |
|
AATG |
6 |
63.1 |
|
3 |
|
ACAG |
6 |
62.6 |
|
3 |
|
ACAT |
8 |
62.0 |
|
4 |
|
ACCC |
|
|
|
|
|
ACCG |
|
|
|
|
|
ACCT |
6 |
61.0 |
|
3 |
|
ACGC |
|
|
|
|
|
ACGG |
|
|
|
|
|
ACTC |
6 |
61.7 |
|
3 |
|
ACTG |
6 |
62.6 |
|
3 |
|
AGAT |
8 |
58.2 |
|
4 |
|
AGCC |
|
|
|
|
|
AGCG |
|
|
|
|
|
AGGC |
|
|
|
|
|
AGGG |
|
|
|
|
|
ATCC |
5 |
|
65.8 |
1, 6 |
|
CCCG |
|
|
|
|
|
|
|
|
|
|
|
Extra Probes |
|
|
|
|
|
TG |
12 |
|
68.3 |
2, 5 |
|
AG |
14 |
65.3 |
|
|
|
|
|
|
|
|
TM- calculated assuming 1M NaCl (6x SSC), and the Nearest Neighbor Method
using NBI's Oligo.
Tm-1 used version 4.0. Tm-2 used version6.6.
(Note: Version 6.6 gives a Tm about 0.5C higher than version 4.0 for the same
sequences).
For more information, contact: Glenn@srel.edu
Webpage from CrocDNA Workshop website
Last updated 31 January 2001
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