Nearest Neighbour Method & Watson Crick Interactions - Why just ten?

[Prewitt]

i'm currently writing a piece of c++ code for improved primer selection for our lab. nothing fancy really. lately i was annoyed by the incorrect melting temperature calculated by 4+2 rule therefore i upgraded to nearest neighbour method. i read the papers by breslauer, santalucia, sugimoto and the rather crappy one by panjkovich - but i'm not really into the subject matter. question is: why are there only ten watson crick interactions that all authors provide thermodynamic data for?

 

They provide data for AA, AT, TA, CA, CT, GA, GT, CG, GC and GG (with complementary nucleotides) but not for AC, AG, CC, TC, TG, TT.

 

I wouldn't really care, but since i want to calculate it right: do i just skip those pairs in calculating the integrals?

[Prewitt]

*bump* anyone got a clue or a theory?

[Dak]

if we take the first two base sequence that's not given a Tm:

 

3'-AC-5'

 

this, with it's complimentary base pairs is

 

3'-AC-5'

5'-TG-3'

 

 

if you look through the list of ones that have Tm's given, you'll find GT.

 

or, in other words, you'll find

 

3'-GT-5'

5'-CA-3'

 

which is the same two base sequence with complimentary w/c pairs as above, just written different.

 

so the missing one's Tm would be the Tm of it's compliment backwards, if that makes sense? (above: AC --compliment--> TG --backwards--> GT)

[CharonY]

Yup that's precisely the reason. The seemingly missing neighbours are nothing more than the reverse complement of the given ones and read from the opposite strands they are identical to one of the "primary" ten neighbours.

[Prewitt]

hm. might be, i'll check it out...thanks for the input

[Prewitt]

it is appearently the correct solution

 

values are ΔH0 from Breslauer 1986

AA 9,1

AC 6,5

AG 7,8

AT 8,6

CA 5,8

CC 11,0

CG 11,9

CT 7,8

GA 5,6

GC 11,1

GG 11,0

GT 6,5

TA 6,0

TC 5,6

TG 5,8

TT 9,1

 

 

5’-AA-3’: 9,1

3’-TT-5’ --> 5’-TT-3’: 9,1

 

5’-AT-3’: 8,6

3’-TA-5’ --> 5’-AT-3’

 

5’-TA-3’: 6,0

3’-AT-5’ --> 5’-TA-3’

 

5’-CA-3’: 5,8

3’-GT-5’ --> 5’-TG-3’: 5,85

 

5’-GT-3’: 6,5

3’-CA-5’ --> 5’-AC-3’: 6,5

 

5’-CT-3’: 7,8

3’-GA-5’ --> 5’-AG-3’: 7,8

 

5’-GA-3’: 5,6

3’-CT-5’ --> 5’-TC-3’: 5,6

 

5’-CG-3’: 11,9

3’-GC-5’ --> 5’-CG-3’

 

5’-GC-3’: 11,1

3’-CG-5’ --> 5’-GC-3’

 

5’-GG-3’: 11,0

3’-CC-5’ --> 5’-CC-3’: 11,0