Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes.
The thermodynamic contributions of rA·dA, rC·dC, rG·dG and rU·dT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°(37), ΔH° and melting temperature (T(m)) of duplexes containing these single mismatches within an average of 0.33 kcal/mol, 4.5 kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rG·dG > rU·dT > rA·dA > rC·dC. The stability trend for the base pairs 5' of the single internal mismatch is rG·dC > rC·dG > rA·dT > rU·dA. The stability trend for the base pairs 3' of the single internal mismatch is rC·dG > rG·dC >> rA·dT > rU·dA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST.
DNA Software Inc., Ann Arbor, MI 48104, USA. norm@dnasoftware.com
Norman E
NE
Watkins
William J
WJ
Kennelly
Mike J
MJ
Tsay
Astrid
A
Tuin
Lara
L
Swenson
Hyung-Ran
HR
Lee
Svetlana
S
Morosyuk
Donald A
DA
Hicks
John
J
Santalucia
D000225:Adenine / Q000737:chemistry; D020137:Base Pair Mismatch; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry; D014498:Uracil / Q000737:chemistry
D014498:Uracil; D006147:Guanine; D012313:RNA; D003596:Cytosine; D004247:DNA; D000225:Adenine; D013941:Thymine