Measurement of Nucleobase pK sub(a) Values in Model Mononucleotides Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes

• Published in: Journal of the American Chemical Society Vol. 126; no. 9; pp. 2862 - 2869
• Main Authors: Acharya, P, Cheruku, P, Chatterjee, S, Acharya, S, Chattopadhyaya, J
• Format: Journal Article
• Language: English
• Published: 10.03.2004
• ISSN: 0002-7863
• DOI: 10.1021/ja0386546

To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK sub(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is completely absent, the 3'-ethyl phosphates, (d/rN)pEt, mimic the nucleotide at the 5'-end. The pK sub(a) values of the nucleobase in each of these model nucleoside phosphates have been determined with low pK sub(a) error ( sigma = plus or minus 0.01 to 0.02) by super(1)H NMR (at 500 MHz) with 20-33 different pH measurements for each compound. This study has led us to show the following: (1) All monomeric DNA nucleobases are more basic than the corresponding RNA nucleobases in their respective Etp(d/rN)pEt and (d/rN)pEt. (2) The pK sub(a) values of the monomeric nucleotide blocks as well as Delta pK sub(a) values between the donor and acceptor can be used to understand the relative base-pairing strength in the oligomeric duplexes in the RNA and DNA series. (3) The Delta G degree sub(pKa) of the donor and acceptor of the base pair in duplexes enables a qualitative dissection of the relative strength of the base-pairing and stacking in the RNA-RNA over the DNA-DNA duplexes. (4) It is also found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases. This interdependency of stacking and hydrogen bonding can be potentially important in the molecular design of the base-pair mimicks to expand the alphabet of the genetic code.