Role of pKa of Nucleobases in the Origins of Chemical Evolution

R Krishnamurthy - Accounts of chemical research, 2012 - ACS Publications
The formation of canonical base pairs through Watson–Crick hydrogen bonding sits at the
heart of the genetic apparatus. The specificity of the base pairing of adenine with …

Model systems for understanding DNA base pairing

AT Krueger, ET Kool - Current opinion in chemical biology, 2007 - Elsevier
The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the
dogma of biology. However, they do not recognize each other well enough in water to …

Watson–Crick versus Hoogsteen base pairs: chemical strategy to encode and express genetic information in life

S Takahashi, N Sugimoto - Accounts of chemical research, 2021 - ACS Publications
Conspectus Nucleic acids typically form a double helix structure through Watson–Crick base-
pairing. In contrast, non-Watson–Crick base pairs can form other three-dimensional …

Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies

I Hirao, M Kimoto, R Yamashige - Accounts of chemical research, 2012 - ACS Publications
Since life began on Earth, the four types of bases (A, G, C, and T (U)) that form two sets of
base pairs have remained unchanged as the components of nucleic acids that replicate and …

Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes

P Acharya, P Cheruku, S Chatterjee… - Journal of the …, 2004 - ACS Publications
To understand why the RNA− RNA duplexes in general has a higher thermodynamic
stability over the corresponding DNA− DNA duplexes, we have measured the p K a values …

Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA

BA Schweitzer, ET Kool - Journal of the american chemical …, 1995 - ACS Publications
We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic
DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine …

Redesigning the architecture of the base pair: toward biochemical and biological function of new genetic sets

AT Krueger, ET Kool - Chemistry & biology, 2009 - cell.com
Recognition of the nucleic acid bases within the DNA scaffold comprises the basis for
transmission of genetic information, dictating protein and cell assembly, organismal …

Expanded-Size Bases in Naturally Sized DNA: Evaluation of Steric Effects in Watson− Crick Pairing

J Gao, H Liu, ET Kool - Journal of the American Chemical Society, 2004 - ACS Publications
We describe physicochemical properties in DNA of altered-size nucleobases that retain
Watson− Crick analogous hydrogen-bonding ability. Size-expanded analogues of adenine …

Minor groove hydrogen bonds and the replication of unnatural base pairs

S Matsuda, AM Leconte… - Journal of the American …, 2007 - ACS Publications
As part of an effort to expand the genetic alphabet, we examined the synthesis of DNA with
six different unnatural nucleotides bearing methoxy-derivatized nucleobase analogues …

A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties

TW Kim, ET Kool - The Journal of Organic Chemistry, 2005 - ACS Publications
We describe the properties in DNA of a set of five nonpolar nucleoside mimics in which
shape is similar but size is increased gradually. The compounds vary in the size of their …