ABSTRACTIn 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)‐poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized such a noncanonical A–T base‐pair through X‐ray analysis of co‐crystals containing 9‐methyladenine and 1‐methylthymine. Subsequent X‐ray analyses of guanine and cytosine derivatives yielded the expected Watson–Crick base‐pairing, but those of adenine and thymine (or uridine) did not yield Watson–Crick base‐pairs, instead favoring “Hoogsteen” base‐pairing. More than two decades ensued without experimental “proof” for A–T Watson–Crick base‐pairs, while Hoogsteen base‐pairs continued to surface in AT‐rich sequences, closing base‐pairs of apical loops, in structures of DNA bound to antibiotics and proteins, damaged and chemically modified DNA, and in polymerases that replicate DNA via Hoogsteen pairing. Recently, NMR studies have shown that base‐pairs in duplex DNA exist as a dynamic equilibrium between Watson–Crick and Hoogsteen forms. There is now little doubt that Hoogsteen base‐pairs exist in significant abundance in genomic DNA, where they can expand the structural and functional versatility of duplex DNA beyond that which can be achieved based only on Watson–Crick base‐pairing. Here, we provide a historical account of the discovery and characterization of Hoogsteen base‐pairs, hoping that this will inform future studies exploring the occurrence and functional importance of these alternative base‐pairs. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 955–968, 2013.

Abstract The electrosorption of two-base mixtures of adenine, uracil and 1,3-dimethyluracil at the mercury electrode|solution interface has been studied at pH 8.0. Mixtures of adenine or uracil with 1,3-dimethyluracil, i.e., non-complementary bases, exhibit an initial dilute region of adsorption where the bases adsorb in a flat orientation on the electrode surface. At critically defined bulk solution concentrations of adenine or uracil a surface reorientation occurs and the latter compounds adopt a perpendicular surface stance. The presence of 1,3-dimethyluracil has very little effect on the ability of adenine or uracil to undergo the latter surface reorientation process. However, mixtures of adenine and uracil, a complementary base pair, exhibit only a flat surface orientation. Even at bulk solution concentrations considerably greater than those required to observe the flat-to-perpendicular reorientation for the single bases the mixed base system does not exhibit such a surface phenomenon. It is proposed that one of the contributing factors to stabilization of the dilute (flat) adsorption layer in the mixed complementary base system is Watson-Crick hydrogen bonding between the base pairs on the electrode surface.

[Eight types of stacking interaction in dinucleotides. Conformational analysis of ApA, ApC, CpA, CpC, GpG]. On the basis of general stereochemical considerations the classification of the stacking state of dinucleoside phosphate (DNP) including eight types of stacks of nucleic bases has been suggested. With the use of the algorithm, which makes possible determination of the backbone conformation for the given nucleic bases arrangement, the stacking conformes of DNP were analysed by atom-atom potential method. For all compounds different types of stacking conformes were obtained with energy values lower than that for the unstacking state. It follows from the results of calculations that for description of the conformational situation of DNP in solution the "non-canonical" conformers should be born in mind. In particular the forms having different sugar conformations in Np- and in pN-parts of the dimers are of interest. The effect of choice of the atom-atom potential functions on optimal conformation of DNP is discussed. For single-stranded RNA several regular and non-regular structures are proposed. Published in Molekuliarnaia biologiia

Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs - PMC Biochemistry . Author manuscript; available in PMC: 2020 May 21. Published in final edited form as: Biochemistry. 2019 May 8;58(20):2474–2487. doi: 10.1021/acs.biochem.9b00122 # Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs Wilma K Olson 1, Shuxiang Li 1, Thomas Kaukonen 1, Andrew V Colasanti 1, Yurong Xin 1, Xiang-Jun Lu 2 - Copyright and License information - Article notes - Author information 1Department of Chemistry & Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA 2Department of Biological Sciences, Columbia University, New York, New York 10027, USA ✉ Corresponding Authors Wilma K. Olson – wilma.olson@rutgers.edu. Phone: +1 848-445-3993., Xiang-Jun Lu – xiangjun@3dna.org. Phone: +1 732-447-7806. Issue date 2019 May 21. PMC Copyright notice PMCID: PMC6729125 NIHMSID: NIHMS1029965 PMID: 31008589 ## Abstract Noncanonical base pairs play important roles in assembling the three-dimensional structures