Hoogsteen DNA duplexes of 3'-3'- and 5'-5'-linked oligonucleotides and trip formation with RNA and DNA pyrimidine single strands: experimental and molecular modeling studies

Biochemistry
E R Kandimalla, S Agrawal

Abstract

DNA oligonucleotide sequences containing two parallel complementary strands attached through 3'-3' and 5'-5' linkages were synthesized. These oligonucleotides from Hoogsteen base-paired parallel-stranded (PS) hairpin duplexes under appropriate conditions [Kandimalla, E. R., Agrawal, S., Venkataraman, G., & Sasisekharan, V. (1995a) J. Am. Chem. Soc. 117, 6416-6417]. UV melting experiments show that these Hoogsteen hairpin duplexes have a lower thermal stability than that of the Watson-Crick (WC) hairpin duplex (antiparallel) of the same sequence. The circular dichroism (CD) spectrum of the Hoogsteen duplex is different from the canonical B-DNA WC duplex spectrum. The formation of the Hoogsteen duplex is pH-dependent since protonation of cytosine requires lower pH conditions. Studies with oligonucleotides of different loop sizes revel that three- and two-base loops are optimum for the formation of stable Hoogsteen duplexes with 3'-3' and 5'-5' linkages, respectively. The guanine residues in the loop stabilize the duplex as a result of G-G interactions as confirmed by molecular modeling studies. The new PS Hoogsteen duplexes form stable triplexes with complementary (antiparallel to the purine domain) single-stranded RNA and DNA py...Continue Reading

References

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Aug 1, 1996·Journal of Biomolecular Structure & Dynamics·E R KandimallaS Agrawal

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Citations

Jun 27, 2001·Bioorganic & Medicinal Chemistry Letters·A AviñóR Eritja
Dec 7, 2007·Nucleosides, Nucleotides & Nucleic Acids·Anna AviñóCarlos González
Jun 13, 2002·Nucleic Acids Research·Anna AviñóRamon Eritja
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May 10, 2005·Chembiochem : a European Journal of Chemical Biology·Anna NadalMaria Pla
Apr 27, 2017·Angewandte Chemie·Yuwei HuItamar Willner
Mar 27, 2019·Current Protocols in Nucleic Acid Chemistry·Anna AviñóVerónica Noé
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Jun 5, 2007·Journal of the American Chemical Society·Ivan Trkulja, Robert Häner
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