Single stand targeted triplex formation: physicochemical and biochemical properties of foldback triplexes. NLM AIDSLINE Important note: Information in this article was accurate in 1997. The state of the art may have changed since the publication date.

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Single stand targeted triplex formation: physicochemical and biochemical properties of foldback triplexes.

J Biomol Struct Dyn. 1996 Aug;14(1):79-90. Unique Identifier : AIDSLINE MED/97031658
Kandimalla ER; Manning A; Agrawal S; Hybridon, Inc Worcester, MA 01605, USA.

Abstract: Oligodeoxyribonucleotides containing both Watson-Crick and Hoogsteen hydrogen bonding domains joined by a nucleotide loop FTFOs) are studied for their binding affinity and specificity to the DNA and RNA single-stranded targets. Thermal denaturation studies reveal that FTFOs have high binding affinity for their targets than do antisense (duplex forming) and antigene (triplex forming) oligonucleotides, because of involvement of both the Watson-Crick and Hoogsteen domains in the interaction. Studies with FTFOs containing different sizes and sequences of loops show that 4-6 bases long loops are optimum for binding; loop sequence does not have a dramatic effect on binding. The FTFOs have greater sequence specificity than do antisense and antigene oligonucleotides because they read the target sequence twice. SI-, PI- and mung bean nuclease protection assays show that the DNA FTFO forms a stable triplex with the DNA target strand, but a weak or no triplex with the RNA target strand. Gel mobility shift assay is used to determine binding of FTFOs to DNA and RNA targets. The circular dichroism (CD) spectrum of the foldback triplex formed with the DNA target strand resembles the B-DNA spectrum, suggesting that the triplex has a B-type of conformation.
Keywords: *DNA/CHEMISTRY *DNA/METABOLISM *Nucleic Acid Heteroduplexes/CHEMISTRYKWDdna/chemistryKWDdna/metabolismKWDnucleicacidheteroduplexes/chemistry
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Copyright © 1997 - National Library of Medicine. Reproduced under license with the National Library of Medicine, Bethesda, MD.

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