NDLI: Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A(+)-G)10.

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Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A(+)-G)10.

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Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A(+)-G)10.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Dolinnaya, N. G. Fresco, J. R.
Description	Author Affiliation: Dolinnaya NG ( Department of Molecular Biology, Princeton University, NJ 08544.);
Abstract	We have identified a type of secondary structure for the homopurine oligomer d(A-G)10 below pH 6 in 0.01 M Na+ that is characterized by intense CD but only minor hypochromicity. The stability of this helix, designated d(A(+)-G)10, does not depend on oligomer concentration and increases sharply as ionic strength or pH drops, reaching a maximum at 4.0 (melting temperature, 37 degrees C). The pKa for the transition, 5.3 at 25 degrees C and even higher with decreasing temperature and [Na+], is much higher than the intrinsic pKa values for dA or dG residues. While the dA residues are protonated in the helix, further protonation of the dG residues disrupts it. When observed at 280 nm, melting of the helix first results in hypochromicity due to stacking of extrahelical dG residues with neighboring dA residues. The character and temperature dependence of the CD spectra of the constituent dinucleoside monophosphates indicate minimal chirality and base overlap for the A+pG sequences in d(A(+)-G)10 but left-handed twist with some base overlap for the GpA+ sequences. The observed properties are best satisfied by a model for an intramolecular helix with limited base overlap, stabilized by ionic bonds between dA residues protonated at N-1 and downstream negatively charged phosphates brought close due to the backbone helical twist, while Gsyn residues lie external to the helix. This structure could provide additional stabilizing energy for biologically relevant protonated non-B-DNA structures adopted by homopurine.homopyrimidine sequences due to topological stress or specific protein binding.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	19
Volume Number	89
Language	English
Publisher	National Academy of Sciences
Publisher Date	1992-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Nucleic Acid Conformation Oligodeoxyribonucleotides Chemistry Circular Dichroism Deoxyadenine Nucleotides Deoxyguanine Nucleotides Hydrogen-Ion Concentration Nucleic Acid Denaturation Spectrophotometry, Ultraviolet Thermodynamics Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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