PROTONATED CARBONYL GROUPS: VIII. ALKYLURACIL SALTS

With 1,3-dimethyluracil and 1,3,6-trimethyluracil as models for nucleic acid bases, it was found by infrared spectroscopic methods that the site of protonation is a carbonyl group. Analysis of other evidence makes it likely that it is the carbonyl group in position 4. In 1,3,6-trimethyluracil salts, activation of the 5 position under acid conditions permits ready hydrogen–deuterium exchange.Some anomalous 2 base – 1 acid salts with complex acids are considered in the light of base pairing errors in nucleic acids.

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Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.10.220 ◽

2014 ◽

Vol 10 ◽

pp. 2131-2138 ◽

Cited By ~ 1

Author(s):

Keunsoo Kim ◽

Venkateshwarlu Punna ◽

Phaneendrasai Karri ◽

Ramanarayanan Krishnamurthy

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Structural Unit ◽

Easy Access ◽

Alternative Route ◽

Base Pairing ◽

Limited Base ◽

Glycerol Nucleic Acid ◽

Adenine Derivative

IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.

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Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520619001999 ◽

2019 ◽

Vol 75 (3) ◽

pp. 301-309

Author(s):

Jelena M. Andrić ◽

Ivana M. Stanković ◽

Snežana D. Zarić

Keyword(s):

Nucleic Acid ◽

Hydrogen Bonds ◽

Nucleic Acids ◽

Metal Ions ◽

Quantum Chemical Calculations ◽

Quantum Chemical ◽

Metal Ion ◽

Water Molecules ◽

Nucleic Acid Bases ◽

Coordinated Water

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

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