The Dipole Moments of Purines and Pyrimidines

Bergmann, Ernst D.; Weiler‐Feilchenfeld, Hannah

doi:10.1016/b978-0-12-222901-5.50008-0

Cited by 3 publications

(36 citation statements)

References 38 publications

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“…Oligomers were desalted on Sep-Pak C18 cartridges (Millipore), eluted with 40% aqueous acetonitrile, and freeze-dried. The average yield of pyrimidine oligomers was 60.6%; of (dA) 24 , 33.4%.…”

Section: Methodsmentioning

confidence: 99%

“…16 Molar extinction coefficients at max were measured as described previously. 16 e (LM À1 cm À1 ) 6 SE (n ¼ 6): (dA) 24 , 9780 6 140, (dT) 24 , 9580 6 130, (dU) 24 , 8930 6 130, (dU 12 -dT 12 ), 9100 6 200, (dU-dT) 12 , 8980 6 120, (dU 2 -dT 2 ) 6 , 9420 6 130, and (dU 3 -dT 3 ) 4 , 9260 6 110 for oligomers in 2.0 mM sodium cacodylate, pH 7, 0.10M NaCl, 20.08.…”

Section: Methodsmentioning

confidence: 99%

“…T m was defined as the temperature at half the change in absorbance of the thermal transition and was calculated with the program LAP. To estimate accuracy, we measured the T m of (dA) 24 Á (dT) 24 18 Cells of 1-and 2-mm path lengths were used at higher oligomer concentrations.…”

Section: Methodsmentioning

confidence: 99%

“…Melting curves of (dA) 24 interacted with (dT) 24 , (dU) 24 , (dU 12 -dT 12 ), (dU-dT) 12 , (dU 2 -dT 2 ) 6 , and (dU 3 -dT 3 ) 4 at the 1:1 ratio have single transitions (2 ? 1 transition) at 257 nm over the range 0.01…”

Section: Ultraviolet Melting Curves: Salt Dependence and Dependence Omentioning

confidence: 99%

“…In this article, we examine the effect of adjacent T residues upon the stability of (dA) 24 interacted with (dU) 24 , (dT) 24 , (dU-dT) 12 , (dU 12 -dT 12 ), (dU 2 -dT 2 ) 6 , or (dU 3 -dT 3 ) 4 , thus determining the influence of composition, neighboring interactions, and next-nearest neighboring interactions of thymine residues. We also find that the major part of the increase in T m of a duplex occurs regardless of the nature of its nearest neighbor, but we attribute this increase to enhanced dipoleinduced dipole as well as to dispersion forces.…”

Section: Introductionmentioning

confidence: 99%

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The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects

Howard¹

2005

Biopolymers

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Ultraviolet melting curves are used to determine the effect of the pyrimidine 5-methyl group on the stability of duplexes of (dA)(24) with (dU)(24), (dT)(24), (dU(12)-dT(12)), (dU-dT)(12), (dU(2)-dT(2))(6), and (dU(3)-dT(3))(4). Substitution of a T for a U results in an increase in stability, which is attributed to an increase in strength of dipole-induced dipole and dispersion (van der Waals) interactions. Significant additional enhancement occurs when two T residues are adjacent. A further increase in the number of adjacent T's has a relatively slight effect on T(m). The sequence effect appears to be largely attributable to an increment in dispersion forces. The CD spectra of the duplexes are all closely similar except in the region between 260 and 290 nm. A band near 272 nm associated with the presence of U in the spectrum of (dA)(24).(dU)(24) decreases in intensity when T's are incorporated in the pyrimidine strand. The band is completely replaced in the spectrum of (dA)(24).(dT)(24) with a new maximum at 282 nm and a minimum at 268 nm, both of lower magnitude. The emergence of the two new bands is correlated with the presence of adjacent T's once more, and only two adjacent T's appear necessary for a major part of the change to occur. The degree of cation release on thermal dissociation of the oligomer dimers ranges from Deltai = 0.14 to 0.16, about the same or slightly less than values reported for polynucleotide duplexes and less than predicted from theoretical calculations.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Ultraviolet Melting Curves: Salt Dependence and Dependence Omentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects

Howard¹

2005

Biopolymers

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Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code

Seligmann

Amzallag

2002

Naturwissenschaften

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The emergence of the genetic code remains an enigma. Proposed mechanisms are based on random, historical, thermodynamic and natural selection. However, they introduce chance as a key factor for overcoming the difficulties encountered by the model. We propose here a model in which three successive levels of chemical specificity generated the nucleotide assignments of amino acids in the genetic code. The first level results from hydrophobic and stereospecific interactions between amino acids and short oligonucleotides (termed oligons). The second and third levels of specificity are determined by conditions of energy transfer from loaded oligons (amino acid-oligomer covalently linked) to formation of phosphodiester bond (second level of specificity) and peptidic bond (third level of specificity), while these reactions are catalyzed by RNA templates. This model is sustained by the relationships observed between dipole moments of the nucleotides (forming the anticodon) and reactivity of the amino acyl linkage of the loaded oligon. Moreover, analysis of modern tRNAs reveals that they were probably generated by loose duplication of the nucleotide sequence forming the oligons, after emergence of the 'genetic code.' Indeed, the similarity of nucleotide composition with that of the anticodon decreases with the tRNA domain's distance from the anticodon, but the acceptor stem is relatively more similar to the anticodon than other stems closer to it. This would be because energy transfer constraints that existed between anticodon and amino acid in prebiotic loaded oligonucleotides still affect the structures of modern tRNA acceptor stems. In the model presented, the genetic code is inherent to the most archaic 'molecular physiology' in protolife, even before emergence of a functional 'protein world.' Simple physical processes, in which a level of specificity is integrated in an emerging meta-structure expressing new properties, generate a parsimonious and realistic explanation of emergence of the genetic code.

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Optimization of Interstrand Hydrophobic Packing Interactions within Unnatural DNA Base Pairs

Matsuda

Romesberg

2004

J. Am. Chem. Soc.

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As part of an effort to expand the genetic alphabet, we have evaluated a large number of predominantly hydrophobic unnatural base pairs. We now report the synthesis and stability of unnatural base pairs formed between simple phenyl rings modified at different positions with methyl groups. Surprisingly, several of the unnatural base pairs are virtually as stable as a natural base pair in the same sequence context. The results show that neither hydrogen-bonding nor large aromatic surface area are required for base pair stability within duplex DNA and that interstrand interactions between small aromatic rings may be optimized for both stability and selectivity. These smaller nucleobases are not expected to induce the distortions in duplex DNA or at the primer terminus that seem to limit replication of larger unnatural base pairs, and they therefore represent a promising approach to the expansion of the genetic alphabet.

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The Dipole Moments of Purines and Pyrimidines

Cited by 3 publications

References 38 publications

The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects

The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects

Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code

Optimization of Interstrand Hydrophobic Packing Interactions within Unnatural DNA Base Pairs

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The Dipole Moments of Purines and Pyrimidines

Cited by 3 publications

References 38 publications

The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12–dT12), (dU–dT)12, (dU2–dT2)6, or (dU3–dT3)4: Nearest neighbor and next‐nearest neighbor effects

The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12–dT12), (dU–dT)12, (dU2–dT2)6, or (dU3–dT3)4: Nearest neighbor and next‐nearest neighbor effects

Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code

Optimization of Interstrand Hydrophobic Packing Interactions within Unnatural DNA Base Pairs

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Product

Resources

About

The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects

The stabilizing contribution of thymine in duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, or (dU₃–dT₃)₄: Nearest neighbor and next‐nearest neighbor effects