Can configuration of solitary wobble base pairs determine the specificity and degeneracy of the genetic code? Clues from molecular orbital modelling studies

Das, Gunajyoti; Lyngdoh, R. H. Duncan

doi:10.1016/j.theochem.2007.11.027

Cited by 9 publications

(10 citation statements)

References 28 publications

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“…Before going into the discussion, it is important to recall the configuration of a solitary base pair 10,11 which is used to predict whether a base pair will occur at the wobble position or not. Since the total number of anticodon wobble bases (AWB) is not known fully to date, the anticodon uracil is taken as the reference and its combination with four codon wobble bases (CWB) such as adenine (Ade), cytosine (Cyt), guanine (Gua) and uracil (Ura) have been chosen here.…”

Section: Resultsmentioning

confidence: 99%

“…The structure, stability, strength and nature of interactions of hydrogen and halogen bonded base pairs with the uracil anticodon are discussed here. Before going into the discussion, it is important to recall the configuration of a solitary base pair 10,11 which is used to predict whether a base pair will occur at the wobble position or not. The following conditions should be satisfied by the base pairs for them to be observed at the wobble position:…”

Section: Resultsmentioning

confidence: 99%

“…1 Base pairs at this position are unique, featuring elongated distances and loose binding, enabling degeneracy. [5][6][7][8][9][10][11][12][13] The HBs were reported to break synergy with delocalization of the p-electrons and charge transfer character, which stabilizes the duplex. [2][3][4] The hydrogen bonds in these base pairs and wobble base pairs have been a target for researchers over the years.…”

Section: Introductionmentioning

confidence: 99%

“…In a surge to find answers to these, we retrieved the codonanticodon base pair geometries with uracil, cytosine, guanine & adenine as codons and uracil as an anticodon from earlier reports 10,11 and replaced both the hydrogens that are involved in hydrogen bonding with halogens (Cl, Br and I). There have been number of previous studies that dealt with individual base pairs available in the literature.…”

Section: Introductionmentioning

confidence: 99%

“…[2][3][4] The hydrogen bonds in these base pairs and wobble base pairs have been a target for researchers over the years. [5][6][7][8][9][10][11][12][13] The HBs were reported to break synergy with delocalization of the p-electrons and charge transfer character, which stabilizes the duplex. On the other hand, a relatively less characterized form of intermolecular interactions that attract much attention in literature is the halogen bond (XB).…”

Section: Introductionmentioning

confidence: 99%

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A new turn in codon–anticodon selection through halogen bonds

Solomon

Vedha

Venuvanalingam

2014

Phys. Chem. Chem. Phys.

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The halogen bond is relatively a less characterized intermolecular interaction compared to the hydrogen bond and the structure, stability and electronic structures of halogenated base pairs, particularly at the wobble junction have been investigated using DFT. Three halogens, namely Cl, Br and I, have been tested for their role in such situations with uracil as the anticodon base. Computed results reveal that when halogen atoms replace protons in the hydrogen bonding positions they induce lot of geometric changes that flip some of the observed base pairs into unobserved base pairs and vice versa. NCI, NBO and AIM analyses explain these changes at the electronic level. The new codons will have lot of impact in future applications, particularly in self assembly of biomaterials and t-RNA synthetic strategies.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A new turn in codon–anticodon selection through halogen bonds

Solomon

Vedha

Venuvanalingam

2014

Phys. Chem. Chem. Phys.

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Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position

Das

Lyngdoh

2012

J Mol Model

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Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.

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