Molecular Recognition of Watson-Crick-Like Purine-Purine Base Pairs

ChemBioChem ◽  
2011 ◽  
Vol 12 (14) ◽  
pp. 2155-2158 ◽  
Author(s):  
Ragan Buckley ◽  
C. Denise Enekwa ◽  
Loren Dean Williams ◽  
Nicholas V. Hud
Keyword(s):  
Molecular Recognition ◽  
Base Pairs ◽  
Purine Base

Purine-purine base pairs and the origin of transversion-type mutation

2009 ◽  
Vol 12 (S4) ◽  
pp. 197-204
Author(s):  
Ramon Gardun̄to ◽  
Robert Rein ◽  
John T. Egan ◽  
Yves Coeckelenbergh ◽  
Robert D. Macelroy
Keyword(s):  
Base Pairs ◽  
Purine Base

scholarly journals Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

2017 ◽  
Author(s):  
Abhinav Mittal ◽  
Antarip Halder ◽  
Sohini Bhattacharya ◽  
Dhananjay Bhattacharyya ◽  
Abhijit Mitra
Keyword(s):  
Structural Alignment ◽  
Bimodal Distribution ◽  
Base Pairs ◽  
Purine Base ◽  
Functional Roles ◽  
Nmr Structures ◽  
Sharp Turn ◽  
Interesting Class ◽  
Functional Rnas ◽  
Noncanonical Base Pairs

AbstractIdentification of static and/or dynamic roles of different noncanonical base pairs is essential for a comprehensive understanding of the sequence-structure-function space of RNA. In this context, reverse Watson-Crick purine-purine base pairs (A:A, G:G&A:GW:W Trans) constitute an interesting class of noncanonical base pairs in RNA due to their characteristic C1′–C1′ distance (highest among all base pairing geometries) and parallel local strand orientation. Structural alignment of the RNA stretches containing these W:W Trans base pairs with their corresponding homologous sites in a non-redundant set of RNA crystal structures show that, as expected, these base pairs are associated with specific structural folds or functional roles. Detailed analysis of these contexts further revealed a bimodal distribution in the local backbone geometry parameters associated with these base pairs. One mode, populated by both A:A and G:G W:W Trans pairs, manifests itself as a characteristic backbone fold. We call this fold a ‘Sharp-turn’ motif. The other mode is exclusively associated with A:A W:W Trans pairs involved in mediating higher order interactions. The same trend is also observed in available solution NMR structures. We have also characterized the importance of recurrent hydrogen bonding interactions between adenine and guanine in W:W Trans geometry. Quantum chemical calculations performed at M05-2X/6-31++(2d,2p) level explain how the characteristic electronic properties of these W:W Trans base pairs facilitate their occurrence in such exclusive structural folds that are important for RNA functionalities.

Binding of an HIV Rev peptide to Rev responsive element RNA induces formation of purine-purine base pairs

Biochemistry ◽  
1994 ◽  
Vol 33 (10) ◽  
pp. 2741-2747 ◽  
Author(s):  
John L. Battiste ◽  
Ruoying Tan ◽  
Alan D. Frankel ◽  
James R. Williamson
Keyword(s):  
Base Pairs ◽  
Purine Base ◽  
Responsive Element

The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences

2015 ◽  
Vol 71 (10) ◽  
pp. 2119-2126 ◽  
Author(s):  
Arunachalam Thirugnanasambandam ◽  
Selvam Karthik ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Hydrogen Bonds ◽  
Dna Sequences ◽  
Single Strand ◽  
Triplet Repeat ◽  
The Novel ◽  
Base Pairs ◽  
Purine Base ◽  
Ion Interactions ◽  
Folded Structure ◽  
Triplet Repeat Sequences

The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson–Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.

IMPORTANCE OF CHARGE TRANSFER EXCITATIONS IN DNA ELECTRON SPECTRUM: A ZINDO SEMIEMPIRICAL QUANTUM-CHEMICAL STUDY

2004 ◽  
Vol 18 (16) ◽  
pp. 825-831 ◽  
Author(s):  
E. B. STARIKOV
Keyword(s):  
Charge Transfer ◽  
Quantum Chemical ◽  
Spectral Band ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Molecular Orbitals ◽  
Base Pairs ◽  
Purine Base ◽  
Dna Conformations

Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempirical quantum-chemical method. This work confirms that, in DNA with intact Watson–Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band is discussed.

scholarly journals 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization

2020 ◽  
Vol 76 (5) ◽  
pp. 513-523
Author(s):  
Dasharath Kondhare ◽  
Simone Budow-Busse ◽  
Constantin Daniliuc ◽  
Frank Seela
Keyword(s):  
Base Pair ◽  
Crystal Packing ◽  
Donor Site ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Acceptor Site ◽  
Base Pairs ◽  
Purine Base ◽  
Value Differences ◽  
Ribose Moiety

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′-endo) for the ribose moiety, with an antiperiplanar orientation of the 5′-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2′ of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H...O and N—H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.

trans-a2Pt(II) (a=NH3, CH3NH2) modified purine base pairs and triples: Hydrogen bonding between self-complementary pairs and triples and heterometal (Ag+) coordination leading to a 1 D helix

2000 ◽  
Vol 300-302 ◽  
pp. 339-352 ◽  
Author(s):  
Irene B. Rother ◽  
Eva Freisinger ◽  
Andrea Erxleben ◽  
Bernhard Lippert
Keyword(s):  
Hydrogen Bonding ◽  
Base Pairs ◽  
Purine Base

Molecular Recognition by Glycoside Pseudo Base Pairs and Triples in an Apramycin-RNA Complex

2005 ◽  
Vol 44 (18) ◽  
pp. 2694-2700 ◽  
Author(s):  
Qing Han ◽  
Qiang Zhao ◽  
Sarah Fish ◽  
Klaus B. Simonsen ◽  
Dionisios Vourloumis ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Base Pairs ◽  
Rna Complex
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