Literature DB >> 28524232

Robust IR-based detection of stable and fractionally populated G-C+ and A-T Hoogsteen base pairs in duplex DNA.

Allison L Stelling1, Yu Xu2, Huiqing Zhou1, Seung H Choi1, Mary C Clay1, Dawn K Merriman2, Hashim M Al-Hashimi1,2.   

Abstract

Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
© 2017 Federation of European Biochemical Societies.

Entities:  

Keywords:  DNA; Hoogsteen; NMR; infrared; m1A; m1G

Mesh：

Substances：

Year:  2017        PMID： 28524232      PMCID： PMC5584567          DOI： 10.1002/1873-3468.12681

Source DB:  PubMed          Journal:  FEBS Lett        ISSN： 0014-5793            Impact factor:   4.124


  90 in total

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Journal:  J Phys Chem Lett       Date:  2016-02-25       Impact factor: 6.475

2.  The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

Authors:  Attila Bende; Cristina M Muntean
Journal:  J Mol Model       Date:  2014-02-25       Impact factor: 1.810

3.  An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences.

Authors:  X Huang; P Yu; E LeProust; X Gao
Journal:  Nucleic Acids Res       Date:  1997-12-01       Impact factor: 16.971

4.  Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA.

Authors:  J M Benevides; G J Thomas
Journal:  Nucleic Acids Res       Date:  1983-08-25       Impact factor: 16.971

5.  Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin A-d(GCGTACGC) complex.

Authors:  A H Wang; G Ughetto; G J Quigley; A Rich
Journal:  J Biomol Struct Dyn       Date:  1986-12

6.  Interpretation of DNA vibration modes. II--The adenosine and thymidine residues involved in oligonucleotides and polynucleotides.

Authors:  R Letellier; M Ghomi; E Taillandier
Journal:  J Biomol Struct Dyn       Date:  1987-02

7.  FTIR study of a nonclassical dT10*dA10-dT10 intramolecular triple helix.

Authors:  C Dagneaux; J Liquier; E Taillandier
Journal:  Biochemistry       Date:  1995-11-14       Impact factor: 3.162

8.  The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions.

Authors:  T J Thamann; R C Lord; A H Wang; A Rich
Journal:  Nucleic Acids Res       Date:  1981-10-24       Impact factor: 16.971

9.  Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

Authors:  Francisco J Acosta-Reyes; Elida Alechaga; Juan A Subirana; J Lourdes Campos
Journal:  PLoS One       Date:  2015-03-17       Impact factor: 3.240

10.  m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.

Authors:  Huiqing Zhou; Isaac J Kimsey; Evgenia N Nikolova; Bharathwaj Sathyamoorthy; Gianmarc Grazioli; James McSally; Tianyu Bai; Christoph H Wunderlich; Christoph Kreutz; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Nat Struct Mol Biol       Date:  2016-08-01       Impact factor: 15.369
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  7 in total

1.  5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex.

Authors:  Brennan Ashwood; Paul J Sanstead; Qing Dai; Chuan He; Andrei Tokmakoff
Journal:  J Phys Chem B       Date:  2020-01-14       Impact factor: 2.991

2.  Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Authors:  Allison L Stelling; Amy Y Liu; Wenjie Zeng; Raul Salinas; Maria A Schumacher; Hashim M Al-Hashimi
Journal:  Angew Chem Int Ed Engl       Date:  2019-07-25       Impact factor: 15.336

3.  Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?

Authors:  Atul Rangadurai; Huiqing Zhou; Dawn K Merriman; Nathalie Meiser; Bei Liu; Honglue Shi; Eric S Szymanski; Hashim M Al-Hashimi
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

4.  Modeling the vibrational couplings of nucleobases.

Authors:  Yaoyukun Jiang; Lu Wang
Journal:  J Chem Phys       Date:  2020-02-28       Impact factor: 3.488

5.  Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.

Authors:  Jocelyne Vreede; Alberto Pérez de Alba Ortíz; Peter G Bolhuis; David W H Swenson
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

6.  Modulation of Hoogsteen dynamics on DNA recognition.

Authors:  Yu Xu; James McSally; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Nat Commun       Date:  2018-04-16       Impact factor: 14.919

7.  Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy.

Authors:  Robert J Fick; Amy Y Liu; Felix Nussbaumer; Christoph Kreutz; Atul Rangadurai; Yu Xu; Roger D Sommer; Honglue Shi; Steve Scheiner; Allison L Stelling
Journal:  J Phys Chem B       Date:  2021-07-08       Impact factor: 2.991
  7 in total

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