Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study.

No abstract is available for this paper.

• Publication year

  1988

• Venue

  Nucleic Acids Research

• Publication date

  1988-04-11

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1093/NAR/16.7.2971PMID 3368313PMCID PMC336445
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution.

  1987cited by this paper
• Conformational perturbation due to an extra adenosine in a self‐complementary oligodeoxynucleotide duplex

  1987cited by this paper
• Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence.

  1987cited by this paper
• Conformational transitions of synthetic DNA sequences with inserted bases, related to the dodecamer d(CGCGAATTCGCG).

  1987cited by this paper
• The B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz two-dimensional NMR study.

  1986cited by this paper
• Extrahelical adenosine stacks into right-handed DNA: solution conformation of the d(C-G-C-A-G-A-G-C-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra.

  1986cited by this paper
• Predicting DNA duplex stability from the base sequence.

  1986cited by this paper
• Wobble dG X dT pairing in right-handed DNA: solution conformation of the d(C-G-T-G-A-A-T-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra.

  1986cited by this paper
• Mechanism of oligonucleotide loop formation in solution.

  1986cited by this paper
• An all atom force field for simulations of proteins and nucleic acids

  1986cited by this paper
• Characterization of imperfect DNA duplexes containing unpaired bases and non-Watson-Crick base pairs.

  1986cited by this paper
• Consequences of methylation on the amino group of adenine. A proton two-dimensional NMR study of d(GGATATCC) and d(GGm6ATATCC).

  1985cited by this paper
• Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy.

  1984cited by this paper
• Effective water resonance suppression in 1D- and 2D-FT-1H-NMR spectroscopy of biopolymers in aqueous solution.

  1983cited by this paper
• Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods.

  1983cited by this paper
• Conformational analysis of a hybrid DNA-RNA double helical oligonucleotide in aqueous solution: d(CG)r(CG)d(CG) studied by 1D- and 2D-1H NMR spectroscopy.

  1983cited by this paper
• Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution.

  1982cited by this paper
• Extrahelical bases in duplex DNA.

  1982cited by this paper
• Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G . T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G).

  1982cited by this paper
• Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method.

  1982cited by this paper
• Local destabilisation of a DNA double helix by a T–T wobble pair

  1979cited by this paper
• Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday.

  1966cited by this paper

• Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions

  2016cites this paper
• Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions.

  2016cites this paper
• Structure of the 1,N2-Etheno-2′-deoxyguanosine Lesion in the 3′-G(εdG)T-5′ Sequence Opposite a One-Base Deletion†

  2010cites this paper
• Bulge migration of the malondialdehyde OPdG DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene.

  2007cites this paper
• DNA Structures of Biological Relevance, Studies of Unusual Sequences

  2006cites this paper
• Mechanics of DNA flexibility visualized by selective 2'-amine acylation at nucleotide bulges.

  2004cites this paper
• Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics.

  2003cites this paper
• Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

  2001cites this paper
• Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges.

  2001cites this paper
• The exocyclic 1,N2-deoxyguanosine pyrimidopurinone M1G is a chemically stable DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene.

  2001cites this paper
• Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).

  2000cites this paper
• 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects.

  1998cites this paper
• Solution structure of N-(2-deoxy-D-erythro-pentofuranosyl)urea frameshifts, one intrahelical and the other extrahelical, by nuclear magnetic resonance and molecular dynamics.

  1998cites this paper
• Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases.

  1998cites this paper
• Solution conformation of a five-nucleotide RNA bulge loop from a group I intron.

  1997cites this paper
• Interaction of MutS Protein with the Major and Minor Grooves of a Heteroduplex DNA*

  1997cites this paper
• Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC) x d(GCGTGTGTGCG): the unpaired thymine stacks inside the helix.

  1997cites this paper
• Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.

  1997cites this paper
• Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.

  1996cites this paper
• Sequence effects on RNA bulge-induced helix bending and a conserved five-nucleotide bulge from the group I introns.

  1996cites this paper
• Bulge-induced bends in RNA: quantification by transient electric birefringence.

  1995cites this paper
• Structure of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frame shift hotspot of Salmonella typhimurium hisD3052 determined by 1H NMR and restrained molecular dynamics.

  1995cites this paper
• Kinking of DNA and RNA by base bulges.

  1995cites this paper
• Bulge defects in intramolecular pyrimidine.purine.pyrimidine DNA triplexes in solution.

  1995cites this paper
• RNA Structure and Interactions With Proteins

  1995cites this paper
• Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment.

  1995cites this paper
• 1H NMR characterization of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frameshift hotspot of Salmonella typhimurium hisD3052.

  1994cites this paper
• Characterization of the effects of a thymine glycol residue on the structure, dynamics, and stability of duplex DNA by NMR.

  1993cites this paper
• Site-specific cleavage at a DNA bulge by neocarzinostatin chromophore via a novel mechanism.

  1993cites this paper
• RecA binding to bulge- and mismatch-containing DNAs. Certain single base mismatches provide strong signals for RecA binding equal to multiple base bulges.

  1993cites this paper
• Nuclear magnetic resonance study of a deoxyoligonucleotide duplex containing a three base bulge.

  1993cites this paper
• Imperfectly matched nucleic acid complexes and their biochemical manifestation

  1993cites this paper
• The structure of branched DNA species

  1993cites this paper
• Nmr studies of an extrahelical cytosine in an A·T rich region of a deoxyribodecanucleotide

  1993cites this paper
• Comparative NMR study of A(n)-bulge loops in DNA duplexes: intrahelical stacking of A, A-A, and A-A-A bulge loops.

  1992cites this paper
• Visualization of diagnostic heteroduplex DNAs from cystic fibrosis deletion heterozygotes provides an estimate of the kinking of DNA by bulged bases.

  1992cites this paper
• Solution structure of a trinucleotide A-T-A bulge loop within a DNA duplex.

  1992cites this paper
• Three-dimensional structures of bulge-containing DNA fragments.

  1992cites this paper
• Solution conformation of an oligonucleotide containing a urea deoxyribose residue in front of a thymine.

  1992cites this paper
• RNA pseudoknots

  1992cites this paper
• Structure and in vitro replication of DNA templates containing 7,8-dihydro-8-oxoadenine.

  1991cites this paper
• Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases.

  1991cites this paper
• Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges.

  1991cites this paper
• Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states.

  1990cites this paper
• [Chemical reactions of double-helical nucleic acids. XI. Interaction between kinetic parameters of chemical ligation in modified DNA-duplexes and structure of the reaction site].

  1990cites this paper
• NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA).oligo(dT) tract.

  1990cites this paper
• Sequence- and structure-dependent DNA base dynamics: synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA.

  1989cites this paper
• Conformational consequences of the incorporation of arabinofuranosylcytidine in DNA. An NMR study of the DNA fragments d(CGCTAGCG) and d(CGaCTAGCG) in solution.

  1989cites this paper
• Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution.

  1989cites this paper
• Complexes of oligo(poly)nucleotides with structural anomalies

  1989cites this paper