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steric hindrance

Overview page. Subjects: Chemistry.

An effect in which a chemical reaction is slowed down or prevented because large groups on a reactant molecule hinder the approach of another reactant molecule.

See overview in Oxford Index

The interaction of 2-phenylbenzimidazole compounds with DNA: The influence of terminal substituents

Yukio Kubota, Seiji Tani and Junichi Nakamura.

in Nucleic Acids Symposium Series

November 2002; p ublished online November 2002 .

Journal Article. Subjects: Chemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 0 words.

We have studied the influence of terminal substituents, amidinium group and N-methylpiperazine ring, of 2-phenylbenzimidazole compounds (1–6; Figure 1) on their DNA-binding modes....

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Steric Factors Influencing Hybridisation Of Nucleic Acids To Oligonucleotide Arrays

M. S. Shchepinov, S. C. Case-Green and E. M. Southern.

in Nucleic Acids Research

March 1997; p ublished online March 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4048 words.

We have investigated the use of spacer molecules to reduce steric interference of the support on the hybridisation behaviour of immobilised oligonucleo-tides. These spacers are built up...

Biochemical analysis of human Dna2

Taro Masuda-Sasa, Osamu Imamura and Judith L. Campbell.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7807 words.

Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5′ flaps. It is also...

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Repair of DNA-protein crosslink damage: Coordinated actions of nucleotide excision repair and homologous recombination

Hiroshi Ide, Toshiaki Nakano, Amir M.H. Salem, Hiroaki Terato, Seung Pil Pack and Keisuke Makino.

in Nucleic Acids Symposium Series

September 2008; p ublished online September 2008 .

Journal Article. Subjects: Chemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 0 words.

DNA-protein crosslinks (DPCs) are extremely bulky DNA lesions, and steric hindrance imposed by covalently trapped proteins would hamper the transaction of DNA such as replication,...

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Molecular basis for the enantioselectivity of HIV-1 reverse transcriptase: Role of the 3′-hydroxyl group of the L-(β)-ribose in chiral discrimination between D- and L-enantiomers of deoxy- and dideoxy-nucleoside triphosphate analogs

Giovanni Maga, Silvio Spadari, Mario Amacker, Ulrich Hübscher, Gilles Gosselin, Jean-Luis Imbach, Christophe Mathé, Abdesslem Faraj and Jean-Pierre Sommadossi.

in Nucleic Acids Research

February 1999; p ublished online February 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3918 words.

In order to identify the basis for the relaxed enantioselectivity of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and to evaluate possible cross-resistance...

Intermolecular ‘cross-torque’: the N4 -cytosine propargyl residue is rotated to the ‘CH’-edge as a result of Watson–Crick interaction

Olwen Domingo, Isabell Hellmuth, Andres Jäschke, Christoph Kreutz and Mark Helm.

in Nucleic Acids Research

June 2015; p ublished online April 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5770 words.

Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being...

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Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation

Shunnichi Kashida, Tan Inoue and Hirohide Saito.

in Nucleic Acids Research

October 2012; p ublished online July 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5440 words.

The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to...

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NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

Peter Podbevšek, Nicholas V. Hud and Janez Plavec.

in Nucleic Acids Research

April 2007; p ublished online April 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7309 words.

d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15[math] ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure...

Fluorescence protection assay: a novel homogeneous assay platform toward development of aptamer sensors for protein detection

Hong-Qi Wang, Zhan Wu, Li-Juan Tang, Ru-Qin Yu and Jian-Hui Jiang.

in Nucleic Acids Research

October 2011; p ublished online July 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3527 words.

Development of novel aptamer sensor strategies for rapid and selective assays of protein biomarkers plays crucial roles in proteomics and clinical diagnostics. Herein, we have developed a...

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The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system

Esther E. A. Verhoeven, Marian van Kesteren, John J. Turner, Gijs A. van der Marel, Jacques H. van Boom, Geri F. Moolenaar and Nora Goosen.

in Nucleic Acids Research

June 2002; p ublished online June 2002 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6949 words.

Nucleotide excision repair in Escherichia coli involves formation of the UvrB–DNA complex and subsequent DNA incisions on either site of the damage by UvrC. In this paper, we studied the...

Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence

Jiafeng Gu, Haihui Lu, Albert G. Tsai, Klaus Schwarz and Michael R. Lieber.

in Nucleic Acids Research

September 2007; p ublished online August 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4064 words.

The double-strand DNA break repair pathway, non-homologous DNA end joining (NHEJ), is distinctive for the flexibility of its nuclease, polymerase and ligase activities. Here we find that...

Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids

Ki-Hyun Kim, Peter E. Nielsen and Peter M. Glazer.

in Nucleic Acids Research

December 2007; p ublished online October 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5855 words.

Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in...

The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms

Sven Sewitz, Paul Crellin and Ronald Chalmers.

in Nucleic Acids Research

October 2003; p ublished online October 2003 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7165 words.

The Tn10 transpososome has symmetrical components on either side: there are two transposon ends each of which has binding sites for a monomer of transposase and an IHF heterodimer. The DNA...

Efficient in vitro inhibition of HIV-1 gag reverse transcription by peptide nucleic acid (PNA) at minimal ratios of PNA/RNA

Uffe Koppelhus, Vladimir Zachar, Peter E. Nielsen, Xiangdon Liu, Jesper Eugen-Olsen and Peter Ebbesen.

in Nucleic Acids Research

June 1997; p ublished online June 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4513 words.

We have tested the inhibitory potential of peptide nucleic acid (PNA) on in vitro reverse transcription of the HIV-1 gag gene. PNA was designed to target different regions of the HIV-1 gag...

Chiral and steric effects in the efficient binding of α-anomeric deoxyoligonucleoside N-alkylphosphoramidates to ssDNA and RNA

Alain Laurent, Magali Naval, Françoise Debart, Jean-Jacques Vasseur and Bernard Rayner.

in Nucleic Acids Research

November 1999; p ublished online November 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4771 words.

We report hybridization properties of new phosphate-modified α-oligonucleoside analogs with non-ionic or cationic internucleotide linkages such as methoxy-ethylphosphoramidate (PNHME),...

Electrochemical detection of low-copy number salivary RNA based on specific signal amplification with a hairpin probe

Fang Wei, Jianghua Wang, Wei Liao, Bernhard G. Zimmermann, David T. Wong and Chih-Ming Ho.

in Nucleic Acids Research

June 2008; p ublished online May 2008 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4015 words.

We developed a technique for electrochemical detection of salivary mRNA employing a hairpin probe (HP). Steric hindrance (SH) suppresses unspecific signal and generates a signal-on...

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Targeted correction of a thalassemia-associated β-globin mutation induced by pseudo-complementary peptide nucleic acids

Pallavi Lonkar, Ki-Hyun Kim, Jean Y. Kuan, Joanna Y. Chin, Faye A. Rogers, Melissa P. Knauert, Ryszard Kole, Peter E. Nielsen and Peter M. Glazer.

in Nucleic Acids Research

June 2009; p ublished online April 2009 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6256 words.

β-Thalassemia is a genetic disorder caused by mutations in the β-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate...

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Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates

Pernilla Lagerbäck, Evalena Andersson, Christer Malmberg and Karin Carlson.

in Nucleic Acids Research

October 2009; p ublished online August 2009 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7714 words.

The oligomerization state and mode of binding to DNA of the GIY-YIG endonuclease II (EndoII) from bacteriophage T4 was studied using gel filtration and electrophoretic mobility shift assays...

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Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad

Vee Vee Cheong, Brahim Heddi, Christopher Jacques Lech and Anh Tuân Phan.

in Nucleic Acids Research

December 2015; p ublished online September 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5902 words.

G-quadruplexes are four-stranded structures built from stacked G-tetrads (G·G·G·G), which are planar cyclical assemblies of four guanine bases interacting through Hoogsteen hydrogen bonds....

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Effect of Geometric Isomerism in Dinuclear Platinum Antitumour Complexes on the Rate of Formation and Structure of Intrastrand Adducts with Oligonucleotides

Kirste J. Mellish, Yun Qu, Neel Scarsdale and Nicholas Farrell.

in Nucleic Acids Research

March 1997; p ublished online March 1997 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3858 words.

The dinuclear platinum complexes [{trans-PtCl (NH3)2}2µ-{HNH2(CH2) n NH2}](NO3)2 [1,1/t,t (n = 4,6)] and [{cis-PtCl(NH3)2}2µ-{NH2(CH2) nnull...