Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Abstract Text:

Randall K Walker,Amanda K McCullough,R Stephen Lloyd,

Bacteriophage T4 pyrimidine dimer glycosylase (T4-Pdg) is a base excision repair protein that incises DNA at cyclobutane pyrimidine dimers that are formed as a consequence of exposure to ultraviolet light. Cocrystallization of T4-Pdg with substrate DNA has shown that the adenosine opposite the 5'-thymine of a thymine-thymine (TT) dimer is flipped into an extrahelical conformation and that the DNA backbone is kinked 60 degrees in the enzyme-substrate (ES) complex. To examine the kinetic details of the precatalytic events in the T4-Pdg reaction mechanism, investigations were designed to separately assess nucleotide flipping and DNA bending. The fluorescent adenine base analogue, 2-aminopurine (2-AP), placed opposite an abasic site analogue, tetrahydrofuran, exhibited a 2.8-fold increase in emission intensity when flipped in the ES complex. Using the 2-AP fluorescence signal for nucleotide flipping, kon and koff pre-steady-state kinetic measurements were determined. DNA bending was assessed by fluorescence resonance energy transfer using fluorescent donor-acceptor pairs located at the 5'-ends of oligonucleotides in duplex DNA. The fluorescence intensity of the donor fluorophore was quenched by 15% in the ES complex as a result of an increased efficiency of energy transfer between the labeled ends of the DNA in the bent conformation. Kinetic analyses of the bending signal revealed an off rate that was 2.5-fold faster than the off rate for nucleotide flipping. These results demonstrate that the nucleotide flipping step can be uncoupled from the bending of DNA in the formation of an ES complex.

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Publishing Authors By Initials

RK Walker,AK McCullough,RS Lloyd,

For similar investigative techniques: chemistry, analytical: photometry: luminescent measurements: fluorometry: spectrometry, fluorescence research abstracts see: investigative techniques: chemistry, analytical: photometry: luminescent measurements: fluorometry: spectrometry, fluorescence research

PUBMED ID PMID:

MEDLINE DATE:

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Biochemistry

VOLUME: 45

Page Numbers: 14192-200

Journal Abbreviation: Biochemistry

ISSN: 0006-2960

DAY: 28

MONTH: Nov

YEAR: 2006

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 370623

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Keywords Mesh Terms:

KEYWORDS: Spectrometry, Fluorescence

MESH TERMS: metabolism

Chemical & Substance for Abstract: Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. Information

Substance Name: DNA Glycosylases

Registry Number: EC 3.2.2.-

Grant and Affiliation Information for Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.

AFFILIATION: PerkinElmer Life and Analytical Sciences, Boston, Massachusetts 02118-2512, USA.

Country: United States

AGENCY: United States NIEHS

GRANT: P30 ES06676

ACRONYM: ES

MEDLINETA: Biochemistry

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase Related Publications

• Associations between common mental disorders and the Mental Illness Needs Index in community settings. Multilevel analysis.
• AtMAP70-5, a divergent member of the MAP70 family of microtubule-associated proteins, is required for anisotropic cell growth in Arabidopsis.
• Civil conflict in Northern Ireland and the prevalence of psychiatric disturbance across the United Kingdom: a population study using the British household panel survey and the Northern Ireland household panel survey.
• Cost-effectiveness of first- v. second-generation antipsychotic drugs: results from a randomised controlled trial in schizophrenia responding poorly to previous therapy.
• Diallyl disulphide depletes glutathione in Candida albicans: oxidative stress-mediated cell death studied by two-photon microscopy.
• Disruption of Rxra gene in thymocytes and T lymphocytes modestly alters lymphocyte frequencies, proliferation, survival and T helper type 1/type 2 balance.
• Doxorubicin eluting beads - 1: effects of drug loading on bead characteristics and drug distribution.
• Dr Brian Gibberd (1931-2006): a pioneering clinician in Refsum's disease.
• EGF and TGF-alpha supplementation enhances development of cloned mouse embryos.
• EKLF and KLF2 have compensatory roles in embryonic beta-globin gene expression and primitive erythropoiesis.
• Expressed emotion in families of children and adults with intellectual disabilities.
• First report of multiresistant, mecA-positive Staphylococcus intermedius in Europe: 12 cases from a veterinary dermatology referral clinic in Germany.
• Geographic variation in avian incubation periods and parental influences on embryonic temperature.
• Human polymorphic variants of the NEIL1 DNA glycosylase.
• Long-term storage of mouse spermatozoa after evaporative drying.
• Modeling community-based, self-help mental health rehabilitation reform.
• Mutagenic bypass of the butadiene-derived 2'-deoxyuridine adducts by polymerases eta and zeta.
• Observational studies: More than high standards needed.
• Phenotypic analysis of C57BL/6J and FVB/NJ mice generated using evaporatively dried spermatozoa.
• Pituitary adenoma with tumoral granulomatous reaction.
• Postinfective fatigue syndrome is not associated with altered cytokine production.
• Probing the biogeochemistry of arsenic: response of two contrasting aquifer sediments from Cambodia to stimulation by arsenate and ferric iron.
• Target specific virtual screening: optimization of an estrogen receptor screening platform.
• Th2-driven, allergen-induced airway inflammation is reduced after treatment with anti-Tim-3 antibody in vivo.
• The value of productivity standards.
• Trans-hepatic cannulation: a novel approach for placement of a pediatric percutaneous ventricular assist device.
• Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.
• Use of stable isotopically enriched proteins and directly coupled high-performance liquid chromatography inductively coupled plasma mass spectrometry for quantitatively monitoring the transfer of metals between proteins.
• Virus inactivation by protein denaturants used in affinity chromatography.
• Why buying a test is tougher than buying a car.