Biomaterial Database

Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase. 1995

Y K Kang, and H B Lee, and M J Noh, and N Y Cho, and O J Yoo

Department of Life Science, Korea Advanced Institute of Science and Technology, Taejon, Korea.

BamHI endonuclease and BamHI methylase were used to investigate their specific interaction with the common recognition sequence, GGATCC. Five derivatives of the oligonucleotide, GACGGATCCGTC, containing a variety of single-base analog substitutions within the hexameric recognition core were synthesized. Steady-state kinetics for the reaction of the endonuclease and the methylase showed that both enzymes recognize the sequences by contacting with functional groups exposed in both major and minor grooves of the site but in different ways. Removal or substitution of the 5-methyl group in thymidine blocked the endonuclease reaction completely but still allowed the methylase reaction with less efficiency. The data also showed that the methylase made a critical minor groove contact with the 2-amino group of the first G but the endonuclease did with that of the second G.

UI	MeSH Term	Description	Entries
D007288	Inosine	A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009841	Oligonucleotides	Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)	Oligonucleotide
D001976	Bromouracil	5-Bromo-2,4(1H,3H)-pyrimidinedione. Brominated derivative of uracil that acts as an antimetabolite, substituting for thymine in DNA. It is used mainly as an experimental mutagen, but its deoxyriboside (BROMODEOXYURIDINE) is used to treat neoplasms.	5-Bromouracil,Bromuracil,5 Bromouracil
D006147	Guanine
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D013329	Structure-Activity Relationship	The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.	Relationship, Structure-Activity,Relationships, Structure-Activity,Structure Activity Relationship,Structure-Activity Relationships
D013379	Substrate Specificity	A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.	Specificities, Substrate,Specificity, Substrate,Substrate Specificities