Biomaterial Database

Synthesis and hybridization properties of 2'-O-methyl-RNA incorporating 3-deazaguanine derivatives. 2005

Kohji Seio, and Takeshi Sasami, and Akihiro Ohkubo, and Mitsuo Sekine

Frontier Collaborative Research Center, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.

3-Deazaguanine (3DG) and its 2-N-acylated derivatives were incorporated into 2'-O-methyl-RNAs, and the hybridization and base discrimination properties were clarified by measuring UV-melting profiles. The 2'-O-methyl-RNA incorporating a 3DG hybridized less strongly in comparison to that without 3-deaza modification to both fully-matched and singly mismatched target strands. The T(m) decrease was the largest in the case of the fully matched duplex so that the base discrimination ability was decreased. Interestingly, the acetylation of the amino group of 3DG could compensate the T(m) decrease of the fully matched duplex by 3DG. Moreover, it was also proved that the base pair of 2-N-acetyl-3-deazaguanine and uracil was much weaker than the G-U pair. These results indicate the possibility of the development of guanine analogs that can recognize cytosine more precisely than guanine by use of the 2-N-acyl-3-deazaguanine skeleton.

UI	MeSH Term	Description	Entries
D008745	Methylation	Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)	Methylations
D009693	Nucleic Acid Hybridization	Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)	Genomic Hybridization,Acid Hybridization, Nucleic,Acid Hybridizations, Nucleic,Genomic Hybridizations,Hybridization, Genomic,Hybridization, Nucleic Acid,Hybridizations, Genomic,Hybridizations, Nucleic Acid,Nucleic Acid Hybridizations
D006147	Guanine
D012313	RNA	A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)	RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D013696	Temperature	The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.	Temperatures
D020029	Base Pairing	Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.	Base Pair,Base Pairs,Base Pairings
D020137	Base Pair Mismatch	The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).	Base Pair Mismatches,Mismatch, Base Pair,Mismatches, Base Pair