DNA/RNA duplexes

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

The antisense approach is use of nucleic acids to reduce the expression of a specific target gene. As shown in Figure 58.2, a small piece of DNA, an oligodeoxynu-cleotide that is in the reverse orientation (antisense) to a portion of a target messenger RNA (mRNA) species, is introduced into a cell and a DNA-RNA duplex is formed by complementary Watson-Crick base pairing. Cessation of protein synthesis then may result from the rapid... 

Although all the RNA-RNA and DNA-RNA duplexes we have examined so far belong to the same tg g tg+ genus in the A-family, there is the exception of poly d(l)-poly(C) whose... 

The terms A/T and G/C refer to the number of A-to-T and G-to-C base pairs, respectively, in the duplex strand. The Wallace rule was designed for duplex strands of 14 to 20 base pairs. The Tm of RNA-RNA and DNA-RNA duplexes may be estimated with Equation 6.2.7... 

Ribonuclease H An endonuclease that degrades the RNA strand in a DNA-RNA duplex... 

The substitution of pentose by hexose sugars has received much attention because oligonucleotides containing hexose sugars have many useful properties. The first hybridisation system between pyranose and furanose nucleic acids has been reported. a-Pyranose oligonucleotides (a-homo-DNA) forms stable duplexes with RNA in a parallel orientation. NMR studies show that the a-homo-DNA bases (in a-homo-DNA RNA duplexes) are equatorially arranged, whilst in the RNA strand they are pseudoaxial. The helical structure does not conform to either A- or B-forms. 

In addition to the detection of antigens and antibodies, EIA will, undoubtedly, play an increasingly important role in molecular biology. For example, the bio-blot method (Leary et al., 1983) for the detection of DNA-DNA or DNA-RNA duplexes on nitrocellulose membranes offers important advantages over conventional procedures in which radioactive probes are used and autoradiographic detection. In this method, biotinylated DNA probes are prepared by nick translation (Rigby et al., 1977) in the presence of biotinylated analogs and hybridized with the DNA or RNA on filters. Biotin is then detected by avidin-labeled enzyme (Section 3.1). 

The structure of a hybrid DNA-RNA duplex containing a single MMI (3 -CH2N(CH3)-0-5 ) linker in the centre of the DNA strand has been studied by NMR. The lipophilic N-methyl group is peripheral to the duplex and the linker promotes a 3 -endo conformation for both adjacent sugar moieties. 

Mature mRNA transcripts (sense strand) from eukaryotic cells can be purified and then reverse transcribed, with the assistance of a reverse transcriptase enzyme (from Moloney murine leukemia virus, MMLV), into complementary DNAs (cDNAs) that will anneal with the mRNA transcripts by Watson-Crick base pairing to give anti-parallel DNA/RNA duplexes or double helices. The poly(A) tail in each mature mRNA transcript is actually a usefiil handle for each reverse transcriptase reaction. Thereafter, DNA/RNA duplexes must be broken down with the assistance ofRNAse enzymes (specific for the hydrolysis of RNA phospho diester links) and a sense strand of DNA constructed instead on each cDNA single strand so that equivalent, more stable antiparallel DNA/DNA duplexes are generated instead, with the assistance of a DNA polymerase enzyme. In this instance, the poly(T) tail in each cDNA molecule turns out to be important for the DNA polymerase reaction ... 

Figure 27. Visualization of biomesogenic nucleic-acid selforganizations by molecular-resolving microscopies (top to bottom and left to right) nucleic acid strand patterns B-DNA and A-RNA duplexes, DNA/ RNA triplex, G-quadruplex, DNA/RNA-duplex/pro-tein-)3-sheet complexations STM and SFM-investi-gations of nucleic acid organizational behavior DNA-plasmid [74 c] RNA- and RNA/peptide-organiza-tions (U) (A) -duplexes (U) (A) (U) -tri-plexes (G) -quadruplexes, (L-Lys) /(U) (A) -com-plexes in 2D and 3D representation [7 a, 17, 18, 33 a, c, f, p, q, 75].

Freier SM, Altmarm K-H (1997) The ups and downs of nucleic acid duplex stability structure-stability studies on chemically-modified DNA RNA duplexes. Nucleic Acids Res 25 4429 443... 

Odom DT, Barton JK Long-range oxidative damage in DNA/RNA duplexes. Biochemistry 2001, 40(30) 8727—8737. 

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