Novel oligomers are disclosed which have enhanced ability with respect to forming duplexes or triplexes compared with oligomers containing only conventional bases. The oligomers contain the bases 5-(1-propynyl)uracil, 5-(1-propynyl)cytosine or related analogs. The oligomers of the invention are capable of (i) forming triplexes with various target sequences such as virus or oncogene sequences by coupling into the major groove of a target DNA duplex at physiological pH or (ii) forming duplexes by binding to single-stranded DNA or to RNA encoded by target genes. The oligomers of the invention can be incorporated into pharmaceutically acceptable carriers and can be constructed to have any desired sequence, provided the sequence normally includes one or more bases that is replaced with the analogs of the invention. Compositions of the invention can be used as pharmaceutical agents to treat various diseases such as those caused by viruses and can be used for diagnostic purposes in order to detect viruses or disease conditions.

Enhanced triple-helix and double-helix formation with oligomers containing modified pyrimidines

Oligonucleotides with enhanced hybridization binding possessing 5-propynyluracil and/or 5-propynylcytosine in place of uracil and cytosine, respectively. These oligonucleotides are useful in traditional hybridization assays for detection of a specific DNA sequence.

Oligonucleotides containing 5-propynyl pyrimidines

Method for purification and synthesis of RNA molecules and enzymatic RNA molecules in enzymatically active form.

Synthesis, deprotection, analysis and purification of RNA and ribozymes

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.

Short cycle methods for sequencing polynucleotides

Compound 1 (F), a nonpolar nucleoside analog that is isosteric with thymidine, has been proposed as a probe for the importance of hydrogen bonds in biological systems. Consistent with its lack of strong H-bond donors or acceptors, F is shown here by thermal denaturation studies to pair very poorly and with no significant selectivity among natural bases in DNA oligonucleotides. We report the synthesis of the 5′-triphosphate derivative of 1 and the study of its ability to be inserted into replicating DNA strands by the Klenow fragment (KF, exo− mutant) of Escherichia coli DNA polymerase I. We find that this nucleotide derivative (dFTP) is a surprisingly good substrate for KF; steady-state measurements indicate it is inserted into a template opposite adenine with efficiency (Vmax/Km) only 40-fold lower than dTTP. Moreover, it is inserted opposite A (relative to C, G, or T) with selectivity nearly as high as that observed for dTTP. Elongation of the strand past F in an F–A pair is associated with a brief pause, whereas that beyond A in the inverted A–F pair is not. Combined with data from studies with F in the template strand, the results show that KF can efficiently replicate a base pair (A–F/F–A) that is inherently very unstable, and the replication occurs with very high fidelity despite a lack of inherent base-pairing selectivity. The results suggest that hydrogen bonds may be less important in the fidelity of replication than commonly believed and that nucleotide/template shape complementarity may play a more important role than previously believed.

https://www.pnas.org/content/pnas/94/20/10506.full.pdf

A thymidine triphosphate shape analog lacking Watson–Crick pairing ability is replicated with high sequence selectivity

Simple synthesis of 5-vinyl- and5-ethynyl-2′-deoxyuridine-5′-triphosphates

A series of (E)-5-(1-alkenyl)-dUTPs as well as 5-vinyl-and (Z)-5-(1-propenyl)-dUTP have been synthesized to study steric requirements in DNA polymerase reactions. Experiments were carried out in E. coli DNA polymerase I Klenow fragment enzyme system. Substrates were characterized by KM and Vmax-values, initial incorporation rates as well as by total extent of incorporation of the analogues into poly(dA-dT) as a template-primer. Incorporation of the analogues could be best correlated with Vmax-values as well as the very similar initial incorporation rate values. Reactivity (Vmax/KM) showed no correlation with the extent of incorporation. 5-Vinyl-dUTP proved to be as good a substrate of the enzyme as dTTP, whereas (E)-5-(1-heptenyl)-and (E)-5-(1-octenyl)-dUTPs were very poor substrates, their incorporation was strongly limited and they also proved to be very efficient inhibitors of DNA replication, as shown by Ki-values. Substrate specificity of the Klenow enzyme can be explained by the steric hindrance of C-5 substituent, by the "orientational steric substituent effect" concept.

Substrate specificity of DNA polymerases I. Enzyme-catalysed incorporation of 5-(1-alkenyl)-2′-deoxyuridines into DNA

Crystal structures of (Z)-5-(2-bromovinyl)-2'-deoxyuridine, 3',5'-di-O-acetyl-(E)-5-(2-bromovinyl)-2'-deoxyuridine and 3',5'-di-O-p-chlorobenzoyl-5-(2-dibromovinyl)-2'-deoxyuridine are compared with each other and with that of the most potent antiviral agent (E)-5-(2-bromovinyl)-2'-deoxyuridine (E-BVDU) reported earlier. A comparison of the conformation of 3',5'-di-O-acetyl-pyrimidine nucleoside structures in which intermolecular hydrogen bond network formation is minimized, with those of their parent compounds has shown that the greatest change in rotation about the glycosyl bond and in the sugar ring pucker is exhibited by E-BVDU. Upon acylation this molecule changes from C2'-endo/C3'-exo conformation to C3'-endo/C4'-exo conformation. The relevance of these structures upon the biological activity of the nucleosides and in particular to their ability to be a substrate for thymidine kinase is discussed.

A comparison of the conformations adopted by some 5-bromovinyl-2'-deoxyuridines and a correlation with their antiviral properties: an X-ray study

(E)-5-(2-bromovinyl-2'-deoxyuridine) crystallizes in the space group P2(1) with a = 12.976(1), b = 4.800(1), c = 20.385(2) A, beta = 96.88(1) degrees, Z = (two molecules a and b in the asymmetric unit). The structure has been determined by the use of 2400 diffractometer reflexions and refined by least-squares to R of 0.053. Conformational features of both molecules a and b resemble those of thymidine. The ribofuranose rings assume the rare C(3')-exo form observed also in thymidine. Similarly, the torsion angles around the glycosidic bonds (mean = 40(1) and 56(1) degrees fall in the anti range. In each molecule the best plane of the 2-bromovinyl moiety is bent out of the least-squares plane of the pyrimidine base by 6 degrees, so that the positively charged C(8)-H(8) group can donate an intramolecular hydrogen bond to 0(4) atom. Eight strong and weak intermolecular hydrogen bridges are built up between the symmetry independent and related molecules forming a complicated three dimensional hydrogen bond network.

Crystal and molecular structure of (E)-5-(2-bromoviayl-2′-deoxyuridine)

Crystal structures of(Z)-5-(2-bromovinyl)-2 '-deoxyuridine, 3',5'-di-0-acetyl-(E)-5-(2-bromovinyl)-2 '-deoxyuridine and3',5'-di-O-p-chlorobenzoyl-5-(2-dibromovinyl)-2'-deoxyuridine arecomparedwitheachotherandwith thatofthemostpotentantiviral agent(E)-5-(2-bromovinyl)-2'-deoxyuridine (E-BVDU)reportedearlier. A comparison oftheconformation of3',5'-di-O -acetyl-pyrimidine nucleoside structures inwhichintermolecular hydrogen bondnetworkformation isminimized, withthoseoftheirparentcompounds hasshownthatthegreatest changeinrotation abouttheglycosyl bondand inthesugarringpuckerisexhibited by E-BVDU.Uponacylation thismoleculechangesfromC2'endIC3'xoconformation toC31an Q/C4'"gconformation.Therelevance ofthesestructures uponthebiological activity ofthe nucleosides andinparticular totheirability tobe a substrate forthymidine kinase isdiscussed.

Teréz Kovács

Papers

Simple synthesis of 5-vinyl- and5-ethynyl-2′-deoxyuridine-5′-triphosphates

Substrate specificity of DNA polymerases I. Enzyme-catalysed incorporation of 5-(1-alkenyl)-2′-deoxyuridines into DNA

A comparison of the conformations adopted by some 5-bromovinyl-2'-deoxyuridines and a correlation with their antiviral properties: an X-ray study

Crystal and molecular structure of (E)-5-(2-bromoviayl-2′-deoxyuridine)

A comparison oftheconformations adopted bysome5-bromovinyl-2'-deoxyuridines anda correlation withtheir antiviral properties: anX-ray study