Chemically defined polyethylene glycol siRNA conjugates with enhanced gene silencing effect

The therapeutic application of siRNA suffers from poor bioavailability caused by rapid degradation and elimination. The covalent attachment of PEG is a universal concept to increase molecular size and enhance the pharmacokinetic properties of biomacromolecules. We devised a facile approach for attachment of PEG molecules with a defined molecular weight, and successful purification of the resulting conjugates. We directly conjugated structurally defined PEG chains with twelve ethylene glycol units to the 3′-terminal hydroxyl group of both sense and antisense strands via an aminoalkyl linker. The conjugates were easily purified by HPLC and successful PEGylation and molecule integrity were confirmed by ESI-MS. The evaluation of in vitro gene knockdown of two different targets in MCF-7 breast cancer cells showed stable pharmacologic activity when combined with a standard transfection reagent. Sense strand PEGylation even increased the silencing potency of a CRCX4-siRNA which had modest activity in its wild-type form. The results indicate that PEG chains at the 3′-terminus of both strands of siRNA are well tolerated by the RNAi effector. The attachment of short, chemically defined PEG chains is a feasible approach to improve the pharmacokinetic properties of siRNA, and can be combined with other targeted and untargeted delivery vehicles.     

DNA sequence patterns in human,mouse, and rabbit immunoglobulin kappa-genes

Summary DNA sequences of the human, mouse, and rabbit immunoglobulin kappa-gene (J-C regions) are compared with respect to various DNA patterns, including dyad symmetry pairings, runs of nucleotides, repeat clusters, and repeats that occur with unusually high frequency. The significant dyad symmetry pairings within each of the sequences emphasize the two control-enhancer elements of the J₅-C intron. Dyad symmetry pairs between the J-C region and a number of kappa variable (V)-gene domains suggest differences in the affinities between the V and J segments. It is the consensus heptamer rather than the consensus nonamer that embodies the longest V-J dyad symmetry combinations. In the rabbit there are long runs and repeat clusters of the sequences that identify regions of high duplication; these regions are absent in the human and mouse sequences. High-frequency oligonucleotides feature the consensus nonamer 5 to the J segments, especially in the mouse sequence.     

Selectively 13C-enriched DNA: 13C and 1H assignments of a triple helix by two-dimensional relayed HMQC experiments

Summary We present NMR studies of an intramolecular triple helix, the three strands of which have been linked by a hexaethylene glycol chain. To overcome the generally encountered difficulties of assignment in the homopyrimidine strands, the carbon C1 of the pyrimidines were selectively ¹³C-enriched. Assignments of the aromatic and sugar protons were obtained from NOESY-HMQC and TOCSY-HMQC spectra. We show that the recognition of a DNA duplex by a third strand via triplex formation is easily carried out in solution by observing the changes of the ¹H1–¹³C1 connectivities as a function of pH. Furthermore, the conformation of the sugars has been found to be C2-endo, on the basis of the coupling constant values directly measured in an HSQC spectrum.     

A 19-kb CpG Island Associated with Single-minded Gene 2 in Down Syndrome Chromosomal Region

To help in isolating the genes involved in Down syndrome, wesought CpG islands in 4 Mb cosmid/PAC contigs spanning mostof the 21q.22.2 band using seven rare cutting enzymes. A strikingfeature was observed upstream of hSIM2 where at least 41 rare-cuttingsites were clustered within a 20-kb region. To investigate thestructure of the cluster, a cosmid containing hSIM2 was submittedto shotgun sequencing. Sequence analysis revealed that the clusterwas a long CpG island extending 19, 128 nucleotides which includesin the first and second exons of hSIM2. Taken together withour observation in which the CpG islands were concentrated within1.2 Mb around hSIM2, we propose that this region functions asan R-band, and the cluster provides a unique element for markingof DNA for the spatial and temporal expression of the hSIM2locus.     

Brief overview of control of genetic expression by antisense oligonucleotides and in vivo applications

Over the past several years, the use of synthetic oligonucleotides and functional analogs thereof as a possibly general means of controlling genetic expression has received widespread attention. Following a brief overview of some of the basic principles and strategies for this approach, attention is focused here on summarizing some recent reports of in vitro and, in particular, in vivo investigations in various animal models using phosphorothioate analogs of 2′-deoxyoligo-nucleotides. In view of these findings, which include studies related to neurobiology, this field should find significant utility in applications of the antisense method for controlling genetic expression.     

An apparatus for simultaneous manual solid-phase synthesis of multiple peptide analogs

A new design of reaction vessel for simultaneous manual solid-phase synthesis of multiple peptide analogs is described. Simultaneous use of four of these vessels attached to a single rotary mixer has been successfully applied to synthesis of two sets of four decapeptide amide analogs. Efficient coupling was indicated by chemical determination at the end of each synthesis cycle and overall final yields of between 78 and 84% were obtained. The products obtained were of a high quality, as assessed by high-performance liquid chromatography and amino acid analysis. This system allows expeditious synthesis of multiple peptide analogs for structure-function studies with economical use of efficiently ventilated laboratory space.     

The influence of nearest neighbors on the rate and pattern of spontaneous point mutations

Summary The numbers and local sequence environments of the two types of substitution mutation plus additions and deletions have been obtained directly in this study from differences between a large number of extant primate gene and pseudogene sequences. A total of 3786 mutations were scored in regions where similarities between pseudogene and corresponding gene sequences is 85%, comprising 30% of the pseudogene database of 80,584 bp. The pattern of mutations obtained in this fashion is almost identical to that obtained by Li et al. (1984) using a slightly different, more direct approach and with a smaller database. When mutations were scored, the neighbor pairs on the 5 and 3 sides were also noted, leading to a large 16 × 12 matrix of transitions and transversions. Biases of varying magnitude are found in the rates of substitution of the same base pair in different local sequence environments. The overall order for the effect of the 5 neighbor on the rates of substitution mutation of a pyrimidine is A > C T > G, and G > A > T > C for the 3 neighbor; where these results represent the average of substitution rates for the complement purine with complement neighbors of bases ordered above. The order for the 3 neighbor is essentially the same for the two transitions and most of the four transversions as well; however, the order for the 5 neighbor is more variable. The overall rate for the C · G T · A transition is not unusual, however the presence of a 3 neighboring G · C pair boosts the rate substantially, presumably due to specific cytosine methylation of the CG doublet in primate DNAs. The rate of the T · A C · G transition is also well above average when the 3 neighbor is an A · T, and to a lesser extent a G · C, pair. The latter bias is typical in that it reflects the association of alternating pyrimidine-purine sequences with increasing mutation rates. The substitution of the pyrimidine in a 5 purine-pyrimi-dine-purine3 sequence generally occurs much faster than in a pyrimidine tract and points to the local conformation as a major determining factor of the substitution rate. An apparent inverse relationship is found between starting and product doublet frequencies of base pairs undergoing mutations with specific 3 neighbors, indicating that differences in intrinsic substitution rates of base pairs with specific neighbors are a key factor in producing the familiar biases of nearest-neighbor frequencies.Offprint requests to: R. D. Blake