Base Pairing
Long-Distance Base Pairing in Flock House Virus RNA1 Regulates Subgenomic RNA3 Synthesis and RNA2 Replication
... long-distance base pairing (23, ...via base pairing between the 5⬘ noncoding region and an octamer sequence located upstream of both viral sgRNAs ...via base pairing of 12-nt ...
15
Partition function and base pairing probabilities of RNA heterodimers
... Difference dot Plot of native and mutated secondary struc- ture of a 3 GU mutation of the CXCR4 siRNA gene. The red part on the right hand side shows the base pairing probability of the 5' part of the micro ...
10
Base Pairing between the 5′ Half of ε and a cis-Acting Sequence, Φ, Makes a Contribution to the Synthesis of Minus-Strand DNA for Human Hepatitis B Virus
... Base pairing between ⌽ and is not sufficient for minus- strand DNA ...potential base pairing ( ⌽ 6/ε6, ⌽ 7/ε7, ⌽ 8/ε8, and ⌽ 10) did not make minus-strand DNA to levels signifi- cantly ...
8
Long-range vibrational dynamics are directed by Watson-Crick base-pairing in duplex DNA
... (base pairing and stacking; deoxyribose rings; phosphodiester groups) combine cooperatively to stabilize double helical DNA or contribute to duplex unwinding in transcription and replica- tion are not ...
11
Striking conformational similarities between the transcription promoters of Thogoto and influenza A viruses: evidence for intrastrand base pairing in the 5' promoter arm.
... interstrand base pairing throughout the length of the ...interstrand base pairing between the first 9 and 10 residues of the 3 9 and 5 9 promoter arms, respectively (4, ...interstrand, ...
5
Small DNA Hairpin Negatively Regulates In Situ Priming during Duck Hepatitis B Virus Reverse Transcription
... sheared base pairing between the G and A residues ...sheared base pair, and the mutant loop, 5⬘-AAA-3⬘, has increased in situ priming (data not ...sheared base pair contributing to function, ...
10
Essential Role of Cyclization Sequences in Flavivirus RNA Replication
... the base-pairing interactions between the covalently linked 5 ⴕ genomic region (first ⬃ 160 nucleotides) and the 3 ⴕ untranslated region (last ⬃ 115 nucleotides) for a range of mosquito-borne Flavivirus ...
10
An RNA stem-loop structure directs hepatitis B virus genomic RNA encapsidation.
... These studies reveal that i in the lower stem, base pairing but not specific primary sequence is required for function; ii there is no requirement for base pairing in the lower portion o[r] ...
10
The Stability of the Duplex between Sense and Antisense Transcription-Regulating Sequences Is a Crucial Factor in Arterivirus Subgenomic mRNA Synthesis
... The data presented above confirm and extend our previous findings (24, 25, 32) in which an important role in EAV sg mRNA synthesis was attributed to the stability of the leader TRS-body TRS duplex. Previously, we ...
9
In Vivo Selection of Rous Sarcoma Virus Mutants with Randomized Sequences in the Packaging Signal
... the base of element O3 was highly favored; only sequences which maintained base pairing were ...the base and in the middle of element L3, were not conserved: neither base pairing ...
10
Conserved determinants of lentiviral genome dimerization
... U5:AUG base pairing. To directly probe for U5:AUG base pairing, we employed a recently developed NMR-based approach that takes advantage of the unique NMR chemical shift patterns of adenosine ...
16
5098.pdf
... In a second approach, tRNA was modeled by representing each nucleotide as a single bead centered at the C3' atom, enforcing base pairing, and filtering structures based on hydroxyl radical cleavage and SAXS ...
162
Supplementary site interactions are critical for the regulation of microsomal triglyceride transfer protein by microRNA-30c
... These studies clearly show that supplementary interac- tions play a role in determining specificity and enhan- cing binding between miR-30c and MTTP. Previously, the importance of the interactions at the supplementary ...
9
Critical chemical features in trans-acting-responsive RNA are required for interaction with human immunodeficiency virus type 1 Tat protein.
... Structural requirements for trans activation of human immunodeficiency virus type 1 long terminal repeat-directed gene expression by tat: importance of base pairing, loop sequence, and b[r] ...
7
Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA.
... Third, the palindrome and flanking A’s normally reside within the loop atop an 11-bp stem structure interrupted by a four-base bulge. Our studies (Fig. 3) show that the bulge is dispensable, at least in vitro, but ...
7
Genetic repair Bruce A Sullenger, Series EditorRibozyme mediated revision of RNA and DNA
... by base-pairing between the exon sequence and the internal guide sequence (IGS) of the ...step. Pairing between the 5 ′ end of the intron and the 3 ′ exon form P10, which has been implicated in ...
8
Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element
... as base pairing interactions at the proximal end of helix II (C19·G37 base pairing) have been implicated in proper tem- plate boundary definition (19,20) (Figure ...
10
Mutational analysis of the equine infectious anemia virus Tat-responsive element.
... Structural requirements for trans-activation of human immunodeficiency virus type 1 long terminal repeat-directed gene expression by tat: importance of base pairing, loop sequence, and b[r] ...
7
Subgenomic RNA synthesis directed by a synthetic defective interfering RNA of mouse hepatitis virus: a study of coronavirus transcription initiation.
... However, the results obtained for the promoter mutants Bi and C3, both containing the same A->C substitution Table 2, seem difficult to interpret in terms of base pairing: introduction o[r] ...
11
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
... The three-dimensional structure is important for the functionality and/or the proper processing of a large and important subgroup of ncRNAs. The most promi- nent representatives are ribosomal RNAs (rRNAs), trans- fer ...
11