Abstract：
:We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Cabaj MK,Dominiak PMdoi
10.1093/nar/gkaa629subject
Has Abstractpub_date
2020-09-04 00:00:00pages
8302-8319issue
15eissn
0305-1048issn
1362-4962pii
5877809journal_volume
48pub_type
杂志文章abstract：:The polypeptides recognized by a monoclonal antibody against calf thymus DNA polymerase alpha (secreted from a hybridoma CL22 -2- 42B , Nucleic Acids Res. (1982) 10, 4703-4713) were identified by the immunoblot method as the large polypeptides of the partially-purified 10S DNA polymerase alpha fraction. Using an immun...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.11.4455
更新日期：1984-06-11 00:00:00
abstract：:Vaccinia virus DNA topoisomerase catalyzes resolution of synthetic Holliday junctions in vitro. The mechanism entails concerted transesterifications at two recognition sites, 5'-CCCTT/, that are opposed within a partially mobile four-way junction. Efficient resolution occurs on a junction with a 10 bp segment of branc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.14.2658
更新日期：2000-07-15 00:00:00
abstract：:Guanine-quadruplexes (G4) consist of non-canonical four-stranded helical arrangements of guanine-rich nucleic acid sequences. The bulky and thermodynamically stable features of G4 structures have been shown in many respects to affect normal nucleic acid metabolism. In vivo conversion of G4 structures to single-strande...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr630
更新日期：2011-11-01 00:00:00
abstract：:The nucleotide sequence of the promoter region and the first five genes of the atp (or unc) operon of Escherichia coli has been determined. The first proposed gene in the operon contains four AUA codons and may be poorly expressed; it encodes a basic but yet hydrophobic protein which could function as a pilot protein ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.16.3919
更新日期：1981-08-25 00:00:00
abstract：:The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.25.5737
更新日期：1994-12-25 00:00:00
abstract：:The Moloney murine leukemia virus (MLV) is a prototype gammaretrovirus requiring nuclear disassembly before DNA integration. In the nucleus, integration site selection towards promoter/enhancer elements is mediated by the host factor bromo- and extraterminal domain (BET) proteins (bromodomain (Brd) proteins 2, 3 and 4...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1157
更新日期：2019-02-20 00:00:00
abstract：:To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein-DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt051
更新日期：2013-03-01 00:00:00
abstract：:HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh289
更新日期：2004-02-23 00:00:00
abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.6.2215
更新日期：1989-03-25 00:00:00
abstract：:Many microRNAs (miRNAs) are co-regulated during the same physiological process but the underlying cellular logic is often little understood. The conserved, immunomodulatory miRNAs miR-146 and miR-155, for instance, are co-induced in many cell types in response to microbial lipopolysaccharide (LPS) to feedback-repress ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1030
更新日期：2013-01-07 00:00:00
abstract：:Computer programs, implemented on an Univac II00/80 computer system, for the identification and characterization of protein coding genes and for the analysis of nucleic acid sequences, are described. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part1.281
更新日期：1984-01-11 00:00:00
abstract：:The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.5.1965
更新日期：1989-03-11 00:00:00
abstract：:An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.9.2963
更新日期：1979-07-11 00:00:00
abstract：:A novel method combining elements of suppression subtractive hybridization with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The poten...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.13.2598
更新日期：1997-07-01 00:00:00
abstract：:Traditional chromatin analysis methods only test one locus at the time or use different templates for each locus, making a standardized analysis of large genomic regions or many co-regulated genes at different loci a difficult task. On the other hand, genome-wide high-resolution mapping of chromatin accessibility empl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp037
更新日期：2009-04-01 00:00:00
abstract：:The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.8.1319
更新日期：1995-04-25 00:00:00
abstract：:Human Ape2 protein has 3' phosphodiesterase activity for processing 3'-damaged DNA termini, 3'-5' exonuclease activity that supports removal of mismatched nucleotides from the 3'-end of DNA, and a somewhat weak AP-endonuclease activity. However, very little is known about the role of Ape2 in DNA repair processes. Here...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp357
更新日期：2009-07-01 00:00:00
abstract：:We describe the unique features of an aberrantly rearranged mu immunoglobulin heavy chain gene isolated from MPC-11 cells (a gamma 2b producing Balb/c plasmacytoma). A novel rearrangement has occurred 1.5 Kb 5' of the MPC-11 mu gene (denoted 18b mu) resulting in the deletion of the majority of the repetitive switch re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.23.7751
更新日期：1982-12-11 00:00:00
abstract：:Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj007
更新日期：2006-01-01 00:00:00
abstract：:Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.22.4607
更新日期：2001-11-15 00:00:00
abstract：:During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw375
更新日期：2016-07-27 00:00:00
abstract：:During DNA replication replicative polymerases move in discrete mechanical steps along the DNA template. To address how the chemical cycle is coupled to mechanical motion of the enzyme, here we use optical tweezers to study the translocation mechanism of individual bacteriophage Phi29 DNA polymerases during processive...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv204
更新日期：2015-04-20 00:00:00
abstract：:Predictably regulating protein expression levels to improve recombinant protein production has become an important tool, but is still rarely applied to engineer mammalian cells. We therefore sought to set-up an easy-to-implement toolbox to facilitate fast and reliable regulation of protein expression in mammalian cell...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa847
更新日期：2020-11-18 00:00:00
abstract：:The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute G...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv808
更新日期：2016-01-08 00:00:00
abstract：:Bcg I and Bcg I-like restriction endonucleases cleave double stranded DNA specifically on both sides of their asymmetric recognition sequences which are interrupted by several ambiguous base pairs. Their heterosubunit structure, bifunctionality and stimulation by AdoMet make them different from other classified restri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.22.4444
更新日期：1997-11-15 00:00:00
abstract：:The DNA repair enzyme human uracil DNA glycosylase (UNG) scans short stretches of genomic DNA and captures rare uracil bases as they transiently emerge from the DNA duplex via spontaneous base pair breathing motions. The process of DNA scanning requires that the enzyme transiently loosen its grip on DNA to allow stoch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp161
更新日期：2009-06-01 00:00:00
abstract：:The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5423
更新日期：1992-10-25 00:00:00
abstract：:Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often preve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq953
更新日期：2011-03-01 00:00:00
abstract：:E2F transcription factors (E2F1-8) are known to coordinately regulate the expression of a plethora of target genes, including those coding for microRNAs (miRNAs), to control cell cycle progression. Recent work has described the atypical E2F factor E2F7 as a transcriptional repressor of cell cycle-related protein-codin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw146
更新日期：2016-07-08 00:00:00
abstract：:The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/29.5.1013
更新日期：2001-03-01 00:00:00
