scholarly journals Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays

2003 ◽  
Vol 69 (5) ◽  
pp. 2848-2856 ◽  
Author(s):  
Hidetoshi Urakawa ◽  
Said El Fantroussi ◽  
Hauke Smidt ◽  
James C. Smoot ◽  
Erik H. Tribou ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Microarrays ◽  
Perfect Match ◽  
Analytical Framework ◽  
Single Base ◽  
Dna And Rna ◽  
Base Pair Mismatch ◽  
Nonequilibrium Dissociation ◽  
Single Base Pair ◽  
Mismatch Discrimination

ABSTRACT The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

scholarly journals Single-Base-Pair Discrimination of Terminal Mismatches by Using Oligonucleotide Microarrays and Neural Network Analyses

2002 ◽  
Vol 68 (1) ◽  
pp. 235-244 ◽  
Author(s):  
Hidetoshi Urakawa ◽  
Peter A. Noble ◽  
Said El Fantroussi ◽  
John J. Kelly ◽  
David A. Stahl
Keyword(s):  
Neural Network ◽  
Base Pair ◽  
Signal Intensity ◽  
Perfect Match ◽  
Oligonucleotide Microarrays ◽  
Single Base ◽  
Probe Target ◽  
Network Analyses ◽  
Base Pair Mismatch ◽  
Single Base Pair

ABSTRACT The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T d) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5′ terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T d and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T d and signal intensity, and it decreased the variability of the signal. Although T ds of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T ds than those with mismatches in the first or second position. The trained NNs predicted the T d with high accuracies (R 2 = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R 2 = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T ds, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5′ terminus plays a greater role in determining the T d and signal intensity of duplexes than the type of mismatch.

scholarly journals Hybridization of synthetic oligodeoxyribonucleotides to ΦX174 DNA: the effect of single base pair mismatch

1979 ◽  
Vol 6 (11) ◽  
pp. 3543-3558 ◽  
Author(s):  
R. Bruce Wallace ◽  
J. Shaffer ◽  
R.F. Murphy ◽  
J. Bonner ◽  
T. Hirose ◽  
...  
Keyword(s):  
Base Pair ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair

scholarly journals Amplified Single Base-Pair Mismatch Detection via Aggregation of Exonuclease-Sheared Gold Nanoparticles

2014 ◽  
Vol 86 (7) ◽  
pp. 3461-3467 ◽  
Author(s):  
Shuo Wu ◽  
Pingping Liang ◽  
Haixiang Yu ◽  
Xiaowen Xu ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Base Pair ◽  
Single Base ◽  
Mismatch Detection ◽  
Base Pair Mismatch ◽  
Single Base Pair

Sequence Context and Thermodynamic Stability of a Single Base Pair Mismatch in Short Deoxyoligonucleotide Duplexes

2001 ◽  
Vol 123 (47) ◽  
pp. 11811-11812 ◽  
Author(s):  
Timothy S. Hall ◽  
Petr Pancoska ◽  
Peter V. Riccelli ◽  
Kathleen Mandell ◽  
Albert S. Benight
Keyword(s):  
Thermodynamic Stability ◽  
Base Pair ◽  
Sequence Context ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair

scholarly journals Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anustup Poddar ◽  
Muhammad S. Azam ◽  
Tunc Kayikcioglu ◽  
Maksym Bobrovskyy ◽  
Jichuan Zhang ◽  
...  
Keyword(s):  
Small Rna ◽  
Base Pair ◽  
High Throughput Sequencing ◽  
Base Pairing ◽  
Target Search ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair ◽  
Bacterial Small Rna

AbstractBase-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff by 14–25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.

Sign in / Sign up

Export Citation Format

Share Document